Mon 24 Dec 00:50:03 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 2prr-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-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/2prr-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-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 00:50:08 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/2prr-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-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 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-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: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-3.8-parrot-mrncs.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 20859 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3197 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2822 (Rfree = 0.000) for 20859 atoms. Found 114 (114 requested) and removed 100 (57 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.52 Search for helices and strands: 0 residues in 0 chains, 21523 seeds are put forward NCS extension: 0 residues added, 21523 seeds are put forward Round 1: 1076 peptides, 201 chains. Longest chain 13 peptides. Score 0.344 Round 2: 1245 peptides, 185 chains. Longest chain 19 peptides. Score 0.476 Round 3: 1288 peptides, 175 chains. Longest chain 31 peptides. Score 0.520 Round 4: 1323 peptides, 162 chains. Longest chain 25 peptides. Score 0.564 Round 5: 1350 peptides, 159 chains. Longest chain 34 peptides. Score 0.583 Taking the results from Round 5 Chains 169, Residues 1191, Estimated correctness of the model 0.0 % 13 chains (153 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 5170 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2069 (Rfree = 0.000) for 17106 atoms. Found 37 (94 requested) and removed 88 (47 requested) atoms. Cycle 2: After refmac, R = 0.1938 (Rfree = 0.000) for 17055 atoms. Found 45 (93 requested) and removed 95 (46 requested) atoms. Cycle 3: After refmac, R = 0.1811 (Rfree = 0.000) for 17005 atoms. Found 40 (93 requested) and removed 90 (46 requested) atoms. Cycle 4: After refmac, R = 0.1357 (Rfree = 0.000) for 16955 atoms. Found 7 (93 requested) and removed 79 (46 requested) atoms. Cycle 5: After refmac, R = 0.1271 (Rfree = 0.000) for 16883 atoms. Found 9 (92 requested) and removed 72 (46 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.47 Search for helices and strands: 0 residues in 0 chains, 17619 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 17652 seeds are put forward Round 1: 1088 peptides, 190 chains. Longest chain 16 peptides. Score 0.378 Round 2: 1293 peptides, 183 chains. Longest chain 21 peptides. Score 0.505 Round 3: 1299 peptides, 179 chains. Longest chain 18 peptides. Score 0.517 Round 4: 1315 peptides, 175 chains. Longest chain 21 peptides. Score 0.533 Round 5: 1322 peptides, 173 chains. Longest chain 26 peptides. Score 0.541 Taking the results from Round 5 Chains 176, Residues 1149, Estimated correctness of the model 0.0 % 4 chains (45 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4591 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1923 (Rfree = 0.000) for 17106 atoms. Found 73 (94 requested) and removed 88 (47 requested) atoms. Cycle 7: After refmac, R = 0.1825 (Rfree = 0.000) for 17091 atoms. Found 78 (93 requested) and removed 73 (46 requested) atoms. Cycle 8: After refmac, R = 0.1353 (Rfree = 0.000) for 17096 atoms. Found 11 (94 requested) and removed 71 (47 requested) atoms. Cycle 9: After refmac, R = 0.1262 (Rfree = 0.000) for 17036 atoms. Found 7 (93 requested) and removed 52 (46 requested) atoms. Cycle 10: After refmac, R = 0.1231 (Rfree = 0.000) for 16991 atoms. Found 10 (93 requested) and removed 62 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.48 Search for helices and strands: 0 residues in 0 chains, 17626 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 17644 seeds are put forward Round 1: 1074 peptides, 180 chains. Longest chain 23 peptides. Score 0.395 Round 2: 1290 peptides, 184 chains. Longest chain 22 peptides. Score 0.501 Round 3: 1270 peptides, 171 chains. Longest chain 16 peptides. Score 0.520 Round 4: 1310 peptides, 180 chains. Longest chain 23 peptides. Score 0.520 Round 5: 1280 peptides, 170 chains. Longest chain 24 peptides. Score 0.527 Taking the results from Round 5 Chains 172, Residues 1110, Estimated correctness of the model 0.0 % 6 chains (41 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4411 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1886 (Rfree = 0.000) for 17106 atoms. Found 90 (94 requested) and removed 104 (47 requested) atoms. Cycle 12: After refmac, R = 0.1765 (Rfree = 0.000) for 17092 atoms. Found 62 (93 requested) and removed 80 (46 requested) atoms. Cycle 13: After refmac, R = 0.1293 (Rfree = 0.000) for 17074 atoms. Found 10 (93 requested) and removed 63 (46 requested) atoms. Cycle 14: After