Mon 24 Dec 00:34:50 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.6-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 00:34:58 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.6-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 1816 and 0 Target number of residues in the AU: 1816 Target solvent content: 0.6555 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 81.74 31226 reflections ( 97.59 % complete ) and 0 restraints for refining 20847 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3069 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2625 (Rfree = 0.000) for 20847 atoms. Found 133 (133 requested) and removed 124 (66 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 21496 seeds are put forward NCS extension: 0 residues added, 21496 seeds are put forward Round 1: 1205 peptides, 218 chains. Longest chain 17 peptides. Score 0.377 Round 2: 1370 peptides, 189 chains. Longest chain 22 peptides. Score 0.530 Round 3: 1407 peptides, 178 chains. Longest chain 22 peptides. Score 0.569 Round 4: 1444 peptides, 161 chains. Longest chain 44 peptides. Score 0.618 Round 5: 1445 peptides, 166 chains. Longest chain 23 peptides. Score 0.609 Taking the results from Round 4 Chains 173, Residues 1283, Estimated correctness of the model 21.6 % 18 chains (197 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 5733 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2037 (Rfree = 0.000) for 17144 atoms. Found 79 (109 requested) and removed 95 (54 requested) atoms. Cycle 2: After refmac, R = 0.1849 (Rfree = 0.000) for 17128 atoms. Found 40 (109 requested) and removed 85 (54 requested) atoms. Cycle 3: After refmac, R = 0.1723 (Rfree = 0.000) for 17083 atoms. Found 50 (109 requested) and removed 85 (54 requested) atoms. Cycle 4: After refmac, R = 0.1626 (Rfree = 0.000) for 17048 atoms. Found 41 (109 requested) and removed 76 (54 requested) atoms. Cycle 5: After refmac, R = 0.1302 (Rfree = 0.000) for 17013 atoms. Found 8 (109 requested) and removed 67 (54 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.32 Search for helices and strands: 0 residues in 0 chains, 17686 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 17699 seeds are put forward Round 1: 1262 peptides, 193 chains. Longest chain 21 peptides. Score 0.467 Round 2: 1403 peptides, 182 chains. Longest chain 22 peptides. Score 0.560 Round 3: 1393 peptides, 172 chains. Longest chain 23 peptides. Score 0.575 Round 4: 1415 peptides, 174 chains. Longest chain 25 peptides. Score 0.581 Round 5: 1455 peptides, 173 chains. Longest chain 25 peptides. Score 0.600 Taking the results from Round 5 Chains 184, Residues 1282, Estimated correctness of the model 14.7 % 12 chains (126 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 5435 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1805 (Rfree = 0.000) for 17144 atoms. Found 63 (109 requested) and removed 103 (54 requested) atoms. Cycle 7: After refmac, R = 0.1709 (Rfree = 0.000) for 17104 atoms. Found 70 (109 requested) and removed 79 (54 requested) atoms. Cycle 8: After refmac, R = 0.1646 (Rfree = 0.000) for 17095 atoms. Found 64 (109 requested) and removed 90 (54 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1606 (Rfree = 0.000) for 17069 atoms. Found 64 (109 requested) and removed 81 (54 requested) atoms. Cycle 10: After refmac, R = 0.1283 (Rfree = 0.000) for 17052 atoms. Found 9 (109 requested) and removed 73 (54 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 17689 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 17703 seeds are put forward Round 1: 1254 peptides, 201 chains. Longest chain 23 peptides. Score 0.444 Round 2: 1385 peptides, 178 chains. Longest chain 22 peptides. Score 0.560 Round 3: 1398 peptides, 176 chains. Longest chain 23 peptides. Score 0.570 Round 4: 1408 peptides, 165 chains. Longest chain 23 peptides. Score 0.596 Round 5: 1427 peptides, 178 chains. Longest chain 24 peptides. Score 0.578 Taking the results from Round 4 Chains 175, Residues 1243, Estimated correctness of the model 13.1 % 11 chains (111 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 5222 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1727 (Rfree = 0.000) for 17144 atoms. Found 57 (109 requested) and removed 85 (54 requested) atoms. Cycle 12: After refmac, R = 0.1630 (Rfree = 0.000) for 17116 atoms. Found 48 (109 requested) and removed 81 (54 requested) atoms. Cycle 13: After refmac, R = 0.1590 (Rfree = 0.000) for 17083 atoms. Found 57 (109 requested) and removed 94 (54 requested) atoms. Cycle 14: After refmac, R = 0.1234 (Rfree = 0.000) for 17046 atoms. Found 6 (109 requested) and removed 66 (54 requested) atoms. Cycle 15: After refmac, R = 0.1178 (Rfree = 0.000) for 16986 atoms. Found 7 (108 requested) and removed 67 (54 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 