INFO  : Successfully started log file 'model.loop.log'
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                                     Assembler

                 Protein structure prediction by fragment assembly
                                   (Ver. 0.6.6)
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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/ccadd883d79760cc/input.fasta
PSSM_FILE                                = /bmm/www/servers/phyre2/public_html/phyre2_output/ccadd883d79760cc/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
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[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 - c2cj0A_.20.pdb
________________________________________________________________________________

INFO  : Performing trim back
________________________________________________________________________________

INFO  : Modelling loops
WARN  : Model missing 182 N-terminal residues
WARN  : Model missing 59 C-terminal residues
________________________________________________________________________________

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 = -3.218 (T = 0) : I = 0 : R = 0 : RoG = 24.000 : PP = 1.470 : SP = 1.584 : SE = 0.383 : HO = -32.487 : TE = 1.832119
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INFO  : Model building complete
________________________________________________________________________________

