INFO  : Successfully started log file 'model.loop_uber.log'
________________________________________________________________________________

                                     Assembler

                 Protein structure prediction by fragment assembly
                                   (Ver. 0.6.6)
________________________________________________________________________________

INFO  : Printing configuration for program 'assembler'
INFO  : Configuration file '/bmm/www/servers/phyre2/bin/loop_uber_local.config'
________________________________________________________________________________

[Query Input]
FASTA_FILE                               = /bmm/www/servers/phyre2/public_html/phyre2_output/4f3837bd0100a348/input.fasta
PSSM_FILE                                = /bmm/www/servers/phyre2/public_html/phyre2_output/4f3837bd0100a348/assembler.pssm
MODEL_START_LIST                         = model_start.list
BUILD_INITIAL_REFERENCE                  = 0
BUILD_UP_MAX_MODELS                      = 1
________________________________________________________________________________

[Energy Functions]
PP_STUB                                  = /bmm/www/servers/phyre2/bin/assembler_data/default.pp
SP_STUB                                  = /bmm/www/servers/phyre2/bin/assembler_data/default.sp
BBDEP_LIBRARY_THRESHOLD                  = 0.9
RADIUS_OF_GYRATION_THRESHOLD             = 2
RADIUS_OF_GYRATION_ABSOLUTE              = 0
CBCB_CONTACT_DIST                        = 7.5
CONTACT_GAP                              = 5
MAXSUB_DIST                              = 6
MAXSUB_ITER                              = 1
RMSD_DIST                                = 6
HBOND_SEPARATION                         = 5
RESIDUE_PROB_CUT_OFF                     = 0.2
PP_RESIDUE_PROB_CUT_OFF                  = 0.4
MAX_CALIBRATE_ENERGY                     = 500
CUTOFF_PHI_PSI                           = 0.001
TORSION_BILINEAR                         = 1
LJ_SWITCH_RATIO                          = 0.7
ENERGY_SET_MODE                          = 0
NUMBER_OF_ENERGY_SETS                    = 1
________________________________________________________________________________

[Energy Set 1]
T_LIMIT                                  = 0
WEIGHT_PAIR_POTENTIAL                    = 0.215
WEIGHT_SOLVATION_POTENTIAL               = 1
WEIGHT_STERIC_ENERGY                     = 5.03
WEIGHT_RADIUS_OF_GYRATION                = 2.83
WEIGHT_TORSION_ENERGY                    = 1.14
WEIGHT_HBONDS_ORIENT                     = 5.27
STERIC_CLASH                             = 1
PAIR_SEPARATION_MIN                      = 3
SS_METHOD                                = 0
ENERGY_SCALE_FACTOR                      = 0
PROB_REFINE_HELIX                        = 0.3
PROB_REFINE_SHEET                        = 0.5
PROB_REFINE_COIL                         = 1
PROB_SHEAR_STRAND                        = 0.05
PROB_PHI_PSI_TWIST                       = 0.1
PROB_PHI_PSI_TILT                        = 0.15
PROB_TEMPLATE_SPLICE                     = 0
PROB_FRAG_3                              = 1
PROB_GUNN_COST_9                         = 0
PROB_GUNN_COST_3                         = 0
PROB_STABILISE_TWIST                     = 0
PROB_STABILISE_TILT                      = 0
PROB_STABILISE_TEMPLATE                  = 0
PROB_STABILISE_FRAG_9                    = 0
PROB_STABILISE_FRAG_3                    = 0
PROB_STABILISE_GUNN_9                    = 0
PROB_STABILISE_GUNN_3                    = 0
FULL_ATOM_MODEL                          = 0
________________________________________________________________________________

[Model Building]
MAX_MODELS                               = 1000
MAX_BUILD_ITERATIONS                     = 100
MAX_JOIN_ITERATIONS                      = 5
MAX_JOIN_REFINE_ITERATIONS               = 5
MAX_REFINE_ITERATIONS                    = 5
MAX_SPLICE_ITERATIONS                    = 5
SHEAR_STRAND_DISTANCE                    = 3.8
PHI_PSI_TWIST_LENGTH                     = 3
PHI_PSI_TWIST_RANGE                      = 5
PHI_PSI_TILT_LENGTH                      = 5
PHI_PSI_TILT_RANGE                       = 15
STABILISE_SIZE                           = 5
STABILISE_RESTRICT                       = 1
STABILISE_ITERATIONS                     = 3
STABILISE_BREAK_THRESHOLD                = 1
STABILISE_HELIX                          = 0
STABILISE_STRAND                         = 1
STABILISE_MAX_ANGLE_UPDATE               = 15
SHEAR_LOOP_SIZE                          = 8
SHEAR_LOOP_COIL_SIZE                     = 5
SHEAR_MAX_CCD_ITERATIONS                 = 300
SHEAR_CCD_THRESHOLD                      = 0.3
SHEAR_CCD_NC_THRESHOLD                   = 0.1
SHEAR_CCD_RESTRICT                       = 0
SHEAR_MAX_ANGLE_UPDATE                   = 15
REPACK_FREQUENCY                         = 25
REPACK_RANDOM                            = 2
REPACK_THRESHOLD                         = 0.7
GUNN_COST_UPPER                          = 0.03
GUNN_COST_LOWER                          = 11.4701
MAX_MSD_DEVIATION                        = 16
RESEED_RESTRICTION_INTERVAL              = 0
RANDOM_LIST_L                            = 0
RANDOM_LIST_9                            = 0
RANDOM_LIST_3                            = 0
RANDOM_LIST_TEMPLATE                     = 0
RANDOM_BUILD                             = 0
________________________________________________________________________________

