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/1be3331859e83b7c/input.fasta
PSSM_FILE                                = /bmm/www/servers/phyre2/public_html/phyre2_output/1be3331859e83b7c/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.c3dw8B_.model.1.pdb
________________________________________________________________________________

INFO  : Performing trim back
INFO  : Chain break between residues 39 - 40
INFO  : Trim Back   39 -   40 : Calculating loop extraction success
INFO  : Trim Back   39 -   40 : Extraction identifed 0 loops
INFO  : Trim Back   39 -   41 : Calculating loop extraction success
INFO  : Trim Back   39 -   41 : Extraction identifed 0 loops
INFO  : Trim Back   39 -   42 : Calculating loop extraction success
INFO  : Trim Back   39 -   42 : Extraction identifed 0 loops
INFO  : Trim Back   39 -   43 : Calculating loop extraction success
INFO  : Trim Back   39 -   43 : Extraction identifed 0 loops
INFO  : Trim Back   38 -   40 : Calculating loop extraction success
INFO  : Trim Back   38 -   40 : Extraction identifed 0 loops
INFO  : Trim Back   38 -   41 : Calculating loop extraction success
INFO  : Trim Back   38 -   41 : Extraction identifed 0 loops
INFO  : Trim Back   38 -   42 : Calculating loop extraction success
INFO  : Trim Back   38 -   42 : Extraction identifed 0 loops
INFO  : Trim Back   38 -   43 : Calculating loop extraction success
INFO  : Trim Back   38 -   43 : Extraction identifed 0 loops
INFO  : Trim Back   37 -   40 : Calculating loop extraction success
INFO  : Trim Back   37 -   40 : Extraction identifed 0 loops
INFO  : Trim Back   37 -   41 : Calculating loop extraction success
INFO  : Trim Back   37 -   41 : Extraction identifed 0 loops
INFO  : Trim Back   37 -   42 : Calculating loop extraction success
INFO  : Trim Back   37 -   42 : Extraction identifed 0 loops
INFO  : Trim Back   37 -   43 : Calculating loop extraction success
INFO  : Trim Back   37 -   43 : Extraction identifed 0 loops
INFO  : Trim Back   36 -   40 : Calculating loop extraction success
INFO  : Trim Back   36 -   40 : Extraction identifed 0 loops
INFO  : Trim Back   36 -   41 : Calculating loop extraction success
INFO  : Trim Back   36 -   41 : Extraction identifed 0 loops
INFO  : Trim Back   36 -   42 : Calculating loop extraction success
INFO  : Trim Back   36 -   42 : Extraction identifed 1 loops
INFO  : Trim back to residues 36 - 42
________________________________________________________________________________

INFO  : Modelling loops
________________________________________________________________________________

INFO  : Gap size 6 between position 36 and 42 : Seq = 'EWRYIFS'
INFO  : Stem parameters: x = 18.24; y = 4.05; beta = 2.67; gamma = -2.98
INFO  : Searching loop database file '/data/data/blast/loopdb/17/3/size.6.b'
INFO  : Searching loop database file '/data/data/blast/loopdb/17/4/size.6.b'
INFO  : Searching loop database file '/data/data/blast/loopdb/17/5/size.6.b'
INFO  : Searching loop database file '/data/data/blast/loopdb/18/3/size.6.b'
INFO  : Searching loop database file '/data/data/blast/loopdb/18/4/size.6.b'
INFO  : Searching loop database file '/data/data/blast/loopdb/18/5/size.6.b'
INFO  : Identified 20 potential loops
INFO  : Ranking by goodness
INFO  : Extracting 1 / 20 from database
INFO  : Ranking by loop score
INFO  : Rank   Score    = Seq     - 80.50 *    rms^2 (goodness) : Target seq = EWRYIFS
INFO  :    1      0.300 =   6.000 - 80.50 *  0.266^2 (30.745) : EATATFN : Loop ID =    3 : 1ZXQ_.pdb.bin ( 145 -  151)
INFO  :    2     -0.849 =   6.000 - 80.50 *  0.292^2 (32.139) : HWEFDEY : Loop ID =    5 : 1T3QC.pdb.bin ( 176 -  182)
INFO  :    3     -7.364 =   2.000 - 80.50 *  0.341^2 (42.526) : NWGSYSG : Loop ID =    9 : 1V0AA.pdb.bin (  14 -   20)
INFO  :    4    -10.931 =  -6.000 - 80.50 *  0.247^2 (62.313) : KATLTVD : Loop ID =   19 : 1MREH.pdb.bin (  66 -   72)
INFO  :    5    -10.991 =  -4.000 - 80.50 *  0.295^2 (39.989) : IPSIVAS : Loop ID =    4 : 1W0PA.pdb.bin ( 200 -  206)
INFO  :    6    -12.071 =  -1.000 - 80.50 *  0.371^2 (18.341) : EGVVTLT : Loop ID =   18 : 1SRDA.pdb.bin (  15 -   21)
INFO  :    7    -14.861 =  -1.000 - 80.50 *  0.415^2 (39.438) : KRSAQFE : Loop ID =   20 : 2B3HA.pdb.bin ( 271 -  277)
INFO  :    8    -15.908 =  -7.000 - 80.50 *  0.333^2 (63.161) : DSYEMEE : Loop ID =   10 : 1MOXA.pdb.bin ( 289 -  295)
INFO  :    9    -17.078 =  -7.000 - 80.50 *  0.354^2 (32.818) : GFSAVGI : Loop ID =    8 : 1VRAA.pdb.bin (  17 -   23)
INFO  :   10    -22.608 = -10.000 - 80.50 *  0.396^2 (48.142) : SIVVFCG : Loop ID =   11 : 2BAT_.pdb.bin ( 360 -  366)
INFO  :   11    -22.861 = -10.000 - 80.50 *  0.400^2 (37.041) : AGNVSVR : Loop ID =   16 : 1DZWP.pdb.bin (  26 -   32)
INFO  :   12    -22.908 =  -8.000 - 80.50 *  0.430^2 (24.472) : GRHGTWQ : Loop ID =    6 : 1NQEA.pdb.bin ( 320 -  326)
INFO  :   13    -23.042 = -10.000 - 80.50 *  0.403^2 (41.642) : DAATAVL : Loop ID =    2 : 1T0BA.pdb.bin (  41 -   47)
INFO  :   14    -24.152 = -10.000 - 80.50 *  0.419^2 (34.336) : RLSISKD : Loop ID =   13 : 1CICD.pdb.bin (  65 -   71)
INFO  :   15    -24.660 =  -9.000 - 80.50 *  0.441^2 (32.378) : KTKPREQ : Loop ID =    7 : 1H3UA.pdb.bin (  50 -   56)
INFO  :   16    -25.500 = -10.000 - 80.50 *  0.439^2 (34.193) : AGNVSVR : Loop ID =   14 : 1DZVP.pdb.bin (  26 -   32)
INFO  :   17    -25.999 = -14.000 - 80.50 *  0.386^2 (34.673) : MRSAQVY : Loop ID =   12 : 1FHUA.pdb.bin (   0 -    6)
INFO  :   18    -26.747 = -10.000 - 80.50 *  0.456^2 (38.183) : AGNVSVR : Loop ID =   15 : 1DZUP.pdb.bin (  26 -   32)
INFO  :   19    -27.615 = -14.000 - 80.50 *  0.411^2 (36.827) : KRWCDVV : Loop ID =   17 : 1XI0A.pdb.bin (  74 -   80)
INFO  :   20    -31.586 = -14.000 - 80.50 *  0.467^2 (55.748) : PGLTFGI : Loop ID =    1 : 1AOL_.pdb.bin ( 209 -  215)
INFO  : Identifed 20 loops for gap 36 - 42 : 'EWRYIFS'
WARN  : Model missing 34 N-terminal residues
WARN  : Model missing 36 C-terminal residues
________________________________________________________________________________