refmac, R = 0.1215 (Rfree = 0.000) for 17021 atoms. Found 4 (93 requested) and removed 59 (46 requested) atoms. Cycle 15: After refmac, R = 0.1201 (Rfree = 0.000) for 16966 atoms. Found 4 (93 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, 17620 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 17648 seeds are put forward Round 1: 1089 peptides, 191 chains. Longest chain 15 peptides. Score 0.377 Round 2: 1237 peptides, 179 chains. Longest chain 27 peptides. Score 0.486 Round 3: 1253 peptides, 181 chains. Longest chain 21 peptides. Score 0.490 Round 4: 1254 peptides, 174 chains. Longest chain 31 peptides. Score 0.506 Round 5: 1256 peptides, 170 chains. Longest chain 25 peptides. Score 0.516 Taking the results from Round 5 Chains 173, Residues 1086, Estimated correctness of the model 0.0 % 8 chains (69 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4423 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1808 (Rfree = 0.000) for 17106 atoms. Found 65 (94 requested) and removed 79 (47 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1754 (Rfree = 0.000) for 17092 atoms. Found 71 (93 requested) and removed 78 (46 requested) atoms. Cycle 18: After refmac, R = 0.1701 (Rfree = 0.000) for 17085 atoms. Found 60 (93 requested) and removed 98 (46 requested) atoms. Cycle 19: After refmac, R = 0.1638 (Rfree = 0.000) for 17047 atoms. Found 75 (93 requested) and removed 86 (46 requested) atoms. Cycle 20: After refmac, R = 0.1168 (Rfree = 0.000) for 17036 atoms. Found 11 (93 requested) and removed 64 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.48 Search for helices and strands: 0 residues in 0 chains, 17614 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 17631 seeds are put forward Round 1: 990 peptides, 181 chains. Longest chain 16 peptides. Score 0.343 Round 2: 1157 peptides, 177 chains. Longest chain 18 peptides. Score 0.449 Round 3: 1209 peptides, 178 chains. Longest chain 20 peptides. Score 0.474 Round 4: 1199 peptides, 173 chains. Longest chain 26 peptides. Score 0.480 Round 5: 1215 peptides, 172 chains. Longest chain 29 peptides. Score 0.491 Taking the results from Round 5 Chains 178, Residues 1043, Estimated correctness of the model 0.0 % 10 chains (71 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4288 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1743 (Rfree = 0.000) for 17106 atoms. Found 80 (94 requested) and removed 81 (47 requested) atoms. Cycle 22: After refmac, R = 0.1725 (Rfree = 0.000) for 17105 atoms. Found 94 (94 requested) and removed 84 (47 requested) atoms. Cycle 23: After refmac, R = 0.1676 (Rfree = 0.000) for 17115 atoms. Found 94 (94 requested) and removed 93 (47 requested) atoms. Cycle 24: After refmac, R = 0.1182 (Rfree = 0.000) for 17116 atoms. Found 8 (94 requested) and removed 68 (47 requested) atoms. Cycle 25: After refmac, R = 0.1114 (Rfree = 0.000) for 17056 atoms. Found 9 (93 requested) and removed 60 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.49 Search for helices and strands: 0 residues in 0 chains, 17639 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 17669 seeds are put forward Round 1: 1001 peptides, 181 chains. Longest chain 17 peptides. Score 0.350 Round 2: 1187 peptides, 187 chains. Longest chain 22 peptides. Score 0.441 Round 3: 1189 peptides, 175 chains. Longest chain 25 peptides. Score 0.470 Round 4: 1223 peptides, 175 chains. Longest chain 23 peptides. Score 0.488 Round 5: 1204 peptides, 173 chains. Longest chain 18 peptides. Score 0.483 Taking the results from Round 4 Chains 176, Residues 1048, Estimated correctness of the model 0.0 % 7 chains (53 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4218 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1742 (Rfree = 0.000) for 17106 atoms. Found 83 (94 requested) and removed 89 (47 requested) atoms. Cycle 27: After refmac, R = 0.1686 (Rfree = 0.000) for 17100 atoms. Found 92 (94 requested) and removed 91 (47 requested) atoms. Cycle 28: After refmac, R = 0.1618 (Rfree = 0.000) for 17101 atoms. Found 90 (94 requested) and removed 80 (47 requested) atoms. Cycle 29: After refmac, R = 0.1145 (Rfree = 0.000) for 17111 atoms. Found 14 (94 requested) and removed 78 (47 requested) atoms. Cycle 30: After refmac, R = 0.1070 (Rfree = 0.000) for 17047 atoms. Found 4 (93 requested) and removed 64 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.49 Search for helices and strands: 0 residues in 0 chains, 17577 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 17593 seeds are put forward Round 1: 989 peptides, 183 chains. Longest chain 16 peptides. Score 0.338 Round 2: 1144 peptides, 182 chains. Longest chain 17 peptides. Score 0.430 Round 3: 1140 peptides, 184 chains. Longest chain 17 peptides. Score 0.423 Round 4: 1154 peptides, 174 chains. Longest chain 18 peptides. Score 0.454 Round 5: 1132 peptides, 174 chains. Longest chain 16 