[Simulated Annealing]
T_START_TEMP                             = 10
T_END_TEMP                               = 0
CALIBRATION_SEED                         = 0
T_CALIBRATION_FACTOR                     = 10
ENERGY_CALIBRATION_FACTOR                = 4
MAX_CALIBRATE_START                      = 500
T_CALIBRATION_FACTOR                     = 10
T_REDUCE_FACTOR_EXP                      = 0.5
T_REDUCE_FACTOR_STEPS                    = 50
RATIO_EXP_TO_LINEAR_SWITCH               = 1
MIN_TEMP_THRESHOLD                       = 0
MAX_TEMP_ITER                            = 1000
MAX_TEMP_REFINE                          = 100
MAX_STOP_ITER                            = 30000
MAX_STOP_REFINE                          = 2000
DELTA_ROLL_SIZE                          = 0
DELTA_STOP_THRESHOLD                     = 0
MAX_QUENCH                               = 5000
NO_TEMPLATE_RATIO                        = 0.2
________________________________________________________________________________

[Loop Modelling]
MODEL_LOOPS                              = 1
LOOP_DATABASE                            = /data/data/blast/loopdb
MIN_LOOP_SIZE                            = 2
MAX_LOOP_SIZE                            = 15
POSITIONAL_GAPS                          = 1
TRIM_BACK                                = 1
TRIM_BACK_STERIC_CHECKS                  = 1
MAX_TRIM_RES                             = 5
MAX_TRIM_EDGE                            = 3
TRIM_BACK_GOODNESS                       = 1
SIZE_TRIM_BACK_AV                        = 0
MAX_SELECT_LOOPS                         = 500
TOLERANCE                                = 0.75
RMSD_WEIGHT                              = 80.5
RMSD_BENCHMARK                           = 0
FIT_ON_TRIANGLE                          = 0
CHECK_STERIC_CLASH                       = 1
CHECK_STERIC_ENERGY                      = 0
STERIC_ENERGY_THRESHOLD                  = 0.5
ABINITIO_LOOPS                           = 0
ABINITIO_ENDS                            = 0
ABINITIO_TRIM_COUNT                      = 0
MAX_LOOP_MODELS                          = 1000
CCD_LOOP_CLOSURE_TOLERANCE               = 6
CCD_FAILURE_TOLERANCE                    = 0
LOOP_SELECTION_TOLERANCE                 = 9
MAX_CCD_LOOPS                            = 20
CCD_DIRECTION                            = 1
CCD_CLOSURE_RMSD                         = 0.08
CCD_CLOSURE_NC_DEVIATION                 = 0.1
CCD_MAX_ITER                             = 5000
CCD_RESTRICT                             = 1
CCD_MAX_ANGLE_UPDATE                     = 15
MAX_COMBINE_LOOPS                        = 10
START_T                                  = 2
STEPS_PER_LOOP                           = 100
REPLACE_TRIMMED                          = 1
________________________________________________________________________________

[Logging]
LOG_LEVEL                                = 1
LOG_TIME                                 = 0
LOG_FILE                                 = 0
LOG_FILE_NAME                            = model.loop_uber.log
FOLDING_PATH                             = 0
OUTPUT_DIR                               = loop
USE_COMPRESSION                          = 0
FIT_ON_PREVIOUS                          = 0
USAGE_FILE                               = assembler.model_usage
MODEL_START_NO                           = 1
MODEL_END_NO                             = 0
OUTPUT_FREQUENCY                         = 100
UNWEIGHTED_OUTPUT                        = 0
SPLICE_INFO                              = 1
SPLICE_FILE                              = assembler.splice_info
FRAGVAR_INFO                             = 0
BAD_FRAG_DIR                             = assembler_bad
REFINE_RRG_LIMIT                         = 0
STOP_FILE                                = assembler.stop
OUTPUT_LOOPS                             = 0
________________________________________________________________________________

[Benchmark]
BACKBONE_RMSD                            = 0
OUTPUT_RMSD                              = 0
OUTPUT_MAXSUB                            = 0
MAXSUB_DIST                              = 6
MAXSUB_ITER                              = 0
________________________________________________________________________________

INFO  : Reading FASTA sequence file
INFO  : Reading query PSSM file
INFO  : Reading Pair-potential file
INFO  : Reading Solvation-potential file
INFO  : Reading PDB list file 'model_start.list'
INFO  : Successfully read 0 PDBs
INFO  : Successfully read 1 / 1 PDBs from list file 'model_start.list'
________________________________________________________________________________

INFO  : Entering build loops routine
________________________________________________________________________________

INFO  : Processing starting model 1 - hh.c4ijdA_.model.1.pdb
________________________________________________________________________________

INFO  : Performing trim back
WARN  : Positional gap in chain between position 151 and 177
INFO  : Chain break between residues 151 - 177
WARN  : Positional gap in chain between position 248 and 262
INFO  : Chain break between residues 248 - 262
INFO  : Trim Back  248 -  262 : Calculating loop extraction success
INFO  : Trim Back  248 -  262 : Extraction identifed 0 loops
INFO  : Trim Back  248 -  263 : Calculating loop extraction success
ERROR : Trim Back failed to transform database loops to fit model
INFO  : Trim Back  248 -  263 : Extraction identifed 0 loops
INFO  : Trim Back  247 -  262 : Calculating loop extraction success
INFO  : Trim Back  247 -  262 : Extraction identifed 0 loops
INFO  : Trim back to residues 247 - 262
________________________________________________________________________________

INFO  : Modelling loops
WARN  : Positional gap in chain between position 151 and 177
________________________________________________________________________________

