Mon 24 Dec 00:10:20 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 2aam-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.4-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/2aam-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.4-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 00:10:25 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/2aam-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.4-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 3952 and 0 Target number of residues in the AU: 3952 Target solvent content: 0.6164 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 309 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1854 Adjusted target solvent content: 0.82 Input MTZ file: 2aam-3.4-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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.40 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: 169.060 3.400 Wilson plot Bfac: 59.77 75788 reflections ( 99.05 % complete ) and 0 restraints for refining 16415 atoms. Observations/parameters ratio is 1.15 ------------------------------------------------------ Starting model: R = 0.3319 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2710 (Rfree = 0.000) for 16415 atoms. Found 123 (123 requested) and removed 75 (61 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 1.94 Search for helices and strands: 0 residues in 0 chains, 16830 seeds are put forward NCS extension: 0 residues added, 16830 seeds are put forward Round 1: 1332 peptides, 139 chains. Longest chain 35 peptides. Score 0.458 Round 2: 1318 peptides, 144 chains. Longest chain 22 peptides. Score 0.446 Round 3: 1351 peptides, 141 chains. Longest chain 29 peptides. Score 0.460 Round 4: 1333 peptides, 140 chains. Longest chain 29 peptides. Score 0.456 Round 5: 1332 peptides, 133 chains. Longest chain 30 peptides. Score 0.466 Taking the results from Round 5 Chains 146, Residues 1199, Estimated correctness of the model 0.0 % 16 chains (193 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5474 restraints for refining 15142 atoms. Observations/parameters ratio is 1.25 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2458 (Rfree = 0.000) for 15142 atoms. Found 114 (114 requested) and removed 71 (57 requested) atoms. Cycle 2: After refmac, R = 0.2291 (Rfree = 0.000) for 15185 atoms. Found 114 (114 requested) and removed 60 (57 requested) atoms. Cycle 3: After refmac, R = 0.2206 (Rfree = 0.000) for 15239 atoms. Found 84 (115 requested) and removed 61 (57 requested) atoms. Cycle 4: After refmac, R = 0.2158 (Rfree = 0.000) for 15262 atoms. Found 62 (115 requested) and removed 64 (57 requested) atoms. Cycle 5: After refmac, R = 0.2103 (Rfree = 0.000) for 15260 atoms. Found 58 (115 requested) and removed 63 (57 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 1.93 Search for helices and strands: 0 residues in 0 chains, 15744 seeds are put forward NCS extension: 49 residues added (3 deleted due to clashes), 15793 seeds are put forward Round 1: 1384 peptides, 142 chains. Longest chain 36 peptides. Score 0.468 Round 2: 1404 peptides, 146 chains. Longest chain 46 peptides. Score 0.468 Round 3: 1387 peptides, 133 chains. Longest chain 33 peptides. Score 0.482 Round 4: 1373 peptides, 141 chains. Longest chain 31 peptides. Score 0.466 Round 5: 1373 peptides, 137 chains. Longest chain 28 peptides. Score 0.472 Taking the results from Round 3 Chains 146, Residues 1254, Estimated correctness of the model 0.0 % 15 chains (256 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 6004 restraints for refining 15353 atoms. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2299 (Rfree = 0.000) for 15353 atoms. Found 115 (115 requested) and removed 69 (57 requested) atoms. Cycle 7: After refmac, R = 0.2128 (Rfree = 0.000) for 15399 atoms. Found 99 (116 requested) and removed 70 (58 requested) atoms. Cycle 8: After refmac, R = 0.2050 (Rfree = 0.000) for 15428 atoms. Found 46 (116 requested) and removed 64 (58 requested) atoms. Cycle 9: After refmac, R = 0.2017 (Rfree = 0.000) for 15410 atoms. Found 57 (116 requested) and removed 62 (58 requested) atoms. Cycle 10: After refmac, R = 0.1987 (Rfree = 0.000) for 15405 atoms. Found 50 (116 requested) and removed 69 (58 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 1.93 Search for helices and strands: 0 residues in 0 chains, 15938 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 15962 seeds are put forward Round 1: 1417 peptides, 138 chains. Longest chain 42 peptides. Score 0.483 Round 2: 1379 peptides, 136 chains. Longest chain 57 peptides. Score 0.475 Round 3: 1366 peptides, 129 chains. Longest chain 43 peptides. Score 0.481 Round 4: 1359 peptides, 148 chains. Longest chain 34 peptides. Score 0.452 Round 5: 1351 peptides, 147 chains. Longest chain 47 peptides. Score 0.451 Taking the results from Round 1 Chains 152, Residues 1279, Estimated correctness of the model 0.0 % 18 chains (325 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 6513 restraints for refining 15415 atoms. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2237 (Rfree = 0.000) for 15415 atoms. Found 116 (116 requested) and removed 71 (58 requested) atoms. Cycle 12: After refmac, R = 0.2086 (Rfree = 0.000) for 15460 atoms. Found 90 (116 requested) and removed 70 (58 requested) atoms. Cycle 13: After refmac, R = 0.2031 (Rfree = 0.000) for 15480 atoms. Found 54 (116 requested) and removed 67 (58 requested) atoms. Cycle 14: After refmac, R = 0.1996 (Rfree = 0.000) for 15467 atoms. Found 41 (116 requested) and removed 63 (58 requested) atoms. Cycle 15: After refmac, R = 0.1973 (Rfree = 0.000) for 15445 atoms. Found 46 (116 requested) and removed 64 (58 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 1.92 Search for helices and strands: 0 residues in 0 chains, 15958 seeds are put forward NCS extension: 9 residues added (10 deleted due to clashes), 15967 seeds are put forward Round 1: 1382 peptides, 141 chains. Longest chain 39 peptides. Score 0.469 Round 2: 1361 peptides, 145 chains. Longest chain 47 peptides. Score 0.457 Round 3: 1341 peptides, 151 chains. Longest chain 31 peptides. Score 0.443 Round 4: 1369 peptides, 147 chains. Longest chain 47 peptides. Score 0.457 Round 5: 1360 peptides, 140 chains. Longest chain 50 peptides. Score 0.464 Taking the results from Round 1 Chains 156, Residues 1241, Estimated correctness of the model 0.0 % 18 chains (333 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 6345 restraints for refining 15642 atoms. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2186 (Rfree = 0.000) for 15642 atoms. Found 118 (118 requested) and removed 73 (59 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2053 (Rfree = 0.000) for 15687 atoms. Found 74 (118 requested) and removed 62 (59 requested) atoms. Cycle 18: After refmac, R = 0.2002 (Rfree = 0.000) for 15699 atoms. Found 49 (118 requested) and removed 67 (59 requested) atoms. Cycle 19: After refmac, R = 0.1982 (Rfree = 0.000) for 15681 atoms. Found 65 (118 requested) and removed 64 (59 requested) atoms. Cycle 20: After refmac, R = 0.1968 (Rfree = 0.000) for 15682 atoms. Found 51 (118 requested) and removed 67 (59 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 1.92 Search for helices and strands: 0 residues in 0 chains, 16169 seeds are put forward NCS extension: 24 residues added (12 deleted due to clashes), 16193 seeds are put forward Round 1: 1369 peptides, 144 chains. Longest chain 30 peptides. Score 0.461 Round 2: 1402 peptides, 126 chains. Longest chain 49 peptides. Score 0.495 Round 3: 1359 peptides, 135 chains. Longest chain 37 peptides. Score 0.471 Round 4: 1391 peptides, 151 chains. Longest chain 30 peptides. Score 0.457 Round 5: 1377 peptides, 141 chains. Longest chain 42 peptides. Score 0.468 Taking the results from Round 2 Chains 141, Residues 1276, Estimated correctness of the model 0.0 % 14 chains (293 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 6299 restraints for refining 15903 atoms. Observations/parameters ratio is 1.19 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2237 (Rfree = 0.000) for 15903 atoms. Found 120 (120 requested) and removed 77 (60 requested) atoms. Cycle 