Mon 24 Dec 07:53:36 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prr-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2prr-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2prr-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-parrot-noncs ############### 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 07:53:40 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/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-parrot-noncs/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 1752 and 0 Target number of residues in the AU: 1752 Target solvent content: 0.6676 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 2364 Adjusted target solvent content: 0.55 Input MTZ file: 2prr-3.8-parrot-noncs.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: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.80 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. 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: 119.307 3.800 Wilson plot Bfac: 90.62 26567 reflections ( 97.64 % complete ) and 0 restraints for refining 20876 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3249 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2892 (Rfree = 0.000) for 20876 atoms. Found 114 (114 requested) and removed 128 (57 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.50 Search for helices and strands: 0 residues in 0 chains, 21427 seeds are put forward NCS extension: 0 residues added, 21427 seeds are put forward Round 1: 962 peptides, 189 chains. Longest chain 14 peptides. Score 0.305 Round 2: 1155 peptides, 181 chains. Longest chain 17 peptides. Score 0.438 Round 3: 1190 peptides, 172 chains. Longest chain 18 peptides. Score 0.478 Round 4: 1217 peptides, 177 chains. Longest chain 20 peptides. Score 0.480 Round 5: 1231 peptides, 163 chains. Longest chain 24 peptides. Score 0.519 Taking the results from Round 5 Chains 167, Residues 1068, Estimated correctness of the model 0.0 % 10 chains (100 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4527 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2187 (Rfree = 0.000) for 17106 atoms. Found 73 (94 requested) and removed 83 (47 requested) atoms. Cycle 2: After refmac, R = 0.2071 (Rfree = 0.000) for 17096 atoms. Found 79 (94 requested) and removed 76 (47 requested) atoms. Cycle 3: After refmac, R = 0.1985 (Rfree = 0.000) for 17099 atoms. Found 53 (94 requested) and removed 85 (47 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1874 (Rfree = 0.000) for 17067 atoms. Found 80 (93 requested) and removed 88 (46 requested) atoms. Cycle 5: After refmac, R = 0.1802 (Rfree = 0.000) for 17059 atoms. Found 46 (93 requested) and removed 93 (46 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.47 Search for helices and strands: 0 residues in 0 chains, 17713 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 17740 seeds are put forward Round 1: 1029 peptides, 185 chains. Longest chain 14 peptides. Score 0.356 Round 2: 1201 peptides, 177 chains. Longest chain 19 peptides. Score 0.472 Round 3: 1257 peptides, 181 chains. Longest chain 18 peptides. Score 0.492 Round 4: 1262 peptides, 172 chains. Longest chain 20 peptides. Score 0.514 Round 5: 1264 peptides, 178 chains. Longest chain 20 peptides. Score 0.502 Taking the results from Round 4 Chains 172, Residues 1090, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4269 restraints for refining 16899 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1788 (Rfree = 0.000) for 16899 atoms. Found 44 (92 requested) and removed 124 (46 requested) atoms. Cycle 7: After refmac, R = 0.1766 (Rfree = 0.000) for 16819 atoms. Found 48 (92 requested) and removed 88 (46 requested) atoms. Cycle 8: After refmac, R = 0.1659 (Rfree = 0.000) for 16779 atoms. Found 48 (92 requested) and removed 106 (46 requested) atoms. Cycle 9: After refmac, R = 0.1608 (Rfree = 0.000) for 16721 atoms. Found 50 (91 requested) and removed 96 (45 requested) atoms. Cycle 10: After refmac, R = 0.1572 (Rfree = 0.000) for 16675 atoms. Found 39 (91 requested) and removed 104 (45 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.49 Search for helices and strands: 0 residues in 0 chains, 17301 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 17322 seeds are put forward Round 1: 1044 peptides, 192 chains. Longest chain 19 peptides. Score 0.347 Round 2: 1209 peptides, 186 chains. Longest chain 35 peptides. Score 0.455 Round 3: 1246 peptides, 177 chains. Longest chain 36 peptides. Score 0.495 Round 4: 1286 peptides, 180 chains. Longest chain 31 peptides. Score 0.508 Round 5: 1286 peptides, 181 chains. Longest chain 25 peptides. Score 0.506 Taking the results from Round 4 Chains 184, Residues 1106, Estimated correctness of the model 0.0 % 14 chains (101 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 26567 reflections ( 97.64 % complete ) and 4601 restraints for refining 17087 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1714 (Rfree = 0.000) for 17087 atoms. Found 46 (93 