INFO  : Gap size 15 between position 247 and 262 : Seq = 'NTGAKHRWMVEGHQGA'
INFO  : Stem parameters: x = 3.93; y = 1.72; beta = 2.37; gamma = 0.84
INFO  : Searching loop database file '/data/data/blast/loopdb/3/2/size.15.b'
INFO  : Searching loop database file '/data/data/blast/loopdb/4/2/size.15.b'
INFO  : Searching loop database file '/data/data/blast/loopdb/5/1/size.15.b'
INFO  : Searching loop database file '/data/data/blast/loopdb/5/2/size.15.b'
INFO  : Identified 96 potential loops
INFO  : Ranking by goodness
INFO  : Extracting 1 / 96 from database
INFO  : Extracting 21 / 96 from database
INFO  : Extracting 41 / 96 from database
INFO  : Extracting 61 / 96 from database
INFO  : Extracting 81 / 96 from database
INFO  : Ranking by loop score
INFO  : Rank   Score    = Seq     - 80.50 *    rms^2 (goodness) : Target seq = NTGAKHRWMVEGHQGA
INFO  :    1     -3.176 =   0.000 - 80.50 *  0.199^2 ( 2.096) : GGIESYNDPYQVRDCQ : Loop ID =   38 : 1BVNP.pdb.bin ( 145 -  160)
INFO  :    2     -6.783 =   5.000 - 80.50 *  0.383^2 ( 9.577) : TIIASGYRSALPHGVA : Loop ID =    7 : 1WY2A.pdb.bin ( 182 -  197)
INFO  :    3     -6.865 =   5.000 - 80.50 *  0.384^2 ( 9.497) : TIIASGHRSALPHGVA : Loop ID =    8 : 1PV9A.pdb.bin ( 171 -  186)
INFO  :    4     -8.977 =   0.000 - 80.50 *  0.334^2 ( 3.793) : GGIESYNDPYQVRDCQ : Loop ID =   11 : 1HX0A.pdb.bin ( 144 -  159)
INFO  :    5     -9.007 =   0.000 - 80.50 *  0.334^2 ( 4.782) : GGIESYNDPYQVRDCQ : Loop ID =   13 : 1PIG_.pdb.bin ( 144 -  159)
INFO  :    6    -10.154 =   0.000 - 80.50 *  0.355^2 ( 4.603) : GGIESYNDPYQVRDCQ : Loop ID =    3 : 1DHKA.pdb.bin ( 144 -  159)
INFO  :    7    -14.653 =  -9.000 - 80.50 *  0.265^2 ( 4.316) : NVYNDTSNPLSTPFNT : Loop ID =    5 : 1W9PA.pdb.bin ( 221 -  236)
INFO  :    8    -14.735 =  -8.000 - 80.50 *  0.289^2 ( 2.089) : ESVRFDSDVGEYRAVT : Loop ID =   88 : 1AQDB.pdb.bin (  32 -   47)
INFO  :    9    -18.801 = -12.000 - 80.50 *  0.291^2 ( 3.629) : GDIENYNDATQVRDCR : Loop ID =   50 : 1KGUA.pdb.bin ( 144 -  159)
INFO  :   10    -19.219 = -12.000 - 80.50 *  0.299^2 ( 4.110) : GDIENYNDATQVRDCR : Loop ID =   52 : 1KBBA.pdb.bin ( 144 -  159)
INFO  :   11    -19.646 = -11.000 - 80.50 *  0.328^2 ( 3.729) : EYVRYDSDVGEHRAVT : Loop ID =   22 : 1MUJB.pdb.bin (  33 -   48)
INFO  :   12    -19.655 = -12.000 - 80.50 *  0.308^2 ( 4.598) : GDIENYNDATQVRDCR : Loop ID =   51 : 2CPUA.pdb.bin ( 144 -  159)
INFO  :   13    -19.665 = -12.000 - 80.50 *  0.309^2 ( 3.782) : GDIENYNDATQVRDCR : Loop ID =   34 : 1HNY_.pdb.bin ( 144 -  159)
INFO  :   14    -19.670 = -12.000 - 80.50 *  0.309^2 ( 4.524) : GDIENYNDATQVRDCR : Loop ID =   62 : 1XGZA.pdb.bin ( 144 -  159)
INFO  :   15    -19.993 = -12.000 - 80.50 *  0.315^2 ( 4.708) : GDIENYNDATQVRDCR : Loop ID =   12 : 1KBKA.pdb.bin ( 144 -  159)
INFO  :   16    -20.111 = -12.000 - 80.50 *  0.317^2 ( 4.474) : GDIENYNDATQVRDCR : Loop ID =    4 : 1SMD_.pdb.bin ( 144 -  159)
INFO  :   17    -20.144 = -11.000 - 80.50 *  0.337^2 ( 2.594) : EYVRYDSDVGEYRAVT : Loop ID =   71 : 2IADB.pdb.bin (  32 -   47)
INFO  :   18    -20.173 = -12.000 - 80.50 *  0.319^2 ( 4.123) : GDIENYNDATQVRDCR : Loop ID =   14 : 1Q4NX.pdb.bin ( 144 -  159)
INFO  :   19    -20.325 = -12.000 - 80.50 *  0.322^2 ( 3.923) : GDIENYNDATQVRDCR : Loop ID =   53 : 1KGWA.pdb.bin ( 144 -  159)
INFO  :   20    -20.665 = -12.000 - 80.50 *  0.328^2 ( 4.402) : GDIENYNDATQVRDCR : Loop ID =   16 : 1NM9A.pdb.bin ( 144 -  159)
INFO  :   21    -20.940 = -12.000 - 80.50 *  0.333^2 ( 4.275) : GDIENMNDATQVRDCR : Loop ID =   20 : 1Z32X.pdb.bin ( 144 -  159)
INFO  :   22    -21.427 = -12.000 - 80.50 *  0.342^2 ( 4.188) : GDIENYNDATQVRDCR : Loop ID =   15 : 1JXJA.pdb.bin ( 144 -  159)
INFO  :   23    -21.723 = -12.000 - 80.50 *  0.348^2 ( 4.708) : GDIENYNDATQVRDCR : Loop ID =   17 : 1JXKA.pdb.bin ( 144 -  159)
INFO  :   24    -21.739 = -11.000 - 80.50 *  0.365^2 ( 6.336) : VKSGNNGYGGYGYNAG : Loop ID =   30 : 1GA6A.pdb.bin ( 327 -  342)
