Mon 24 Dec 01:10:21 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2obp-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obp-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obp-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-4.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 01:10:25 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/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-4.0-parrot-mrncs/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 136 and 0 Target number of residues in the AU: 136 Target solvent content: 0.6861 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.56 Input MTZ file: 2obp-4.0-parrot-mrncs.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: 182 Cell parameters: 76.690 76.690 138.090 90.000 90.000 120.000 Input sequence file: 2obp-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1536 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.462 4.001 Wilson plot Bfac: 105.46 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2299 reflections ( 99.14 % complete ) and 0 restraints for refining 1706 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3765 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3970 (Rfree = 0.000) for 1706 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.15 3.83 Search for helices and strands: 0 residues in 0 chains, 1736 seeds are put forward NCS extension: 0 residues added, 1736 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 13 peptides. Score 0.292 Round 2: 76 peptides, 10 chains. Longest chain 14 peptides. Score 0.458 Round 3: 88 peptides, 12 chains. Longest chain 14 peptides. Score 0.477 Round 4: 82 peptides, 11 chains. Longest chain 13 peptides. Score 0.467 Round 5: 78 peptides, 12 chains. Longest chain 12 peptides. Score 0.410 Taking the results from Round 3 Chains 12, Residues 76, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 3288 restraints for refining 1385 atoms. 2974 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3376 (Rfree = 0.000) for 1385 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 2: After refmac, R = 0.3339 (Rfree = 0.000) for 1330 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 3: After refmac, R = 0.3280 (Rfree = 0.000) for 1285 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 4: After refmac, R = 0.3224 (Rfree = 0.000) for 1255 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 5: After refmac, R = 0.3185 (Rfree = 0.000) for 1213 atoms. Found 4 (5 requested) and removed 16 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.08 3.77 Search for helices and strands: 0 residues in 0 chains, 1274 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 1298 seeds are put forward Round 1: 69 peptides, 10 chains. Longest chain 13 peptides. Score 0.410 Round 2: 85 peptides, 13 chains. Longest chain 13 peptides. Score 0.427 Round 3: 87 peptides, 10 chains. Longest chain 17 peptides. Score 0.528 Round 4: 82 peptides, 10 chains. Longest chain 16 peptides. Score 0.497 Round 5: 88 peptides, 10 chains. Longest chain 15 peptides. Score 0.533 Taking the results from Round 5 Chains 11, Residues 78, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2661 restraints for refining 1234 atoms. 2324 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3053 (Rfree = 0.000) for 1234 atoms. Found 4 (5 requested) and removed 14 (2 requested) atoms. Cycle 7: After refmac, R = 0.3078 (Rfree = 0.000) for 1203 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 8: After refmac, R = 0.3027 (Rfree = 0.000) for 1173 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 9: After refmac, R = 0.3507 (Rfree = 0.000) for 1138 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 10: After refmac, R = 0.3127 (Rfree = 0.000) for 1115 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.06 3.75 Search for helices and strands: 0 residues in 0 chains, 1189 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1209 seeds are put forward Round 1: 70 peptides, 12 chains. Longest chain 14 peptides. Score 0.352 Round 2: 84 peptides, 10 chains. Longest chain 17 peptides. Score 0.509 Round 3: 83 peptides, 11 chains. Longest chain 12 peptides. Score 0.474 Round 4: 82 peptides, 12 chains. Longest chain 11 peptides. Score 0.437 Round 5: 81 peptides, 10 chains. Longest chain 15 peptides. Score 0.491 Taking the results from Round 2 Chains 10, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2427 restraints for refining 1122 atoms. 2141 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3230 (Rfree = 0.000) for 1122 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. Cycle 12: After refmac, R = 0.3095 (Rfree = 0.000) for 1103 atoms. Found 4 (5 requested) and removed 9 (2 requested) atoms. Cycle 13: After refmac, R = 0.3098 (Rfree = 0.000) for 1083 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 14: After refmac, R = 0.3010 (Rfree = 0.000) for 1064 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 15: After refmac, R = 0.3203 (Rfree = 0.000) for 1050 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.07 3.76 Search for helices and strands: 0 residues in 0 chains, 1119 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1144 seeds are put forward Round 1: 75 peptides, 12 chains. Longest chain 10 peptides. Score 0.389 Round 2: 86 peptides, 11 chains. Longest chain 13 peptides. Score 0.493 Round 3: 80 peptides, 10 chains. Longest chain 15 peptides. Score 0.484 Round 4: 92 peptides, 10 chains. Longest chain 17 peptides. Score 0.557 Round 5: 92 peptides, 11 chains. Longest chain 15 peptides. Score 0.530 Taking the results from Round 4 Chains 10, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2387 restraints for refining 1119 atoms. 2069 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3305 (Rfree = 0.000) for 1119 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 17: After refmac, R = 0.3159 (Rfree = 0.000) for 1093 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 18: After refmac, R = 0.3041 (Rfree = 0.000) for 1065 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 19: After refmac, R = 0.3460 (Rfree = 0.000) for 1056 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 20: After refmac, R = 0.3234 (Rfree = 0.000) for 1035 atoms. Found 4 (4 requested) and removed 15 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.13 3.81 Search for helices and strands: 0 residues in 0 chains, 1100 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1117 seeds are put forward Round 1: 71 peptides, 11 chains. Longest chain 12 peptides. Score 0.392 Round 2: 75 peptides, 9 chains. Longest chain 13 peptides. Score 0.482 Round 3: 86 peptides, 10 chains. Longest chain 17 peptides. Score 0.522 Round 4: 80 peptides, 9 chains. Longest chain 15 peptides. Score 0.514 Round 5: 79 peptides, 9 chains. Longest chain 14 peptides. Score 0.508 Taking the results from Round 3 Chains 10, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2378 restraints for refining 1111 atoms. 