peptides. Score 0.442 Taking the results from Round 4 Chains 174, Residues 980, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 3746 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1744 (Rfree = 0.000) for 17106 atoms. Found 81 (94 requested) and removed 74 (47 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1753 (Rfree = 0.000) for 17113 atoms. Found 94 (94 requested) and removed 72 (47 requested) atoms. Cycle 33: After refmac, R = 0.1772 (Rfree = 0.000) for 17135 atoms. Found 94 (94 requested) and removed 92 (47 requested) atoms. Cycle 34: After refmac, R = 0.1633 (Rfree = 0.000) for 17137 atoms. Found 94 (94 requested) and removed 88 (47 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1635 (Rfree = 0.000) for 17143 atoms. Found 94 (94 requested) and removed 90 (47 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.49 Search for helices and strands: 0 residues in 0 chains, 17797 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 17814 seeds are put forward Round 1: 854 peptides, 174 chains. Longest chain 15 peptides. Score 0.277 Round 2: 1021 peptides, 176 chains. Longest chain 16 peptides. Score 0.375 Round 3: 1074 peptides, 176 chains. Longest chain 15 peptides. Score 0.405 Round 4: 1069 peptides, 168 chains. Longest chain 17 peptides. Score 0.422 Round 5: 1098 peptides, 166 chains. Longest chain 21 peptides. Score 0.443 Taking the results from Round 5 Chains 169, Residues 932, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 3675 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1676 (Rfree = 0.000) for 17106 atoms. Found 94 (94 requested) and removed 76 (47 requested) atoms. Cycle 37: After refmac, R = 0.1227 (Rfree = 0.000) for 17124 atoms. Found 12 (94 requested) and removed 64 (47 requested) atoms. Cycle 38: After refmac, R = 0.1108 (Rfree = 0.000) for 17072 atoms. Found 5 (93 requested) and removed 57 (46 requested) atoms. Cycle 39: After refmac, R = 0.1061 (Rfree = 0.000) for 17020 atoms. Found 3 (93 requested) and removed 54 (46 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1050 (Rfree = 0.000) for 16969 atoms. Found 8 (93 requested) and removed 54 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.50 Search for helices and strands: 0 residues in 0 chains, 17513 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 17528 seeds are put forward Round 1: 843 peptides, 165 chains. Longest chain 14 peptides. Score 0.294 Round 2: 1030 peptides, 177 chains. Longest chain 15 peptides. Score 0.378 Round 3: 1053 peptides, 178 chains. Longest chain 18 peptides. Score 0.388 Round 4: 1067 peptides, 175 chains. Longest chain 17 peptides. Score 0.404 Round 5: 1081 peptides, 175 chains. Longest chain 17 peptides. Score 0.412 Taking the results from Round 5 Chains 176, Residues 906, Estimated correctness of the model 0.0 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 3559 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1646 (Rfree = 0.000) for 17106 atoms. Found 78 (94 requested) and removed 77 (47 requested) atoms. Cycle 42: After refmac, R = 0.1204 (Rfree = 0.000) for 17107 atoms. Found 20 (94 requested) and removed 67 (47 requested) atoms. Cycle 43: After refmac, R = 0.1098 (Rfree = 0.000) for 17060 atoms. Found 7 (93 requested) and removed 52 (46 requested) atoms. Cycle 44: After refmac, R = 0.1061 (Rfree = 0.000) for 17015 atoms. Found 10 (93 requested) and removed 58 (46 requested) atoms. Cycle 45: After refmac, R = 0.1040 (Rfree = 0.000) for 16967 atoms. Found 5 (93 requested) and removed 49 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.48 Search for helices and strands: 0 residues in 0 chains, 17454 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 17469 seeds are put forward Round 1: 828 peptides, 168 chains. Longest chain 12 peptides. Score 0.276 Round 2: 990 peptides, 170 chains. Longest chain 18 peptides. Score 0.372 Round 3: 983 peptides, 164 chains. Longest chain 21 peptides. Score 0.383 Round 4: 1001 peptides, 160 chains. Longest chain 24 peptides. Score 0.404 Round 5: 993 peptides, 170 chains. Longest chain 17 peptides. Score 0.374 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 161, Residues 841, Estimated correctness of the model 0.0 % 7 chains (48 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 161 chains (841 residues) following loop building 7 chains (48 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26567 reflections ( 97.64 % complete ) and 3395 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1670 (Rfree = 0.000) for 17106 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 47: After refmac, R = 0.1667 (Rfree = 0.000) for 17059 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Cycle 48: After refmac, R = 0.1616 (Rfree = 0.000) for 17013 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Cycle 49: After refmac, R = 0.1087 (Rfree = 0.000) for 16967 atoms. TimeTaking 146.18