INFO  :   25    -22.854 = -11.000 - 80.50 *  0.384^2 ( 3.335) : EIVRFDSDVGEFRAVT : Loop ID =   77 : 1S9VB.pdb.bin (  33 -   48)
INFO  :   26    -23.174 = -13.000 - 80.50 *  0.356^2 ( 6.608) : PIYPTETKKDTRAVQG : Loop ID =   43 : 2TPSA.pdb.bin ( 142 -  157)
INFO  :   27    -23.801 = -14.000 - 80.50 *  0.349^2 (10.976) : TYGDHPGLPKVEDTIG : Loop ID =   42 : 1SB8A.pdb.bin ( 144 -  159)
INFO  :   28    -24.177 = -13.000 - 80.50 *  0.373^2 ( 8.032) : PIYPTETKKDTRAVQG : Loop ID =   57 : 1G6CA.pdb.bin ( 142 -  157)
INFO  :   29    -24.378 = -13.000 - 80.50 *  0.376^2 ( 2.913) : EYLRFDSDVGEYRAVT : Loop ID =   69 : 1K2DB.pdb.bin (  31 -   46)
INFO  :   30    -24.934 = -12.000 - 80.50 *  0.401^2 (12.140) : HGLLVKKNHEYEINHV : Loop ID =   18 : 1E4EB.pdb.bin (  74 -   89)
INFO  :   31    -25.524 =  17.000 - 80.50 *  0.727^2 ( 5.602) : HVTHHPRSKGEVTLRC : Loop ID =   37 : 1LD9A.pdb.bin ( 187 -  202)
INFO  :   32    -25.585 = -11.000 - 80.50 *  0.426^2 ( 8.870) : KGTLSVTSSELYFEVD : Loop ID =    6 : 1T77A.pdb.bin (  18 -   33)
INFO  :   33    -25.634 = -14.000 - 80.50 *  0.380^2 ( 4.890) : FCIERVGERWVVTDAG : Loop ID =   45 : 1Y0UA.pdb.bin (  67 -   82)
INFO  :   34    -25.757 = -10.000 - 80.50 *  0.442^2 ( 2.180) : IDASCLTWEGQQFQGK : Loop ID =   59 : 1U5OA.pdb.bin (  32 -   47)
INFO  :   35    -26.090 = -20.000 - 80.50 *  0.275^2 ( 2.265) : AIASVDASSGQVTLKE : Loop ID =   39 : 1F00I.pdb.bin ( 143 -  158)
INFO  :   36    -27.643 = -22.000 - 80.50 *  0.265^2 ( 2.277) : PLFLYDPLNDKFEPWL : Loop ID =   28 : 1VR5A.pdb.bin (  38 -   53)
INFO  :   37    -28.702 = -18.000 - 80.50 *  0.365^2 ( 1.883) : AQFWTSYNGVTVSVGN : Loop ID =   19 : 8PRN_.pdb.bin (  68 -   83)
INFO  :   38    -29.112 = -12.000 - 80.50 *  0.461^2 (15.023) : HGLLVKKNHEYEINHV : Loop ID =    1 : 1E4EA.pdb.bin (  74 -   89)
INFO  :   39    -29.774 = -19.000 - 80.50 *  0.366^2 ( 6.408) : AHGSWTDSIASPAENR : Loop ID =   33 : 1TF4A.pdb.bin ( 379 -  394)
INFO  :   40    -29.899 = -19.000 - 80.50 *  0.368^2 (10.844) : KEGYLQIGATTQAAQK : Loop ID =   26 : 1K4YA.pdb.bin ( 466 -  481)
INFO  :   41    -31.072 = -21.000 - 80.50 *  0.354^2 ( 4.885) : ISQGGTHYGVSVVGIG : Loop ID =   93 : 1KJOA.pdb.bin ( 243 -  258)
INFO  :   42    -31.133 = -21.000 - 80.50 *  0.355^2 ( 4.923) : ISQGGTHYGVSVVGIG : Loop ID =   87 : 8TLNE.pdb.bin ( 243 -  258)
INFO  :   43    -31.925 = -18.000 - 80.50 *  0.416^2 ( 1.697) : AQFWTSYNGVTVSVGN : Loop ID =   10 : 7PRN_.pdb.bin (  68 -   83)
INFO  :   44    -32.063 = -19.000 - 80.50 *  0.403^2 ( 2.973) : GAFAMDPEIEKAYVKD : Loop ID =   75 : 1FXRA.pdb.bin (  22 -   37)
INFO  :   45    -32.471 = -21.000 - 80.50 *  0.377^2 ( 6.781) : LANGGTHYGVTVTGIG : Loop ID =   67 : 1NPC_.pdb.bin ( 244 -  259)
INFO  :   46    -32.478 = -24.000 - 80.50 *  0.325^2 ( 1.470) : FPEGKYPNRSTHDTGL : Loop ID =   89 : 1QAKA.pdb.bin ( 642 -  657)
INFO  :   47    -32.897 = -24.000 - 80.50 *  0.332^2 ( 1.324) : FPEGKYPNRSTHDTGL : Loop ID =   90 : 1QALA.pdb.bin ( 641 -  656)
INFO  :   48    -34.606 = -15.000 - 80.50 *  0.494^2 ( 3.029) : RGLMQKPSGETFEVPV : Loop ID =   65 : 2A6HD.pdb.bin ( 928 -  943)
INFO  :   49    -34.617 = -22.000 - 80.50 *  0.396^2 ( 7.591) : SCAPGADPKSRLCALC : Loop ID =   61 : 2B6DA.pdb.bin ( 148 -  163)
INFO  :   50    -34.774 = -17.000 - 80.50 *  0.470^2 ( 4.781) : VTKTYKMGEEIIYALK : Loop ID =   41 : 1L2TA.pdb.bin (   6 -   21)
INFO  :   51    -36.175 =   0.000 - 80.50 *  0.670^2 (10.568) : QKSLVMSGPYELKALH : Loop ID =   58 : 1HIB_.pdb.bin (  12 -   27)
INFO  :   52    -36.284 = -24.000 - 80.50 *  0.391^2 ( 6.062) : SCAPGSDPASNLCALC : Loop ID =   48 : 1LFG_.pdb.bin ( 491 -  506)
INFO  :   53    -36.575 = -23.000 - 80.50 *  0.411^2 ( 7.415) : SCAPGSDPRSNLCALC : Loop ID =   66 : 2BJJX.pdb.bin ( 492 -  507)
INFO  :   54    -37.081 = -23.000 - 80.50 *  0.418^2 ( 7.392) : SCAPGSDPRSNLCALC : Loop ID =   49 : 1LCF_.pdb.bin ( 491 -  506)
INFO  :   55    -37.319 = -19.000 - 80.50 *  0.477^2 ( 2.236) : DTQAIVQNNDSTEYGL : Loop ID =   60 : 1FKVA.pdb.bin (  37 -   52)