17644 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 17674 seeds are put forward Round 1: 1249 peptides, 204 chains. Longest chain 17 peptides. Score 0.435 Round 2: 1383 peptides, 188 chains. Longest chain 21 peptides. Score 0.538 Round 3: 1372 peptides, 171 chains. Longest chain 22 peptides. Score 0.568 Round 4: 1393 peptides, 174 chains. Longest chain 24 peptides. Score 0.571 Round 5: 1402 peptides, 176 chains. Longest chain 20 peptides. Score 0.571 Taking the results from Round 5 Chains 180, Residues 1226, Estimated correctness of the model 3.0 % 9 chains (71 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4995 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1731 (Rfree = 0.000) for 17144 atoms. Found 71 (109 requested) and removed 87 (54 requested) atoms. Cycle 17: After refmac, R = 0.1598 (Rfree = 0.000) for 17128 atoms. Found 55 (109 requested) and removed 83 (54 requested) atoms. Cycle 18: After refmac, R = 0.1570 (Rfree = 0.000) for 17100 atoms. Found 49 (109 requested) and removed 78 (54 requested) atoms. Cycle 19: After refmac, R = 0.1483 (Rfree = 0.000) for 17071 atoms. Found 47 (109 requested) and removed 75 (54 requested) atoms. Cycle 20: After refmac, R = 0.1157 (Rfree = 0.000) for 17043 atoms. Found 2 (109 requested) and removed 67 (54 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 17649 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 17667 seeds are put forward Round 1: 1175 peptides, 197 chains. Longest chain 19 peptides. Score 0.411 Round 2: 1340 peptides, 174 chains. Longest chain 22 peptides. Score 0.547 Round 3: 1358 peptides, 186 chains. Longest chain 24 peptides. Score 0.530 Round 4: 1385 peptides, 176 chains. Longest chain 25 peptides. Score 0.564 Round 5: 1363 peptides, 175 chains. Longest chain 28 peptides. Score 0.556 Taking the results from Round 4 Chains 179, Residues 1209, Estimated correctness of the model 0.1 % 7 chains (82 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4977 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1691 (Rfree = 0.000) for 17144 atoms. Found 69 (109 requested) and removed 77 (54 requested) atoms. Cycle 22: After refmac, R = 0.1584 (Rfree = 0.000) for 17136 atoms. Found 58 (109 requested) and removed 82 (54 requested) atoms. Cycle 23: After refmac, R = 0.1522 (Rfree = 0.000) for 17112 atoms. Found 55 (109 requested) and removed 77 (54 requested) atoms. Cycle 24: After refmac, R = 0.1466 (Rfree = 0.000) for 17090 atoms. Found 47 (109 requested) and removed 71 (54 requested) atoms. Cycle 25: After refmac, R = 0.1395 (Rfree = 0.000) for 17066 atoms. Found 39 (109 requested) and removed 72 (54 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 17695 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 17717 seeds are put forward Round 1: 1143 peptides, 192 chains. Longest chain 18 peptides. Score 0.405 Round 2: 1284 peptides, 172 chains. Longest chain 23 peptides. Score 0.525 Round 3: 1296 peptides, 179 chains. Longest chain 18 peptides. Score 0.516 Round 4: 1297 peptides, 177 chains. Longest chain 22 peptides. Score 0.520 Round 5: 1297 peptides, 171 chains. Longest chain 24 peptides. Score 0.533 Taking the results from Round 5 Chains 180, Residues 1126, Estimated correctness of the model 0.0 % 9 chains (95 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 31226 reflections ( 97.59 % complete ) and 4686 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1711 (Rfree = 0.000) for 17144 atoms. Found 78 (109 requested) and removed 79 (54 requested) atoms. Cycle 27: After refmac, R = 0.1609 (Rfree = 0.000) for 17143 atoms. Found 91 (109 requested) and removed 73 (54 requested) atoms. Cycle 28: After refmac, R = 0.1556 (Rfree = 0.000) for 17161 atoms. Found 80 (110 requested) and removed 80 (55 requested) atoms. Cycle 29: After refmac, R = 0.1499 (Rfree = 0.000) for 17161 atoms. Found 81 (110 requested) and removed 69 (55 requested) atoms. Cycle 30: After refmac, R = 0.1151 (Rfree = 0.000) for 17173 atoms. Found 8 (110 requested) and removed 65 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 17772 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 17796 seeds are put forward Round 1: 1083 peptides, 195 chains. Longest chain 16 peptides. Score 0.363 Round 2: 1261 peptides, 183 chains. Longest chain 22 peptides. Score 0.489 Round 3: 1273 peptides, 180 chains. Longest chain 25 peptides. Score 0.502 Round 4: 1319 peptides, 185 chains. Longest chain 20 peptides. Score 0.514 Round 5: 1271 peptides, 177 chains. Longest chain 29 peptides. Score 0.508 Taking the results from Round 4 Chains 189, Residues 1134, Estimated correctness of the model 0.0 % 9 chains (64 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4549 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1618 (Rfree = 