INFO  : Cyclic-Coordinate Descent (CCD) and selection for gap   36 -   42
INFO  : CCD : Closed loop    3 in  1050 N->C cycles (RMSD = 0.0799984 : N-C = 1.29141)
ERROR : CCD : Failed loop    5 in  5000 N->C cycles (RMSD = 0.254655 : N-C = 1.4067)
ERROR : CCD : Failed loop    9 in  5000 N->C cycles (RMSD = 0.125536 : N-C = 1.32483)
ERROR : CCD : Failed loop   19 in  5000 N->C cycles (RMSD = 0.0983241 : N-C = 1.25536)
ERROR : CCD : Failed loop    4 in  5000 N->C cycles (RMSD = 0.146487 : N-C = 1.32127)
ERROR : CCD : Failed loop   18 in  5000 N->C cycles (RMSD = 0.349781 : N-C = 1.34905)
ERROR : CCD : Failed loop   20 in  5000 N->C cycles (RMSD = 0.457262 : N-C = 1.54215)
ERROR : CCD : Failed loop   10 in  5000 N->C cycles (RMSD = 0.126933 : N-C = 1.28704)
ERROR : CCD : Failed loop    8 in  5000 N->C cycles (RMSD = 0.229876 : N-C = 1.39538)
ERROR : CCD : Failed loop   11 in  5000 N->C cycles (RMSD = 0.229675 : N-C = 1.36038)
ERROR : CCD : Failed loop   16 in  5000 N->C cycles (RMSD = 0.31163 : N-C = 1.43248)
ERROR : CCD : Failed loop    6 in  5000 N->C cycles (RMSD = 0.241509 : N-C = 1.37677)
ERROR : CCD : Failed loop    2 in  5000 N->C cycles (RMSD = 0.416691 : N-C = 1.46495)
ERROR : CCD : Failed loop   13 in  5000 N->C cycles (RMSD = 0.199794 : N-C = 1.42523)
ERROR : CCD : Failed loop    7 in  5000 N->C cycles (RMSD = 0.774648 : N-C = 1.75998)
ERROR : CCD : Failed loop   14 in  5000 N->C cycles (RMSD = 0.501022 : N-C = 1.50467)
ERROR : CCD : Failed loop   12 in  5000 N->C cycles (RMSD = 0.191731 : N-C = 1.37745)
ERROR : CCD : Failed loop   15 in  5000 N->C cycles (RMSD = 0.520871 : N-C = 1.5116)
ERROR : CCD : Failed loop   17 in  5000 N->C cycles (RMSD = 0.994084 : N-C = 1.89331)
ERROR : CCD : Failed loop    1 in  5000 N->C cycles (RMSD = 0.377676 : N-C = 1.53072)
________________________________________________________________________________

INFO  : Assembling final models for 1 gaps => 1 combinations
INFO  : Removing single loop lists
INFO  : Removing single loop list for position 36 from enumeration
INFO  : Assembled 1 / 1 combinations
________________________________________________________________________________

INFO  : Ranking final models by energy
INFO  : Outputting models to dir 'loop/model.1'
INFO  : model.1.pdb : Energy = 34.187 (T = 0) : I = 0 : R = 0 : RoG = 36.263 : PP = 7.590 : SP = 4.170 : SE = 3.234 : HO = -29.138 : TE = 12.067979
________________________________________________________________________________

INFO  : Model building complete
________________________________________________________________________________