INFO  :   56    -37.616 = -23.000 - 80.50 *  0.426^2 ( 7.159) : SCAPGSDPRSNLCALC : Loop ID =   91 : 1B0LA.pdb.bin ( 491 -  506)
INFO  :   57    -37.808 = -23.000 - 80.50 *  0.429^2 ( 8.183) : SCAPGSDPRSNLCALC : Loop ID =   92 : 1CB6A.pdb.bin ( 491 -  506)
INFO  :   58    -38.057 = -19.000 - 80.50 *  0.487^2 (13.303) : KEGYLQIGANTQAAQK : Loop ID =   85 : 1MX1A.pdb.bin ( 501 -  516)
INFO  :   59    -38.236 = -17.000 - 80.50 *  0.514^2 ( 2.625) : DTQAIVKNSDHKEYGL : Loop ID =   35 : 1HFX_.pdb.bin (  36 -   51)
INFO  :   60    -39.239 = -22.000 - 80.50 *  0.463^2 (13.472) : DGGCMLLSKTRLDNGN : Loop ID =   36 : 1QO3C.pdb.bin (  98 -  113)
INFO  :   61    -43.486 = -23.000 - 80.50 *  0.504^2 ( 9.952) : RGEVVVIDENFGVRIT : Loop ID =    9 : 1O6AA.pdb.bin (  55 -   70)
INFO  :   62    -45.341 = -19.000 - 80.50 *  0.572^2 ( 8.856) : DINCPSKEGPVPDAGS : Loop ID =   70 : 1VJRA.pdb.bin ( 146 -  161)
INFO  :   63    -46.474 = -10.000 - 80.50 *  0.673^2 ( 7.957) : QNPFYVTPEGEARQAP : Loop ID =   44 : 1UIRA.pdb.bin ( 292 -  307)
INFO  :   64    -47.313 =  -7.000 - 80.50 *  0.708^2 ( 5.795) : IMMEPFNDPGPGTYYK : Loop ID =   95 : 1ZB7A.pdb.bin (  18 -   33)
INFO  :   65    -47.373 = -12.000 - 80.50 *  0.663^2 ( 9.163) : LHWVVPLAPGRLVVRP : Loop ID =   73 : 1UJNA.pdb.bin ( 299 -  314)
INFO  :   66    -47.827 = -22.000 - 80.50 *  0.566^2 ( 9.829) : CFVIISAFDQVYFLEA : Loop ID =    2 : 1RZNA.pdb.bin (  85 -  100)
INFO  :   67    -47.928 = -22.000 - 80.50 *  0.568^2 ( 9.557) : CFVIISAFDQVYFLEA : Loop ID =   21 : 1ZP7A.pdb.bin (  87 -  102)
INFO  :   68    -49.231 =  -8.000 - 80.50 *  0.716^2 ( 5.582) : YKDTVGFGGVSIKNQV : Loop ID =   29 : 1ZAP_.pdb.bin (  94 -  109)
INFO  :   69    -49.524 =  -8.000 - 80.50 *  0.718^2 ( 5.685) : YKDTVGFGGVSIKNQV : Loop ID =   74 : 1EAGA.pdb.bin (  94 -  109)
INFO  :   70    -49.925 =  -9.000 - 80.50 *  0.713^2 ( 5.838) : SLLFVHDHCHRAGVWL : Loop ID =   86 : 1W2FA.pdb.bin ( 207 -  222)
INFO  :   71    -50.048 = -19.000 - 80.50 *  0.621^2 (10.342) : NEDCAEFSGSGWNDNR : Loop ID =   25 : 1XPHA.pdb.bin ( 105 -  120)
INFO  :   72    -51.441 = -13.000 - 80.50 *  0.691^2 ( 9.744) : WNLTIPQGRPAITIST : Loop ID =   82 : 1VAVA.pdb.bin (   5 -   20)
INFO  :   73    -53.461 = -15.000 - 80.50 *  0.691^2 ( 4.989) : SFTIESGAKGPAAGNV : Loop ID =   80 : 1MJC_.pdb.bin (  50 -   65)
INFO  :   74    -59.304 = -22.000 - 80.50 *  0.681^2 ( 5.697) : SGSVQSGFANETVADV : Loop ID =   72 : 2PRN_.pdb.bin ( 267 -  282)
INFO  :   75    -60.991 =  -8.000 - 80.50 *  0.811^2 ( 7.902) : VMVTTVDEEGNINAAP : Loop ID =   32 : 1EJEA.pdb.bin (  29 -   44)
INFO  :   76    -61.331 = -19.000 - 80.50 *  0.725^2 ( 6.163) : EVWMGYYNGHTKVAVK : Loop ID =   78 : 1QPDA.pdb.bin (  27 -   42)
INFO  :   77    -61.405 = -22.000 - 80.50 *  0.700^2 ( 5.467) : SGSVQSGFANETVADV : Loop ID =   94 : 8PRN_.pdb.bin ( 267 -  282)
INFO  :   78    -62.451 = -26.000 - 80.50 *  0.673^2 (10.543) : GFHLEIFPNGTIQGTR : Loop ID =   81 : 1IHKA.pdb.bin (  19 -   34)
INFO  :   79    -62.878 = -16.000 - 80.50 *  0.763^2 ( 6.559) : GIKTGHTDKAGYNLVA : Loop ID =   64 : 1Z6FA.pdb.bin ( 207 -  222)
INFO  :   80    -63.137 = -16.000 - 80.50 *  0.765^2 ( 6.417) : GIKTGHTDKAGYNLVA : Loop ID =   31 : 1NZOA.pdb.bin ( 207 -  222)
INFO  :   81    -63.592 = -15.000 - 80.50 *  0.777^2 ( 6.585) : YDQILIEICGHKAIGT : Loop ID =   68 : 1GNNA.pdb.bin (  58 -   73)
INFO  :   82    -64.046 = -11.000 - 80.50 *  0.812^2 ( 6.564) : ATYVHKKNDGTTVDLT : Loop ID =   27 : 1QA7A.pdb.bin ( 140 -  155)
INFO  :   83    -64.732 = -16.000 - 80.50 *  0.778^2 ( 6.587) : GIKTGHTDKAGYNLVA : Loop ID =   54 : 1NJ4A.pdb.bin ( 198 -  213)
INFO  :   84    -64.807 = -20.000 - 80.50 *  0.746^2 ( 6.162) : GVKTGSGPEAKYCLVF : Loop ID =   56 : 1ES3A.pdb.bin ( 208 -  223)
INFO  :   85    -65.127 = -12.000 - 80.50 *  0.812^2 ( 6.892) : VTVSLWQGETQVASGT : Loop ID =   47 : 1JZ2A.pdb.bin ( 243 -  258)
INFO  :   86    -65.851 = -22.000 - 80.50 *  0.738^2 ( 7.083) : GYDTVQVGGISDTNQI : Loop ID =   79 : 1QRPE.pdb.bin (  84 -   99)
