Mon 24 Dec 00:10:26 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 2pnk-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-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/2pnk-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-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 00:10:31 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/2pnk-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-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 4422 and 0 Target number of residues in the AU: 4422 Target solvent content: 0.6614 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 428 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 5136 Adjusted target solvent content: 0.61 Input MTZ file: 2pnk-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: 5 Cell parameters: 273.720 158.560 181.240 90.000 116.029 90.000 Input sequence file: 2pnk-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 41088 target number of atoms Had to go as low as 1.00 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: 162.857 4.000 Wilson plot Bfac: 85.98 54586 reflections ( 92.59 % complete ) and 0 restraints for refining 45235 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3212 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2944 (Rfree = 0.000) for 45235 atoms. Found 214 (214 requested) and removed 183 (107 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.27 Search for helices and strands: 0 residues in 0 chains, 46309 seeds are put forward NCS extension: 0 residues added, 46309 seeds are put forward Round 1: 2092 peptides, 380 chains. Longest chain 14 peptides. Score 0.327 Round 2: 2649 peptides, 383 chains. Longest chain 21 peptides. Score 0.455 Round 3: 2744 peptides, 378 chains. Longest chain 23 peptides. Score 0.480 Round 4: 2834 peptides, 369 chains. Longest chain 30 peptides. Score 0.507 Round 5: 2848 peptides, 352 chains. Longest chain 33 peptides. Score 0.526 Taking the results from Round 5 Chains 363, Residues 2496, Estimated correctness of the model 0.0 % 11 chains (108 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 10062 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2262 (Rfree = 0.000) for 37106 atoms. Found 168 (176 requested) and removed 129 (88 requested) atoms. Cycle 2: After refmac, R = 0.2081 (Rfree = 0.000) for 37145 atoms. Found 176 (176 requested) and removed 159 (88 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1980 (Rfree = 0.000) for 37162 atoms. Found 176 (176 requested) and removed 168 (88 requested) atoms. Cycle 4: After refmac, R = 0.1494 (Rfree = 0.000) for 37170 atoms. Found 32 (176 requested) and removed 131 (88 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1414 (Rfree = 0.000) for 37071 atoms. Found 24 (176 requested) and removed 121 (88 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.24 Search for helices and strands: 0 residues in 0 chains, 38404 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 38425 seeds are put forward Round 1: 2392 peptides, 408 chains. Longest chain 16 peptides. Score 0.371 Round 2: 2798 peptides, 379 chains. Longest chain 22 peptides. Score 0.491 Round 3: 2828 peptides, 369 chains. Longest chain 27 peptides. Score 0.506 Round 4: 2863 peptides, 368 chains. Longest chain 28 peptides. Score 0.514 Round 5: 2847 peptides, 354 chains. Longest chain 27 peptides. Score 0.524 Taking the results from Round 5 Chains 363, Residues 2493, Estimated correctness of the model 0.0 % 11 chains (122 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 10099 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1957 (Rfree = 0.000) for 37106 atoms. Found 165 (176 requested) and removed 145 (88 requested) atoms. Cycle 7: After refmac, R = 0.1874 (Rfree = 0.000) for 37126 atoms. Found 176 (176 requested) and removed 175 (88 requested) atoms. Cycle 8: After refmac, R = 0.1793 (Rfree = 0.000) for 37127 atoms. Found 176 (176 requested) and removed 212 (88 requested) atoms. Cycle 9: After refmac, R = 0.1279 (Rfree = 0.000) for 37091 atoms. Found 28 (176 requested) and removed 151 (88 requested) atoms. Cycle 10: After refmac, R = 0.1201 (Rfree = 0.000) for 36968 atoms. Found 19 (175 requested) and removed 141 (87 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38223 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 38246 seeds are put forward Round 1: 2433 peptides, 420 chains. Longest chain 19 peptides. Score 0.368 Round 2: 2764 peptides, 375 chains. Longest chain 28 peptides. Score 0.487 Round 3: 2855 peptides, 371 chains. Longest chain 23 peptides. Score 0.510 Round 4: 2811 peptides, 366 chains. Longest chain 26 peptides. Score 0.505 Round 5: 2794 peptides, 366 chains. Longest chain 35 peptides. Score 0.502 Taking the results from Round 3 Chains 378, Residues 2484, Estimated correctness of the model 0.0 % 10 chains (109 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 9980 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1856 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 199 (88 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1799 (Rfree = 0.000) for 37083 atoms. Found 176 (176 requested) and removed 185 (88 requested) atoms. Cycle 13: After refmac, R = 0.1729 (Rfree = 0.000) for 37074 atoms. Found 176 (176 requested) and removed 204 (88 requested) atoms. Cycle 14: After refmac, R = 0.1221 (Rfree = 0.000) for 37046 atoms. Found 37 (176 requested) and removed 153 (88 requested) atoms. Cycle 15: After refmac, R = 0.1140 (Rfree = 0.000) for 36930 atoms. Found 18 (175 requested) and removed 129 (87 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.22 Search for helices and strands: 0 residues in 0 chains, 38116 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 38129 seeds are put forward Round 1: 2502 peptides, 426 chains. Longest chain 17 peptides. Score 0.379 Round 2: 2813 peptides, 402 chains. Longest chain 36 peptides. Score 0.472 Round 3: 2818 peptides, 376 chains. Longest chain 29 peptides. Score 0.497 Round 4: 2836 peptides, 383 chains. Longest chain 23 peptides. Score 0.495 Round 5: 2835 peptides, 371 chains. Longest chain 25 peptides. Score 0.506 Taking the results from Round 5 Chains 376, Residues 2464, Estimated correctness of the model 0.0 % 9 chains (99 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 9872 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1817 (Rfree = 0.000) for 37106 atoms. Found 172 (176 requested) and removed 164 (88 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1785 (Rfree = 0.000) for 37114 atoms. Found 176 (176 requested) and removed 172 (88 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1239 (Rfree = 0.000) for 37118 atoms. Found 21 (176 requested) and removed 152 (88 requested) atoms. Cycle 19: After refmac, R = 0.1137 (Rfree = 0.000) for 36987 atoms. Found 12 (175 requested) and removed 133 (87 requested) atoms. Cycle 20: After refmac, R = 0.1100 (Rfree = 0.000) for 36866 atoms. Found 16 (175 requested) and removed 124 (87 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.22 Search for helices and strands: 0 residues in 0 chains, 38132 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 38150 seeds are put forward Round 1: 2414 peptides, 418 chains. Longest chain 19 peptides. Score 0.366 Round 2: 2690 peptides, 382 chains. Longest chain 19 peptides. Score 0.465 Round 3: 2745 peptides, 372 chains. Longest chain 28 peptides. Score 0.486 Round 4: 2747 peptides, 376 chains. Longest chain 21 peptides. Score 0.483 Round 5: 2765 peptides, 370 chains. Longest chain 21 peptides. Score 0.492 Taking the results from Round 5 Chains 373, Residues 2395, Estimated correctness of the model 0.0 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 9399 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1827 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 137 (88 requested) atoms. Cycle 22: After refmac, R = 0.1795 (Rfree = 0.000) for 37145 atoms. Found 176 (176 requested) and removed 154 (88 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1245 (Rfree = 0.000) for 37167 atoms. Found 20 (176 requested) and removed 127 (88 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1146 (Rfree = 0.000) for 37060 atoms. Found 13 (176 requested) and removed 128 (88 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1099 (Rfree = 0.000) for 36945 atoms. Found 10 (175 requested) and removed 123 (87 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38181 seeds are put forward NCS extension: 0 residues added, 38181 seeds are put forward Round 1: 2369 peptides, 422 chains. Longest chain 18 peptides. Score 0.351 Round 2: 2622 peptides, 378 chains. Longest chain 26 peptides. Score 0.454 Round 3: 2668 peptides, 387 chains. Longest chain 18 peptides. Score 0.455 Round 4: 2717 peptides, 382 chains. Longest chain 23 peptides. Score 0.471 Round 5: 2667 peptides, 377 chains. Longest chain 20 peptides. Score 0.465 Taking the results from Round 4 Chains 384, Residues 2335, Estimated correctness of the model 0.0 % 9 chains (64 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 9209 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1781 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 162 (88 requested) atoms. Cycle 27: After refmac, R = 0.1766 (Rfree = 0.000) for 37120 atoms. Found 176 (176 requested) and removed 183 (88 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1691 (Rfree = 0.000) for 37113 atoms. Found 176 (176 requested) and removed 198 (88 requested) atoms. Cycle 29: After refmac, R = 0.1692 (Rfree = 0.000) for 37091 atoms. Found 176 (176 requested) and removed 186 (88 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1632 (Rfree = 0.000) for 37081 atoms. Found 176 (176 requested) and removed 176 (88 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38390 seeds are put forward NCS extension: 0 residues added, 38390 seeds are put forward Round 1: 2092 peptides, 387 chains. Longest chain 20 peptides. Score 0.319 Round 2: 2452 peptides, 391 chains. Longest chain 21 peptides. Score 0.403 Round 3: 2605 peptides, 387 chains. Longest chain 19 peptides. Score 0.442 Round 4: 2619 peptides, 389 chains. Longest chain 