requested) and removed 125 (46 requested) atoms. Cycle 12: After refmac, R = 0.1655 (Rfree = 0.000) for 17008 atoms. Found 58 (93 requested) and removed 112 (46 requested) atoms. Cycle 13: After refmac, R = 0.1219 (Rfree = 0.000) for 16954 atoms. Found 14 (93 requested) and removed 70 (46 requested) atoms. Cycle 14: After refmac, R = 0.1127 (Rfree = 0.000) for 16898 atoms. Found 7 (92 requested) and removed 66 (46 requested) atoms. Cycle 15: After refmac, R = 0.1119 (Rfree = 0.000) for 16839 atoms. Found 11 (92 requested) and removed 64 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.48 Search for helices and strands: 0 residues in 0 chains, 17433 seeds are put forward NCS extension: 42 residues added (0 deleted due to clashes), 17475 seeds are put forward Round 1: 1086 peptides, 198 chains. Longest chain 16 peptides. Score 0.357 Round 2: 1218 peptides, 189 chains. Longest chain 25 peptides. Score 0.453 Round 3: 1240 peptides, 180 chains. Longest chain 25 peptides. Score 0.485 Round 4: 1233 peptides, 172 chains. Longest chain 21 peptides. Score 0.500 Round 5: 1286 peptides, 178 chains. Longest chain 26 peptides. Score 0.513 Taking the results from Round 5 Chains 179, Residues 1108, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4394 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1690 (Rfree = 0.000) for 17106 atoms. Found 57 (94 requested) and removed 110 (47 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1664 (Rfree = 0.000) for 17053 atoms. Found 92 (93 requested) and removed 81 (46 requested) atoms. Cycle 18: After refmac, R = 0.1225 (Rfree = 0.000) for 17064 atoms. Found 7 (93 requested) and removed 67 (46 requested) atoms. Cycle 19: After refmac, R = 0.1152 (Rfree = 0.000) for 17004 atoms. Found 6 (93 requested) and removed 65 (46 requested) atoms. Cycle 20: After refmac, R = 0.1138 (Rfree = 0.000) for 16945 atoms. Found 4 (93 requested) and removed 56 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.48 Search for helices and strands: 0 residues in 0 chains, 17497 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 17518 seeds are put forward Round 1: 1035 peptides, 194 chains. Longest chain 16 peptides. Score 0.337 Round 2: 1158 peptides, 184 chains. Longest chain 29 peptides. Score 0.433 Round 3: 1181 peptides, 176 chains. Longest chain 20 peptides. Score 0.464 Round 4: 1175 peptides, 180 chains. Longest chain 20 peptides. Score 0.451 Round 5: 1170 peptides, 178 chains. Longest chain 24 peptides. Score 0.453 Taking the results from Round 3 Chains 179, Residues 1005, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4002 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1701 (Rfree = 0.000) for 17106 atoms. Found 77 (94 requested) and removed 95 (47 requested) atoms. Cycle 22: After refmac, R = 0.1671 (Rfree = 0.000) for 17088 atoms. Found 93 (93 requested) and removed 88 (46 requested) atoms. Cycle 23: After refmac, R = 0.1211 (Rfree = 0.000) for 17093 atoms. Found 12 (94 requested) and removed 67 (47 requested) atoms. Cycle 24: After refmac, R = 0.1133 (Rfree = 0.000) for 17038 atoms. Found 8 (93 requested) and removed 60 (46 requested) atoms. Cycle 25: After refmac, R = 0.1123 (Rfree = 0.000) for 16986 atoms. Found 9 (93 requested) and removed 56 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.49 Search for helices and strands: 0 residues in 0 chains, 17508 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 17522 seeds are put forward Round 1: 954 peptides, 179 chains. Longest chain 18 peptides. Score 0.327 Round 2: 1099 peptides, 172 chains. Longest chain 19 peptides. Score 0.429 Round 3: 1111 peptides, 178 chains. Longest chain 21 peptides. Score 0.421 Round 4: 1121 peptides, 170 chains. Longest chain 23 peptides. Score 0.446 Round 5: 1117 peptides, 170 chains. Longest chain 18 peptides. Score 0.444 Taking the results from Round 4 Chains 171, Residues 951, Estimated correctness of the model 0.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 3801 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1717 (Rfree = 0.000) for 17106 atoms. Found 74 (94 requested) and removed 86 (47 requested) atoms. Cycle 27: After refmac, R = 0.1680 (Rfree = 0.000) for 17094 atoms. Found 80 (94 requested) and removed 79 (47 requested) atoms. Cycle 28: After refmac, R = 0.1190 (Rfree = 0.000) for 17095 atoms. Found 10 (94 requested) and removed 62 (47 requested) atoms. Cycle 29: After refmac, R = 0.1112 (Rfree = 0.000) for 17043 atoms. Found 6 (93 requested) and removed 57 (46 requested) atoms. Cycle 30: After refmac, R = 0.1117 (Rfree = 0.000) for 16992 atoms. Found 8 (93 requested) and removed 59 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.47 Search for helices and strands: 0 residues in 0 chains, 17481 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 17505 seeds are put forward Round 1: 928 peptides, 183 chains. Longest chain 13 peptides. Score 0.300 Round 2: 1086 peptides, 178 chains. Longest chain 15 peptides. Score 0.407 