null Sun 23 Dec 22:22:44 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vjx-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjx-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjx-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:52 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 137 and 0 Target number of residues in the AU: 137 Target solvent content: 0.6402 Checking the provided sequence file Detected sequence length: 157 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 157 Adjusted target solvent content: 0.59 Input MTZ file: 1vjx-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 98 Cell parameters: 82.326 82.326 121.618 90.000 90.000 90.000 Input sequence file: 1vjx-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1256 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 68.175 3.602 Wilson plot Bfac: 70.99 2534 reflections ( 96.42 % complete ) and 0 restraints for refining 1393 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3473 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3324 (Rfree = 0.000) for 1393 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.22 Search for helices and strands: 0 residues in 0 chains, 1426 seeds are put forward Round 1: 53 peptides, 10 chains. Longest chain 9 peptides. Score 0.297 Round 2: 67 peptides, 10 chains. Longest chain 13 peptides. Score 0.417 Round 3: 76 peptides, 12 chains. Longest chain 10 peptides. Score 0.417 Round 4: 78 peptides, 11 chains. Longest chain 11 peptides. Score 0.466 Round 5: 79 peptides, 10 chains. Longest chain 14 peptides. Score 0.506 Taking the results from Round 5 Chains 10, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2534 reflections ( 96.42 % complete ) and 2422 restraints for refining 1075 atoms. 2156 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3439 (Rfree = 0.000) for 1075 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 2: After refmac, R = 0.3094 (Rfree = 0.000) for 1055 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.3254 (Rfree = 0.000) for 1048 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.2798 (Rfree = 0.000) for 1040 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.2965 (Rfree = 0.000) for 1039 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.10 Search for helices and strands: 0 residues in 0 chains, 1105 seeds are put forward Round 1: 82 peptides, 14 chains. Longest chain 9 peptides. Score 0.396 Round 2: 86 peptides, 11 chains. Longest chain 17 peptides. Score 0.522 Round 3: 81 peptides, 11 chains. Longest chain 15 peptides. Score 0.488 Round 4: 75 peptides, 11 chains. Longest chain 15 peptides. Score 0.444 Round 5: 78 peptides, 10 chains. Longest chain 11 peptides. Score 0.499 Taking the results from Round 2 Chains 11, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2534 reflections ( 96.42 % complete ) and 2380 restraints for refining 1071 atoms. 2091 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3256 (Rfree = 0.000) for 1071 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 7: After refmac, R = 0.2998 (Rfree = 0.000) for 1053 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 8: After refmac, R = 0.3008 (Rfree = 0.000) for 1049 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.3097 (Rfree = 0.000) for 1043 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.2764 (Rfree = 0.000) for 1041 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 3.10 Search for helices and strands: 0 residues in 0 chains, 1108 seeds are put forward Round 1: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.364 Round 2: 80 peptides, 9 chains. Longest chain 21 peptides. Score 0.544 Round 3: 92 peptides, 13 chains. Longest chain 16 peptides. Score 0.502 Round 4: 91 peptides, 11 chains. Longest chain 25 peptides. Score 0.555 Round 5: 91 peptides, 11 chains. Longest chain 22 peptides. Score 0.555 Taking the results from Round 5 Chains 11, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2534 reflections ( 96.42 % complete ) and 2572 restraints for refining 1120 atoms. 2263 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3182 (Rfree = 0.000) for 1120 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 12: After refmac, R = 0.2978 (Rfree = 0.000) for 1115 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.3084 (Rfree = 0.000) for 1110 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 14: After refmac, R = 0.2776 (Rfree = 0.000) for 1106 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2877 (Rfree = 0.000) for 1103 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 2.94 Search for helices and strands: 0 residues in 0 chains, 1172 seeds are put forward Round 1: 77 peptides, 13 chains. Longest chain 13 peptides. Score 0.391 Round 2: 83 peptides, 15 chains. Longest chain 9 peptides. Score 0.370 Round 3: 85 peptides, 13 chains. Longest chain 14 peptides. Score 0.452 Round 4: 85 peptides, 12 chains. Longest chain 12 peptides. Score 0.484 Round 5: 81 peptides, 10 chains. Longest chain 11 peptides. Score 0.520 Taking the results from Round 5 Chains 10, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2534 reflections ( 96.42 % complete ) and 2643 restraints for refining 1139 atoms. 2369 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3132 (Rfree = 0.000) for 1139 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 17: After refmac, R = 0.3021 (Rfree = 0.000) for 1132 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 18: After refmac, R = 0.3059 (Rfree = 0.000) for 1130 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 19: After refmac, R = 0.2779 (Rfree = 0.000) for 1124 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 20: After refmac, R = 0.2723 (Rfree = 0.000) for 1123 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.82 Search for helices and strands: 0 residues in 0 chains, 1193 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.317 Round 2: 80 peptides, 13 chains. Longest chain 9 peptides. Score 0.414 Round 3: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.367 Round 4: 90 peptides, 12 chains. Longest chain 17 peptides. Score 0.519 Round 5: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.429 Taking the results from Round 4 Chains 12, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2534 reflections ( 96.42 % complete ) and 2618 restraints for refining 1139 atoms. 