INFO  :   87    -66.542 = -20.000 - 80.50 *  0.760^2 ( 6.062) : LSFIVFSSQATIILPL : Loop ID =   24 : 1SHUX.pdb.bin (  42 -   57)
INFO  :   88    -67.145 = -16.000 - 80.50 *  0.797^2 ( 4.260) : RYRLAANGNGQWSLVG : Loop ID =   40 : 1DABA.pdb.bin ( 518 -  533)
INFO  :   89    -67.649 = -27.000 - 80.50 *  0.711^2 ( 9.626) : GFHLQALPDGRIGGAH : Loop ID =   84 : 1IJTA.pdb.bin (  14 -   29)
INFO  :   90    -69.943 = -17.000 - 80.50 *  0.811^2 ( 7.804) : REEAMPYGNQAYYYAM : Loop ID =   46 : 1F58H.pdb.bin (  97 -  112)
INFO  :   91    -71.777 =  -8.000 - 80.50 *  0.890^2 ( 7.779) : LIIRRYSSEKHYGRES : Loop ID =   63 : 1ZETA.pdb.bin ( 317 -  332)
INFO  :   92    -72.212 = -14.000 - 80.50 *  0.850^2 ( 7.277) : GLKTGSSDTANYNHTI : Loop ID =   23 : 1TVFA.pdb.bin ( 242 -  257)
INFO  :   93    -72.430 = -24.000 - 80.50 *  0.776^2 ( 7.659) : GFKVAAHGNDYAVWEK : Loop ID =   83 : 1AVAA.pdb.bin ( 386 -  401)
INFO  :   94    -72.812 = -29.000 - 80.50 *  0.738^2 ( 6.334) : GGLPVIFNEQVIGAVG : Loop ID =   96 : 2A2LA.pdb.bin ( 105 -  120)
INFO  :   95    -75.266 = -20.000 - 80.50 *  0.829^2 ( 7.855) : HTFPAVLQSDLYTLSS : Loop ID =   76 : 1F4XH.pdb.bin ( 167 -  182)
INFO  :   96    -75.378 = -20.000 - 80.50 *  0.829^2 ( 4.474) : GVKTGSGPEAKYCLVF : Loop ID =   55 : 1ESIA.pdb.bin ( 208 -  223)
WARN  : Steric clash between  T  140 -> G  249 = 2.621 in loop   38 - 1BVNP.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.900 in loop   11 - 1HX0A.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.675 in loop   13 - 1PIG_.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.911 in loop    3 - 1DHKA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.555 in loop    5 - 1W9PA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.237 in loop   88 - 1AQDB.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.421 in loop   50 - 1KGUA.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.509 in loop   52 - 1KBBA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.299 in loop   22 - 1MUJB.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.645 in loop   51 - 2CPUA.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.476 in loop   34 - 1HNY_.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.565 in loop   62 - 1XGZA.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.580 in loop   12 - 1KBKA.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.675 in loop    4 - 1SMD_.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.163 in loop   71 - 2IADB.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.709 in loop   14 - 1Q4NX.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.610 in loop   53 - 1KGWA.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.560 in loop   16 - 1NM9A.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.787 in loop   20 - 1Z32X.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.711 in loop   15 - 1JXJA.pdb.bin
WARN  : Steric clash between  T  140 -> G  249 = 2.575 in loop   17 - 1JXKA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 3.043 in loop   30 - 1GA6A.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.199 in loop   77 - 1S9VB.pdb.bin
WARN  : Steric clash between  P  141 -> G  249 = 2.590 in loop   43 - 2TPSA.pdb.bin
WARN  : Steric clash between  P  263 -> A  250 = 2.459 in loop   42 - 1SB8A.pdb.bin
WARN  : Steric clash between  P  141 -> G  249 = 2.887 in loop   57 - 1G6CA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.157 in loop   69 - 1K2DB.pdb.bin
WARN  : Steric clash between  A  300 -> A  250 = 2.227 in loop   18 - 1E4EB.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.859 in loop   37 - 1LD9A.pdb.bin
WARN  : Steric clash between  A  300 -> A  250 = 2.450 in loop    6 - 1T77A.pdb.bin
WARN  : Steric clash between  G  139 -> G  258 = 2.590 in loop   45 - 1Y0UA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.210 in loop   59 - 1U5OA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.123 in loop   39 - 1F00I.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.144 in loop   28 - 1VR5A.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 1.692 in loop   19 - 8PRN_.pdb.bin
