INFO  : Successfully started log file 'model.loop.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_local.config'
________________________________________________________________________________

[Query Input]
FASTA_FILE                               = /bmm/www/servers/phyre2/public_html/phyre2_output/21ab7a63204e9efd/input.fasta
PSSM_FILE                                = /bmm/www/servers/phyre2/public_html/phyre2_output/21ab7a63204e9efd/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                  = 0
MAX_TRIM_RES                             = 6
MAX_TRIM_EDGE                            = 6
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.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 - d1bdga1.20.pdb
________________________________________________________________________________

INFO  : Performing trim back
INFO  : Chain break between residues 11 - 12
INFO  : Trim back to residues 5 - 12
________________________________________________________________________________

INFO  : Modelling loops
________________________________________________________________________________

INFO  : Gap size 7 between position 5 and 12 : Seq = 'IQILASYP'
INFO  : Stem parameters: x = 10.52; y = 19.58; beta = 1.72; gamma = -0.69
INFO  : Searching loop database file '/data/data/blast/loopdb/10/19/size.7.b'
INFO  : Searching loop database file '/data/data/blast/loopdb/11/19/size.7.b'
INFO  : Identified 38 potential loops
INFO  : Ranking by goodness
INFO  : Extracting 1 / 38 from database
INFO  : Extracting 21 / 38 from database
INFO  : Ranking by loop score
INFO  : Rank   Score    = Seq     - 80.50 *    rms^2 (goodness) : Target seq = IQILASYP
INFO  :    1    -12.962 =  -1.000 - 80.50 *  0.385^2 ( 1.746) : NSIVSMCS : Loop ID =   19 : 1NMBN.pdb.bin ( 360 -  367)
INFO  :    2    -14.426 =  -1.000 - 80.50 *  0.408^2 ( 1.956) : YHLVVGRS : Loop ID =   23 : 1GYDB.pdb.bin ( 216 -  223)
INFO  :    3    -14.442 =  -1.000 - 80.50 *  0.409^2 ( 2.194) : NSIVSMCS : Loop ID =   37 : 1INY_.pdb.bin ( 360 -  367)
INFO  :    4    -14.583 =  -1.000 - 80.50 *  0.411^2 ( 1.955) : NSIVSMCS : Loop ID =   38 : 6NN9_.pdb.bin ( 360 -  367)
INFO  :    5    -15.432 =  -1.000 - 80.50 *  0.423^2 ( 1.955) : YHLVVGRS : Loop ID =   10 : 1GYHA.pdb.bin ( 219 -  226)
INFO  :    6    -18.663 =  -4.000 - 80.50 *  0.427^2 ( 1.952) : DGVILGAD : Loop ID =   18 : 1RYPH.pdb.bin (  18 -   25)
INFO  :    7    -18.729 =   0.000 - 80.50 *  0.482^2 ( 2.925) : VSVTSWLV : Loop ID =   33 : 2BS6A.pdb.bin (  47 -   54)
INFO  :    8    -19.423 =  -7.000 - 80.50 *  0.393^2 ( 1.583) : DLYTLSSS : Loop ID =    1 : 1QKZH.pdb.bin ( 178 -  185)
INFO  :    9    -20.589 =   1.000 - 80.50 *  0.518^2 ( 3.797) : TGCNACYM : Loop ID =   12 : 1V4SA.pdb.bin ( 214 -  221)
INFO  :   10    -20.794 =   0.000 - 80.50 *  0.508^2 ( 3.512) : VSVTSWLV : Loop ID =   31 : 2BT9A.pdb.bin (  47 -   54)
INFO  :   11    -20.917 =   1.000 - 80.50 *  0.522^2 ( 3.951) : TGTNACYM : Loop ID =   20 : 1QHAA.pdb.bin ( 220 -  227)
INFO  :   12    -21.589 =  -6.000 - 80.50 *  0.440^2 ( 2.073) : IGARGVCD : Loop ID =   27 : 1YU2A.pdb.bin ( 364 -  371)
INFO  :   13    -21.892 =  -2.000 - 80.50 *  0.497^2 ( 3.074) : LHWMISDI : Loop ID =    8 : 2BJFA.pdb.bin ( 140 -  147)