Round 3: 1082 peptides, 181 chains. Longest chain 19 peptides. Score 0.397 Round 4: 1066 peptides, 173 chains. Longest chain 17 peptides. Score 0.408 Round 5: 1106 peptides, 177 chains. Longest chain 19 peptides. Score 0.421 Taking the results from Round 5 Chains 178, Residues 929, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 3615 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1683 (Rfree = 0.000) for 17106 atoms. Found 62 (94 requested) and removed 92 (47 requested) atoms. Cycle 32: After refmac, R = 0.1652 (Rfree = 0.000) for 17076 atoms. Found 85 (93 requested) and removed 100 (46 requested) atoms. Cycle 33: After refmac, R = 0.1161 (Rfree = 0.000) for 17061 atoms. Found 10 (93 requested) and removed 76 (46 requested) atoms. Cycle 34: After refmac, R = 0.1081 (Rfree = 0.000) for 16995 atoms. Found 3 (93 requested) and removed 64 (46 requested) atoms. Cycle 35: After refmac, R = 0.1062 (Rfree = 0.000) for 16934 atoms. Found 7 (93 requested) and removed 62 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.48 Search for helices and strands: 0 residues in 0 chains, 17397 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 17416 seeds are put forward Round 1: 913 peptides, 177 chains. Longest chain 13 peptides. Score 0.306 Round 2: 1041 peptides, 175 chains. Longest chain 18 peptides. Score 0.389 Round 3: 1074 peptides, 177 chains. Longest chain 18 peptides. Score 0.403 Round 4: 1073 peptides, 178 chains. Longest chain 16 peptides. Score 0.400 Round 5: 1083 peptides, 178 chains. Longest chain 15 peptides. Score 0.405 Taking the results from Round 5 Chains 178, Residues 905, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 3464 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1642 (Rfree = 0.000) for 17106 atoms. Found 75 (94 requested) and removed 86 (47 requested) atoms. Cycle 37: After refmac, R = 0.1624 (Rfree = 0.000) for 17095 atoms. Found 86 (94 requested) and removed 92 (47 requested) atoms. Cycle 38: After refmac, R = 0.1647 (Rfree = 0.000) for 17089 atoms. Found 93 (93 requested) and removed 91 (46 requested) atoms. Cycle 39: After refmac, R = 0.1594 (Rfree = 0.000) for 17091 atoms. Found 92 (93 requested) and removed 94 (46 requested) atoms. Cycle 40: After refmac, R = 0.1577 (Rfree = 0.000) for 17089 atoms. Found 93 (93 requested) and removed 93 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.47 Search for helices and strands: 0 residues in 0 chains, 17701 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 17718 seeds are put forward Round 1: 806 peptides, 164 chains. Longest chain 13 peptides. Score 0.273 Round 2: 986 peptides, 175 chains. Longest chain 14 peptides. Score 0.357 Round 3: 993 peptides, 166 chains. Longest chain 16 peptides. Score 0.384 Round 4: 976 peptides, 166 chains. Longest chain 16 peptides. Score 0.374 Round 5: 1032 peptides, 169 chains. Longest chain 16 peptides. Score 0.399 Taking the results from Round 5 Chains 170, Residues 863, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 26567 reflections ( 97.64 % complete ) and 3374 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1544 (Rfree = 0.000) for 17106 atoms. Found 69 (94 requested) and removed 100 (47 requested) atoms. Cycle 42: After refmac, R = 0.1536 (Rfree = 0.000) for 17075 atoms. Found 93 (93 requested) and removed 93 (46 requested) atoms. Cycle 43: After refmac, R = 0.1512 (Rfree = 0.000) for 17075 atoms. Found 86 (93 requested) and removed 103 (46 requested) atoms. Cycle 44: After refmac, R = 0.1452 (Rfree = 0.000) for 17058 atoms. Found 87 (93 requested) and removed 83 (46 requested) atoms. Cycle 45: After refmac, R = 0.1445 (Rfree = 0.000) for 17062 atoms. Found 93 (93 requested) and removed 81 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.48 Search for helices and strands: 0 residues in 0 chains, 17639 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 17652 seeds are put forward Round 1: 743 peptides, 154 chains. Longest chain 12 peptides. Score 0.259 Round 2: 873 peptides, 160 chains. Longest chain 13 peptides. Score 0.327 Round 3: 887 peptides, 157 chains. Longest chain 14 peptides. Score 0.344 Round 4: 910 peptides, 157 chains. Longest chain 13 peptides. Score 0.358 Round 5: 903 peptides, 150 chains. Longest chain 16 peptides. Score 0.372 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 150, Residues 753, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 150 chains (753 residues) following loop building 2 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26567 reflections ( 97.64 % complete ) and 2919 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1622 (Rfree = 0.000) for 17106 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 47: After refmac, R = 0.1663 (Rfree = 0.000) for 17059 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Cycle 48: After refmac, R = 0.1602 (Rfree = 0.000) for 17013 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1534 (Rfree = 0.000) for 16967 atoms. TimeTaking 138.23