WARN  : Steric clash between  A  300 -> A  250 = 1.841 in loop    1 - 1E4EA.pdb.bin
WARN  : Steric clash between  P  141 -> G  261 = 2.984 in loop   33 - 1TF4A.pdb.bin
WARN  : Steric clash between  P  141 -> G  249 = 2.041 in loop   93 - 1KJOA.pdb.bin
WARN  : Steric clash between  P  141 -> G  249 = 2.320 in loop   87 - 8TLNE.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 1.708 in loop   10 - 7PRN_.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.040 in loop   75 - 1FXRA.pdb.bin
WARN  : Steric clash between  P  141 -> G  249 = 2.019 in loop   67 - 1NPC_.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.658 in loop   89 - 1QAKA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.629 in loop   90 - 1QALA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 3.146 in loop   65 - 2A6HD.pdb.bin
WARN  : Steric clash between  P  120 -> A  250 = 2.925 in loop   61 - 2B6DA.pdb.bin
WARN  : Steric clash between  T  140 -> A  250 = 2.651 in loop   41 - 1L2TA.pdb.bin
WARN  : Steric clash between  P  120 -> A  250 = 2.908 in loop   48 - 1LFG_.pdb.bin
WARN  : Steric clash between  P  120 -> A  250 = 3.068 in loop   66 - 2BJJX.pdb.bin
WARN  : Steric clash between  P  120 -> A  250 = 3.088 in loop   49 - 1LCF_.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 1.879 in loop   60 - 1FKVA.pdb.bin
WARN  : Steric clash between  P  120 -> A  250 = 3.026 in loop   91 - 1B0LA.pdb.bin
WARN  : Steric clash between  P  120 -> A  250 = 2.961 in loop   92 - 1CB6A.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 1.927 in loop   35 - 1HFX_.pdb.bin
WARN  : Steric clash between  A  300 -> A  250 = 2.287 in loop    9 - 1O6AA.pdb.bin
WARN  : Steric clash between  G  139 -> G  258 = 3.044 in loop   70 - 1VJRA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.770 in loop   95 - 1ZB7A.pdb.bin
WARN  : Steric clash between  A  300 -> A  250 = 2.162 in loop    2 - 1RZNA.pdb.bin
WARN  : Steric clash between  A  300 -> A  250 = 2.257 in loop   21 - 1ZP7A.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.946 in loop   29 - 1ZAP_.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 3.049 in loop   74 - 1EAGA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.863 in loop   86 - 1W2FA.pdb.bin
WARN  : Steric clash between  T  140 -> H  259 = 1.308 in loop   80 - 1MJC_.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 1.977 in loop   72 - 2PRN_.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.811 in loop   32 - 1EJEA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.311 in loop   78 - 1QPDA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 1.951 in loop   94 - 8PRN_.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.243 in loop   68 - 1GNNA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.362 in loop   27 - 1QA7A.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 1.899 in loop   47 - 1JZ2A.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.950 in loop   79 - 1QRPE.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.201 in loop   24 - 1SHUX.pdb.bin
WARN  : Steric clash between  T  140 -> Q  260 = 3.123 in loop   40 - 1DABA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.932 in loop   46 - 1F58H.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 2.069 in loop   63 - 1ZETA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 1.880 in loop   96 - 2A2LA.pdb.bin
WARN  : Steric clash between  P  141 -> T  248 = 1.927 in loop   76 - 1F4XH.pdb.bin
WARN  : Steric clash between  T  140 -> Q  260 = 2.960 in loop   55 - 1ESIA.pdb.bin
INFO  : Identifed 18 loops for gap 247 - 262 : 'NTGAKHRWMVEGHQGA'
WARN  : Model missing 70 N-terminal residues
WARN  : Model missing 109 C-terminal residues
________________________________________________________________________________