INFO  :   14    -21.904 =  -5.000 - 80.50 *  0.458^2 ( 2.763) : GHAIACSC : Loop ID =   14 : 1UKFA.pdb.bin ( 130 -  137)
INFO  :   15    -23.158 = -11.000 - 80.50 *  0.389^2 ( 1.372) : YYAWGGGI : Loop ID =   22 : 1G9JA.pdb.bin ( 298 -  305)
INFO  :   16    -23.512 =  -7.000 - 80.50 *  0.453^2 ( 2.338) : DTVYITGN : Loop ID =   29 : 1ITCA.pdb.bin ( 434 -  441)
INFO  :   17    -24.843 =  -5.000 - 80.50 *  0.496^2 ( 2.671) : QNVYLTGS : Loop ID =   21 : 1TCMA.pdb.bin ( 601 -  608)
INFO  :   18    -24.945 =  -7.000 - 80.50 *  0.472^2 ( 2.435) : DTVYITGN : Loop ID =   26 : 1VEMA.pdb.bin ( 434 -  441)
INFO  :   19    -25.507 =  -9.000 - 80.50 *  0.453^2 ( 2.212) : PTLEVEVY : Loop ID =   30 : 1W6TA.pdb.bin (  19 -   26)
INFO  :   20    -25.646 =  11.000 - 80.50 *  0.675^2 ( 8.085) : LEVEAVAP : Loop ID =    9 : 1WUBA.pdb.bin ( 164 -  171)
INFO  :   21    -27.063 = -18.000 - 80.50 *  0.336^2 ( 1.116) : RGQGEGEY : Loop ID =   25 : 2A13A.pdb.bin (  17 -   24)
INFO  :   22    -30.408 = -16.000 - 80.50 *  0.423^2 ( 1.747) : KIEVYMDG : Loop ID =   16 : 1TB3A.pdb.bin ( 254 -  261)
INFO  :   23    -30.631 = -18.000 - 80.50 *  0.396^2 ( 1.661) : DAGSLYEL : Loop ID =    7 : 1UMHA.pdb.bin ( 102 -  109)
INFO  :   24    -31.219 = -14.000 - 80.50 *  0.462^2 ( 2.788) : GTSVKLSC : Loop ID =   28 : 2C1PB.pdb.bin (  13 -   20)
INFO  :   25    -33.676 = -12.000 - 80.50 *  0.519^2 ( 3.140) : PRPINVKI : Loop ID =   15 : 1GUIA.pdb.bin (  85 -   92)
INFO  :   26    -34.298 =  -4.000 - 80.50 *  0.613^2 ( 6.425) : EEWVGSAY : Loop ID =   11 : 1F3VA.pdb.bin (   1 -    8)
INFO  :   27    -34.992 = -11.000 - 80.50 *  0.546^2 ( 4.251) : GVLRGQSL : Loop ID =   34 : 2A50B.pdb.bin (  86 -   93)
INFO  :   28    -35.216 = -11.000 - 80.50 *  0.548^2 ( 4.272) : GVLRGQSL : Loop ID =   32 : 2A53B.pdb.bin (  86 -   93)
INFO  :   29    -36.635 = -21.000 - 80.50 *  0.441^2 ( 2.282) : PITGNYTF : Loop ID =   17 : 1LYQA.pdb.bin (  90 -   97)
INFO  :   30    -39.964 =  -9.000 - 80.50 *  0.620^2 ( 6.964) : EIGAATAT : Loop ID =   24 : 9GAFA.pdb.bin ( 190 -  197)
INFO  :   31    -40.592 =  -7.000 - 80.50 *  0.646^2 ( 7.775) : SELYIMGY : Loop ID =    2 : 1VE6A.pdb.bin ( 429 -  436)
INFO  :   32    -42.821 =  -9.000 - 80.50 *  0.648^2 ( 7.724) : GHYVVYLN : Loop ID =    3 : 1NB8A.pdb.bin ( 239 -  246)
INFO  :   33    -44.794 =   6.000 - 80.50 *  0.794^2 (30.947) : TWRIAAYG : Loop ID =    5 : 1UPSA.pdb.bin ( 164 -  171)
INFO  :   34    -47.709 =   0.000 - 80.50 *  0.770^2 (12.428) : ANATATMD : Loop ID =   35 : 1N7OA.pdb.bin ( 479 -  486)
INFO  :   35    -54.302 =  -3.000 - 80.50 *  0.798^2 (29.114) : SGLAALIT : Loop ID =   36 : 1HVXA.pdb.bin ( 421 -  428)
INFO  :   36    -54.882 = -12.000 - 80.50 *  0.730^2 (10.642) : NCYKKWWS : Loop ID =    6 : 1VB0A.pdb.bin (  21 -   28)
INFO  :   37    -71.185 = -22.000 - 80.50 *  0.782^2 (18.170) : NIGGFLCM : Loop ID =    4 : 1C7GA.pdb.bin ( 261 -  268)
INFO  :   38    -72.611 = -21.000 - 80.50 *  0.801^2 (20.280) : YIGGYVAY : Loop ID =   13 : 1E54A.pdb.bin ( 169 -  176)
INFO  : Identifed 38 loops for gap 5 - 12 : 'IQILASYP'
WARN  : Model missing 4 N-terminal residues
WARN  : Model missing 36 C-terminal residues
________________________________________________________________________________