2318 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3039 (Rfree = 0.000) for 1139 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2883 (Rfree = 0.000) for 1120 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 23: After refmac, R = 0.2864 (Rfree = 0.000) for 1110 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.2758 (Rfree = 0.000) for 1105 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2739 (Rfree = 0.000) for 1103 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 2.98 Search for helices and strands: 0 residues in 0 chains, 1171 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 10 peptides. Score 0.297 Round 2: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.378 Round 3: 80 peptides, 13 chains. Longest chain 12 peptides. Score 0.414 Round 4: 84 peptides, 13 chains. Longest chain 9 peptides. Score 0.444 Round 5: 81 peptides, 12 chains. Longest chain 11 peptides. Score 0.455 Taking the results from Round 5 Chains 12, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2534 reflections ( 96.42 % complete ) and 2703 restraints for refining 1139 atoms. 2439 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3391 (Rfree = 0.000) for 1139 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 27: After refmac, R = 0.3115 (Rfree = 0.000) for 1124 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.2939 (Rfree = 0.000) for 1114 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.2904 (Rfree = 0.000) for 1113 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.3192 (Rfree = 0.000) for 1108 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.01 Search for helices and strands: 0 residues in 0 chains, 1161 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 8 peptides. Score 0.292 Round 2: 80 peptides, 13 chains. Longest chain 14 peptides. Score 0.414 Round 3: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.399 Round 4: 76 peptides, 11 chains. Longest chain 13 peptides. Score 0.451 Round 5: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.385 Taking the results from Round 4 Chains 11, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2534 reflections ( 96.42 % complete ) and 2643 restraints for refining 1137 atoms. 2394 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2947 (Rfree = 0.000) for 1137 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 32: After refmac, R = 0.2698 (Rfree = 0.000) for 1125 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.3235 (Rfree = 0.000) for 1119 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 34: After refmac, R = 0.2756 (Rfree = 0.000) for 1109 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.2865 (Rfree = 0.000) for 1106 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.14 Search for helices and strands: 0 residues in 0 chains, 1180 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 8 peptides. Score 0.243 Round 2: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.366 Round 3: 82 peptides, 14 chains. Longest chain 9 peptides. Score 0.396 Round 4: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.411 Round 5: 74 peptides, 12 chains. Longest chain 12 peptides. Score 0.401 Taking the results from Round 4 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2534 reflections ( 96.42 % complete ) and 2561 restraints for refining 1130 atoms. 2295 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2774 (Rfree = 0.000) for 1130 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 37: After refmac, R = 0.2877 (Rfree = 0.000) for 1120 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2640 (Rfree = 0.000) for 1117 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.2705 (Rfree = 0.000) for 1112 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.2720 (Rfree = 0.000) for 1108 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.03 Search for helices and strands: 0 residues in 0 chains, 1177 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.254 Round 2: 64 peptides, 10 chains. Longest chain 10 peptides. Score 0.392 Round 3: 65 peptides, 10 chains. Longest chain 10 peptides. Score 0.401 Round 4: 63 peptides, 11 chains. Longest chain 8 peptides. Score 0.347 Round 5: 74 peptides, 12 chains. Longest chain 8 peptides. Score 0.401 Taking the results from Round 5 Chains 12, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2534 reflections ( 96.42 % complete ) and 2731 restraints for refining 1139 atoms. 2495 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2827 (Rfree = 0.000) for 1139 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.2676 (Rfree = 0.000) for 1130 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.2552 (Rfree = 0.000) for 1122 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.2497 (Rfree = 0.000) for 1121 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.2473 (Rfree = 0.000) for 1116 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.92 2.59 Search for helices and strands: 0 residues in 0 chains, 1158 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.274 Round 2: 66 peptides, 12 chains. Longest chain 12 peptides. Score 0.336 Round 3: 68 peptides, 11 chains. Longest chain 11 peptides. Score 0.389 Round 4: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.406 Round 5: 74 peptides, 13 chains. Longest chain 8 peptides. Score 0.366 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vjx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2534 reflections ( 96.42 % complete ) and 2685 restraints for refining 1139 atoms. 2434 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3061 (Rfree = 0.000) for 1139 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3084 (Rfree = 0.000) for 1129 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2552 (Rfree = 0.000) for 1122 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2466 (Rfree = 0.000) for 1118 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:49:39 GMT 2018 Job finished. TimeTaking 26.92 Used memory is bytes: 7615552