0.000) for 17144 atoms. Found 68 (109 requested) and removed 69 (54 requested) atoms. Cycle 32: After refmac, R = 0.1562 (Rfree = 0.000) for 17143 atoms. Found 81 (109 requested) and removed 80 (54 requested) atoms. Cycle 33: After refmac, R = 0.1491 (Rfree = 0.000) for 17144 atoms. Found 67 (109 requested) and removed 72 (54 requested) atoms. Cycle 34: After refmac, R = 0.1470 (Rfree = 0.000) for 17139 atoms. Found 63 (109 requested) and removed 78 (54 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1386 (Rfree = 0.000) for 17124 atoms. Found 69 (109 requested) and removed 71 (54 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.36 Search for helices and strands: 0 residues in 0 chains, 17782 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 17802 seeds are put forward Round 1: 1059 peptides, 193 chains. Longest chain 18 peptides. Score 0.354 Round 2: 1187 peptides, 167 chains. Longest chain 22 peptides. Score 0.488 Round 3: 1205 peptides, 173 chains. Longest chain 23 peptides. Score 0.483 Round 4: 1214 peptides, 163 chains. Longest chain 24 peptides. Score 0.511 Round 5: 1196 peptides, 168 chains. Longest chain 22 peptides. Score 0.490 Taking the results from Round 4 Chains 169, Residues 1051, Estimated correctness of the model 0.0 % 8 chains (68 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB 31226 reflections ( 97.59 % complete ) and 4295 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1570 (Rfree = 0.000) for 17144 atoms. Found 68 (109 requested) and removed 75 (54 requested) atoms. Cycle 37: After refmac, R = 0.1258 (Rfree = 0.000) for 17137 atoms. Found 17 (109 requested) and removed 68 (54 requested) atoms. Cycle 38: After refmac, R = 0.1191 (Rfree = 0.000) for 17086 atoms. Found 10 (109 requested) and removed 55 (54 requested) atoms. Cycle 39: After refmac, R = 0.1162 (Rfree = 0.000) for 17041 atoms. Found 7 (109 requested) and removed 55 (54 requested) atoms. Cycle 40: After refmac, R = 0.1141 (Rfree = 0.000) for 16993 atoms. Found 7 (109 requested) and removed 54 (54 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 17538 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 17554 seeds are put forward Round 1: 1005 peptides, 186 chains. Longest chain 13 peptides. Score 0.339 Round 2: 1134 peptides, 171 chains. Longest chain 18 peptides. Score 0.451 Round 3: 1157 peptides, 171 chains. Longest chain 21 peptides. Score 0.463 Round 4: 1133 peptides, 162 chains. Longest chain 19 peptides. Score 0.471 Round 5: 1140 peptides, 166 chains. Longest chain 19 peptides. Score 0.466 Taking the results from Round 4 Chains 163, Residues 971, Estimated correctness of the model 0.0 % 6 chains (63 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 31226 reflections ( 97.59 % complete ) and 3968 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1605 (Rfree = 0.000) for 17144 atoms. Found 77 (109 requested) and removed 72 (54 requested) atoms. Cycle 42: After refmac, R = 0.1613 (Rfree = 0.000) for 17149 atoms. Found 83 (110 requested) and removed 64 (55 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1215 (Rfree = 0.000) for 17168 atoms. Found 15 (110 requested) and removed 60 (55 requested) atoms. Cycle 44: After refmac, R = 0.1309 (Rfree = 0.000) for 17123 atoms. Found 33 (109 requested) and removed 66 (54 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1128 (Rfree = 0.000) for 17090 atoms. Found 7 (109 requested) and removed 55 (54 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 17693 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 17710 seeds are put forward Round 1: 939 peptides, 174 chains. Longest chain 20 peptides. Score 0.331 Round 2: 1067 peptides, 169 chains. Longest chain 21 peptides. Score 0.419 Round 3: 1119 peptides, 168 chains. Longest chain 22 peptides. Score 0.450 Round 4: 1155 peptides, 173 chains. Longest chain 23 peptides. Score 0.457 Round 5: 1149 peptides, 172 chains. Longest chain 23 peptides. Score 0.456 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 178, Residues 982, Estimated correctness of the model 0.0 % 9 chains (91 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 178 chains (982 residues) following loop building 9 chains (91 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 31226 reflections ( 97.59 % complete ) and 4126 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1622 (Rfree = 0.000) for 17144 atoms. Found 0 (109 requested) and removed 54 (54 requested) atoms. Cycle 47: After refmac, R = 0.1564 (Rfree = 0.000) for 17090 atoms. Found 0 (109 requested) and removed 54 (54 requested) atoms. Cycle 48: After refmac, R = 0.1178 (Rfree = 0.000) for 17036 atoms. Found 0 (109 requested) and removed 54 (54 requested) atoms. Cycle 49: After refmac, R = 0.1105 (Rfree = 0.000) for 16982 atoms. TimeTaking 185.37