INFO  : Cyclic-Coordinate Descent (CCD) and selection for gap    5 -   12
ERROR : CCD : Failed loop   19 in  5000 N->C cycles (RMSD = 0.2193 : N-C = 1.4415)
ERROR : CCD : Failed loop   23 in  5000 N->C cycles (RMSD = 0.298897 : N-C = 1.48914)
ERROR : CCD : Failed loop   37 in  5000 N->C cycles (RMSD = 0.223035 : N-C = 1.43378)
ERROR : CCD : Failed loop   38 in  5000 N->C cycles (RMSD = 0.309139 : N-C = 1.48785)
ERROR : CCD : Failed loop   10 in  5000 N->C cycles (RMSD = 0.254299 : N-C = 1.47663)
ERROR : CCD : Failed loop   18 in  5000 N->C cycles (RMSD = 0.455959 : N-C = 1.59317)
ERROR : CCD : Failed loop   33 in  5000 N->C cycles (RMSD = 0.376881 : N-C = 1.57566)
ERROR : CCD : Failed loop    1 in  5000 N->C cycles (RMSD = 0.254805 : N-C = 1.51423)
ERROR : CCD : Failed loop   12 in  5000 N->C cycles (RMSD = 0.412063 : N-C = 1.56923)
ERROR : CCD : Failed loop   31 in  5000 N->C cycles (RMSD = 0.373306 : N-C = 1.60406)
ERROR : CCD : Failed loop   20 in  5000 N->C cycles (RMSD = 0.448043 : N-C = 1.52312)
ERROR : CCD : Failed loop   27 in  5000 N->C cycles (RMSD = 0.288884 : N-C = 1.48911)
ERROR : CCD : Failed loop    8 in  5000 N->C cycles (RMSD = 0.255643 : N-C = 1.46587)
ERROR : CCD : Failed loop   14 in  5000 N->C cycles (RMSD = 0.295798 : N-C = 1.51752)
ERROR : CCD : Failed loop   22 in  5000 N->C cycles (RMSD = 0.342308 : N-C = 1.53024)
ERROR : CCD : Failed loop   29 in  5000 N->C cycles (RMSD = 0.27628 : N-C = 1.44211)
ERROR : CCD : Failed loop   21 in  5000 N->C cycles (RMSD = 0.352991 : N-C = 1.4459)
ERROR : CCD : Failed loop   26 in  5000 N->C cycles (RMSD = 0.331461 : N-C = 1.45468)
ERROR : CCD : Failed loop   30 in  5000 N->C cycles (RMSD = 0.328949 : N-C = 1.5558)
ERROR : CCD : Failed loop    9 in  5000 N->C cycles (RMSD = 0.34734 : N-C = 1.50669)
ERROR : CCD : Failed loop   25 in  5000 N->C cycles (RMSD = 0.353788 : N-C = 1.49763)
ERROR : CCD : Failed loop   16 in  5000 N->C cycles (RMSD = 0.218818 : N-C = 1.46318)
ERROR : CCD : Failed loop    7 in  5000 N->C cycles (RMSD = 0.33449 : N-C = 1.5251)
ERROR : CCD : Failed loop   28 in  5000 N->C cycles (RMSD = 0.493817 : N-C = 1.45169)
ERROR : CCD : Failed loop   15 in  5000 N->C cycles (RMSD = 0.221509 : N-C = 1.50923)
ERROR : CCD : Failed loop   11 in  5000 N->C cycles (RMSD = 0.251012 : N-C = 1.49321)
ERROR : CCD : Failed loop   34 in  5000 N->C cycles (RMSD = 0.31793 : N-C = 1.55758)
ERROR : CCD : Failed loop   32 in  5000 N->C cycles (RMSD = 0.299926 : N-C = 1.54059)
ERROR : CCD : Failed loop   17 in  5000 N->C cycles (RMSD = 0.441796 : N-C = 1.52944)
ERROR : CCD : Failed loop   24 in  5000 N->C cycles (RMSD = 0.434996 : N-C = 1.61332)
ERROR : CCD : Failed loop    2 in  5000 N->C cycles (RMSD = 0.279051 : N-C = 1.49449)
ERROR : CCD : Failed loop    3 in  5000 N->C cycles (RMSD = 0.371289 : N-C = 1.61509)
ERROR : CCD : Failed loop    5 in  5000 N->C cycles (RMSD = 0.22107 : N-C = 1.45248)
ERROR : CCD : Failed loop   35 in  5000 N->C cycles (RMSD = 0.341186 : N-C = 1.53259)
ERROR : CCD : Failed loop   36 in  5000 N->C cycles (RMSD = 0.273879 : N-C = 1.53205)
ERROR : CCD : Failed loop    6 in  5000 N->C cycles (RMSD = 0.311156 : N-C = 1.50026)
ERROR : CCD : Failed loop    4 in  5000 N->C cycles (RMSD = 0.364225 : N-C = 1.55781)
ERROR : CCD : Failed loop   13 in  5000 N->C cycles (RMSD = 0.617791 : N-C = 1.6383)
ERROR : Failed to select any loops for gap 5 - 12
________________________________________________________________________________

INFO  : Assembling final models for 0 gaps => 1 combinations
INFO  : Removing single loop lists
INFO  : Assembled 1 / 1 combinations
________________________________________________________________________________

INFO  : Ranking final models by energy
INFO  : Outputting models to dir 'loop/model.1'
INFO  : model.1.pdb : Energy = 38.410 (T = 0) : I = 0 : R = 0 : RoG = 36.597 : PP = 3.561 : SP = 1.015 : SE = 0.000 : HO = -4.037 : TE = 1.274264
________________________________________________________________________________

INFO  : Model building complete
________________________________________________________________________________