23 peptides. Score 0.443 Round 5: 2609 peptides, 375 chains. Longest chain 22 peptides. Score 0.454 Taking the results from Round 5 Chains 380, Residues 2234, Estimated correctness of the model 0.0 % 7 chains (69 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 8831 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1909 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 169 (88 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 32: After refmac, R = 0.1776 (Rfree = 0.000) for 37113 atoms. Found 176 (176 requested) and removed 164 (88 requested) atoms. Cycle 33: After refmac, R = 0.1691 (Rfree = 0.000) for 37125 atoms. Found 176 (176 requested) and removed 185 (88 requested) atoms. Cycle 34: After refmac, R = 0.1659 (Rfree = 0.000) for 37116 atoms. Found 176 (176 requested) and removed 201 (88 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1144 (Rfree = 0.000) for 37091 atoms. Found 39 (176 requested) and removed 144 (88 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38352 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 38370 seeds are put forward Round 1: 2120 peptides, 402 chains. Longest chain 14 peptides. Score 0.310 Round 2: 2511 peptides, 405 chains. Longest chain 25 peptides. Score 0.402 Round 3: 2513 peptides, 400 chains. Longest chain 25 peptides. Score 0.408 Round 4: 2570 peptides, 379 chains. Longest chain 22 peptides. Score 0.442 Round 5: 2543 peptides, 380 chains. Longest chain 24 peptides. Score 0.435 Taking the results from Round 4 Chains 382, Residues 2191, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 8495 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1838 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 173 (88 requested) atoms. Cycle 37: After refmac, R = 0.1768 (Rfree = 0.000) for 37109 atoms. Found 176 (176 requested) and removed 136 (88 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1718 (Rfree = 0.000) for 37149 atoms. Found 176 (176 requested) and removed 197 (88 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1181 (Rfree = 0.000) for 37128 atoms. Found 26 (176 requested) and removed 137 (88 requested) atoms. Cycle 40: After refmac, R = 0.1097 (Rfree = 0.000) for 37017 atoms. Found 17 (175 requested) and removed 127 (87 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38177 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 38203 seeds are put forward Round 1: 2050 peptides, 400 chains. Longest chain 13 peptides. Score 0.294 Round 2: 2344 peptides, 387 chains. Longest chain 17 peptides. Score 0.382 Round 3: 2423 peptides, 391 chains. Longest chain 19 peptides. Score 0.396 Round 4: 2453 peptides, 391 chains. Longest chain 25 peptides. Score 0.403 Round 5: 2437 peptides, 371 chains. Longest chain 30 peptides. Score 0.420 Taking the results from Round 5 Chains 374, Residues 2066, Estimated correctness of the model 0.0 % 8 chains (58 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 8093 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1805 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 175 (88 requested) atoms. Cycle 42: After refmac, R = 0.1706 (Rfree = 0.000) for 37107 atoms. Found 176 (176 requested) and removed 168 (88 requested) atoms. Cycle 43: After refmac, R = 0.1208 (Rfree = 0.000) for 37115 atoms. Found 44 (176 requested) and removed 132 (88 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1107 (Rfree = 0.000) for 37027 atoms. Found 20 (175 requested) and removed 136 (87 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1084 (Rfree = 0.000) for 36911 atoms. Found 25 (175 requested) and removed 119 (87 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38052 seeds are put forward NCS extension: 0 residues added, 38052 seeds are put forward Round 1: 1961 peptides, 384 chains. Longest chain 14 peptides. Score 0.289 Round 2: 2320 peptides, 394 chains. Longest chain 19 peptides. Score 0.368 Round 3: 2364 peptides, 391 chains. Longest chain 25 peptides. Score 0.382 Round 4: 2339 peptides, 370 chains. Longest chain 19 peptides. Score 0.398 Round 5: 2354 peptides, 381 chains. Longest chain 19 peptides. Score 0.390 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 371, Residues 1969, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2pnk-4_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 259 F and 271 F 370 chains (1974 residues) following loop building 2 chains (35 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 54586 reflections ( 92.59 % complete ) and 7653 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1818 (Rfree = 0.000) for 37106 atoms. Found 0 (176 requested) and removed 88 (88 requested) atoms. Cycle 47: After refmac, R = 0.1769 (Rfree = 0.000) for 37018 atoms. Found 0 (175 requested) and removed 87 (87 requested) atoms. Cycle 48: After refmac, R = 0.1165 (Rfree = 0.000) for 36931 atoms. Found 0 (175 requested) and removed 87 (87 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1062 (Rfree = 0.000) for 36844 atoms. Found 0 (175 requested) and removed 87 (87 requested) atoms. Writing output files ... TimeTaking 412