INFO  : Cyclic-Coordinate Descent (CCD) and selection for gap  247 -  262
INFO  : CCD : Closed loop    7 in    41 N->C cycles (RMSD = 0.0798961 : N-C = 1.36068)
WARN  : Steric clash between  P  141 -> T  248 = 3.126 in loop    7 - 1WY2A.pdb.bin
ERROR : CCD : Altered loop 7 fails steric checks
INFO  : CCD : Closed loop    8 in    41 N->C cycles (RMSD = 0.0775038 : N-C = 1.35411)
WARN  : Steric clash between  P  141 -> T  248 = 3.097 in loop    8 - 1PV9A.pdb.bin
ERROR : CCD : Altered loop 8 fails steric checks
INFO  : CCD : Closed loop   26 in   148 N->C cycles (RMSD = 0.0799529 : N-C = 1.34677)
WARN  : Steric clash between  P  141 -> G  249 = 1.768 in loop   26 - 1K4YA.pdb.bin
ERROR : CCD : Altered loop 26 fails steric checks
INFO  : CCD : Closed loop   58 in   139 N->C cycles (RMSD = 0.0796762 : N-C = 1.37768)
WARN  : Steric clash between  P  141 -> T  248 = 2.078 in loop   58 - 1HIB_.pdb.bin
ERROR : CCD : Altered loop 58 fails steric checks
INFO  : CCD : Closed loop   85 in   215 N->C cycles (RMSD = 0.0799792 : N-C = 1.31705)
WARN  : Steric clash between  P  141 -> G  249 = 0.967 in loop   85 - 1MX1A.pdb.bin
ERROR : CCD : Altered loop 85 fails steric checks
INFO  : CCD : Closed loop   36 in    66 N->C cycles (RMSD = 0.0799606 : N-C = 1.35751)
WARN  : Steric clash between  K   97 -> V  256 = 1.989 in loop   36 - 1QO3C.pdb.bin
ERROR : CCD : Altered loop 36 fails steric checks
INFO  : CCD : Closed loop   44 in   143 N->C cycles (RMSD = 0.0799857 : N-C = 1.29299)
WARN  : Steric clash between  P  141 -> T  248 = 2.898 in loop   44 - 1UIRA.pdb.bin
ERROR : CCD : Altered loop 44 fails steric checks
INFO  : CCD : Closed loop   73 in   253 N->C cycles (RMSD = 0.0799989 : N-C = 1.34846)
WARN  : Steric clash between  P  141 -> T  248 = 2.594 in loop   73 - 1UJNA.pdb.bin
ERROR : CCD : Altered loop 73 fails steric checks
INFO  : CCD : Closed loop   25 in   301 N->C cycles (RMSD = 0.0799827 : N-C = 1.3495)
WARN  : Steric clash between  P  141 -> T  248 = 2.111 in loop   25 - 1XPHA.pdb.bin
ERROR : CCD : Altered loop 25 fails steric checks
INFO  : CCD : Closed loop   82 in   361 N->C cycles (RMSD = 0.0798695 : N-C = 1.36223)
WARN  : Steric clash between  P  141 -> T  248 = 2.252 in loop   82 - 1VAVA.pdb.bin
ERROR : CCD : Altered loop 82 fails steric checks
INFO  : CCD : Closed loop   81 in   215 N->C cycles (RMSD = 0.0799439 : N-C = 1.3365)
WARN  : Steric clash between  P  141 -> T  248 = 2.347 in loop   81 - 1IHKA.pdb.bin
ERROR : CCD : Altered loop 81 fails steric checks
INFO  : CCD : Closed loop   64 in   152 N->C cycles (RMSD = 0.0799645 : N-C = 1.38452)
WARN  : Steric clash between  P  141 -> Q  260 = 2.941 in loop   64 - 1Z6FA.pdb.bin
ERROR : CCD : Altered loop 64 fails steric checks
INFO  : CCD : Closed loop   31 in   273 N->C cycles (RMSD = 0.0799275 : N-C = 1.35605)
WARN  : Steric clash between  P  141 -> Q  260 = 3.057 in loop   31 - 1NZOA.pdb.bin
ERROR : CCD : Altered loop 31 fails steric checks
INFO  : CCD : Closed loop   54 in   212 N->C cycles (RMSD = 0.0798795 : N-C = 1.37099)
INFO  : CCD : Closed loop   56 in   182 N->C cycles (RMSD = 0.0799545 : N-C = 1.33854)
INFO  : CCD : Closed loop   84 in   167 N->C cycles (RMSD = 0.0799159 : N-C = 1.32072)
WARN  : Steric clash between  P  141 -> T  248 = 2.844 in loop   84 - 1IJTA.pdb.bin
ERROR : CCD : Altered loop 84 fails steric checks
INFO  : CCD : Closed loop   23 in   137 N->C cycles (RMSD = 0.0799851 : N-C = 1.39175)
WARN  : Steric clash between  P  141 -> Q  260 = 2.418 in loop   23 - 1TVFA.pdb.bin
ERROR : CCD : Altered loop 23 fails steric checks
INFO  : CCD : Closed loop   83 in   191 N->C cycles (RMSD = 0.0799996 : N-C = 1.32363)
WARN  : Steric clash between  P  141 -> T  248 = 2.525 in loop   83 - 1AVAA.pdb.bin
ERROR : CCD : Altered loop 83 fails steric checks
________________________________________________________________________________

INFO  : Assembling final models for 1 gaps => 2 = 2 combinations
INFO  : Removing single loop lists
INFO  : Assembled 2 / 2 combinations
________________________________________________________________________________

INFO  : Ranking final models by energy
INFO  : Outputting models to dir 'loop/model.1'
INFO  : model.1.pdb : Energy = 95.996 (T = 0) : I = 0 : R = 0 : RoG = 50.822 : PP = 207.426 : SP = 5.987 : SE = 13.488 : HO = -240.483 : TE = 58.755994
INFO  : model.2.pdb : Energy = 101.814 (T = 0) : I = 0 : R = 0 : RoG = 50.612 : PP = 209.357 : SP = 5.788 : SE = 16.652 : HO = -241.542 : TE = 60.947522
________________________________________________________________________________

INFO  : Model building complete
________________________________________________________________________________