2084 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3326 (Rfree = 0.000) for 1111 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 22: After refmac, R = 0.3181 (Rfree = 0.000) for 1089 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 23: After refmac, R = 0.3129 (Rfree = 0.000) for 1062 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 24: After refmac, R = 0.3406 (Rfree = 0.000) for 1046 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 25: After refmac, R = 0.3515 (Rfree = 0.000) for 1028 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.15 3.83 Search for helices and strands: 0 residues in 0 chains, 1123 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1148 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.281 Round 2: 79 peptides, 11 chains. Longest chain 16 peptides. Score 0.448 Round 3: 70 peptides, 10 chains. Longest chain 13 peptides. Score 0.417 Round 4: 82 peptides, 10 chains. Longest chain 14 peptides. Score 0.497 Round 5: 78 peptides, 9 chains. Longest chain 17 peptides. Score 0.501 Taking the results from Round 5 Chains 9, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2418 restraints for refining 1113 atoms. 2151 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3464 (Rfree = 0.000) for 1113 atoms. Found 5 (5 requested) and removed 19 (2 requested) atoms. Cycle 27: After refmac, R = 0.3491 (Rfree = 0.000) for 1084 atoms. Found 5 (5 requested) and removed 21 (2 requested) atoms. Cycle 28: After refmac, R = 0.3419 (Rfree = 0.000) for 1053 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 29: After refmac, R = 0.3694 (Rfree = 0.000) for 1042 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 30: After refmac, R = 0.3453 (Rfree = 0.000) for 1017 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.59 4.24 Search for helices and strands: 0 residues in 0 chains, 1093 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1112 seeds are put forward Round 1: 67 peptides, 10 chains. Longest chain 12 peptides. Score 0.396 Round 2: 78 peptides, 10 chains. Longest chain 15 peptides. Score 0.471 Round 3: 76 peptides, 9 chains. Longest chain 15 peptides. Score 0.489 Round 4: 70 peptides, 9 chains. Longest chain 15 peptides. Score 0.449 Round 5: 74 peptides, 9 chains. Longest chain 13 peptides. Score 0.476 Taking the results from Round 3 Chains 10, Residues 67, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2162 restraints for refining 1083 atoms. 1847 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3357 (Rfree = 0.000) for 1083 atoms. Found 4 (5 requested) and removed 11 (2 requested) atoms. Cycle 32: After refmac, R = 0.3108 (Rfree = 0.000) for 1057 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 33: After refmac, R = 0.3241 (Rfree = 0.000) for 1051 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 34: After refmac, R = 0.3182 (Rfree = 0.000) for 1030 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 35: After refmac, R = 0.2828 (Rfree = 0.000) for 1011 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.22 3.89 Search for helices and strands: 0 residues in 0 chains, 1049 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1068 seeds are put forward Round 1: 63 peptides, 9 chains. Longest chain 10 peptides. Score 0.400 Round 2: 57 peptides, 8 chains. Longest chain 13 peptides. Score 0.390 Round 3: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.421 Round 4: 62 peptides, 8 chains. Longest chain 11 peptides. Score 0.426 Round 5: 71 peptides, 7 chains. Longest chain 16 peptides. Score 0.518 Taking the results from Round 5 Chains 7, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2397 restraints for refining 1087 atoms. 2148 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3542 (Rfree = 0.000) for 1087 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 37: After refmac, R = 0.3093 (Rfree = 0.000) for 1068 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 38: After refmac, R = 0.3022 (Rfree = 0.000) for 1054 atoms. Found 3 (5 requested) and removed 9 (2 requested) atoms. Cycle 39: After refmac, R = 0.2949 (Rfree = 0.000) for 1040 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 40: After refmac, R = 0.3254 (Rfree = 0.000) for 1025 atoms. Found 4 (4 requested) and removed 15 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.15 3.83 Search for helices and strands: 0 residues in 0 chains, 1082 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1104 seeds are put forward Round 1: 62 peptides, 10 chains. Longest chain 12 peptides. Score 0.359 Round 2: 71 peptides, 8 chains. Longest chain 16 peptides. Score 0.487 Round 3: 70 peptides, 10 chains. Longest chain 13 peptides. Score 0.417 Round 4: 68 peptides, 11 chains. Longest chain 11 peptides. Score 0.370 Round 5: 66 peptides, 10 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 2 Chains 8, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2329 restraints for refining 1052 atoms. 2085 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3475 (Rfree = 0.000) for 1052 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 42: After refmac, R = 0.3125 (Rfree = 0.000) for 1030 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 43: After refmac, R = 0.3097 (Rfree = 0.000) for 1015 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.3074 (Rfree = 0.000) for 995 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.3099 (Rfree = 0.000) for 985 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.11 3.79 Search for helices and strands: 0 residues in 0 chains, 1048 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1060 seeds are put forward Round 1: 50 peptides, 9 chains. Longest chain 8 peptides. Score 0.298 Round 2: 67 peptides, 9 chains. Longest chain 16 peptides. Score 0.428 Round 3: 63 peptides, 9 chains. Longest chain 11 peptides. Score 0.400 Round 4: 59 peptides, 7 chains. Longest chain 11 peptides. Score 0.439 Round 5: 57 peptides, 8 chains. Longest chain 12 peptides. Score 0.390 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 52, 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 2obp-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2299 reflections ( 99.14 % complete ) and 2323 restraints for refining 1036 atoms. 2122 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3177 (Rfree = 0.000) for 1036 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3114 (Rfree = 0.000) for 1019 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.3059 (Rfree = 0.000) for 1009 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2862 (Rfree = 0.000) for 1001 atoms. TimeTaking 23.9