22: After refmac, R = 0.2087 (Rfree = 0.000) for 15946 atoms. Found 94 (120 requested) and removed 68 (60 requested) atoms. Cycle 23: After refmac, R = 0.2020 (Rfree = 0.000) for 15972 atoms. Found 56 (120 requested) and removed 72 (60 requested) atoms. Cycle 24: After refmac, R = 0.1997 (Rfree = 0.000) for 15956 atoms. Found 36 (120 requested) and removed 65 (60 requested) atoms. Cycle 25: After refmac, R = 0.1986 (Rfree = 0.000) for 15927 atoms. Found 44 (120 requested) and removed 69 (60 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 1.93 Search for helices and strands: 0 residues in 0 chains, 16406 seeds are put forward NCS extension: 16 residues added (7 deleted due to clashes), 16422 seeds are put forward Round 1: 1364 peptides, 129 chains. Longest chain 37 peptides. Score 0.481 Round 2: 1385 peptides, 136 chains. Longest chain 36 peptides. Score 0.477 Round 3: 1352 peptides, 143 chains. Longest chain 30 peptides. Score 0.458 Round 4: 1352 peptides, 142 chains. Longest chain 32 peptides. Score 0.459 Round 5: 1327 peptides, 148 chains. Longest chain 33 peptides. Score 0.443 Taking the results from Round 1 Chains 140, Residues 1235, Estimated correctness of the model 0.0 % 16 chains (312 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 6296 restraints for refining 15788 atoms. Observations/parameters ratio is 1.20 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2178 (Rfree = 0.000) for 15788 atoms. Found 119 (119 requested) and removed 67 (59 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2048 (Rfree = 0.000) for 15840 atoms. Found 81 (119 requested) and removed 63 (59 requested) atoms. Cycle 28: After refmac, R = 0.2010 (Rfree = 0.000) for 15858 atoms. Found 52 (119 requested) and removed 60 (59 requested) atoms. Cycle 29: After refmac, R = 0.2008 (Rfree = 0.000) for 15850 atoms. Found 51 (119 requested) and removed 63 (59 requested) atoms. Cycle 30: After refmac, R = 0.2012 (Rfree = 0.000) for 15838 atoms. Found 73 (119 requested) and removed 64 (59 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 1.92 Search for helices and strands: 0 residues in 0 chains, 16315 seeds are put forward NCS extension: 23 residues added (11 deleted due to clashes), 16338 seeds are put forward Round 1: 1331 peptides, 145 chains. Longest chain 39 peptides. Score 0.449 Round 2: 1430 peptides, 134 chains. Longest chain 51 peptides. Score 0.492 Round 3: 1398 peptides, 138 chains. Longest chain 40 peptides. Score 0.478 Round 4: 1407 peptides, 131 chains. Longest chain 45 peptides. Score 0.490 Round 5: 1391 peptides, 135 chains. Longest chain 42 peptides. Score 0.480 Taking the results from Round 2 Chains 148, Residues 1296, Estimated correctness of the model 0.0 % 15 chains (277 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 6309 restraints for refining 16073 atoms. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2204 (Rfree = 0.000) for 16073 atoms. Found 121 (121 requested) and removed 73 (60 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2087 (Rfree = 0.000) for 16121 atoms. Found 110 (121 requested) and removed 63 (60 requested) atoms. Cycle 33: After refmac, R = 0.2061 (Rfree = 0.000) for 16168 atoms. Found 75 (122 requested) and removed 63 (61 requested) atoms. Cycle 34: After refmac, R = 0.2047 (Rfree = 0.000) for 16180 atoms. Found 73 (122 requested) and removed 65 (61 requested) atoms. Cycle 35: After refmac, R = 0.2039 (Rfree = 0.000) for 16188 atoms. Found 64 (122 requested) and removed 65 (61 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 1.92 Search for helices and strands: 0 residues in 0 chains, 16636 seeds are put forward NCS extension: 27 residues added (12 deleted due to clashes), 16663 seeds are put forward Round 1: 1359 peptides, 146 chains. Longest chain 42 peptides. Score 0.455 Round 2: 1407 peptides, 132 chains. Longest chain 40 peptides. Score 0.489 Round 3: 1383 peptides, 128 chains. Longest chain 48 peptides. Score 0.487 Round 4: 1356 peptides, 134 chains. Longest chain 32 peptides. Score 0.472 Round 5: 1372 peptides, 130 chains. Longest chain 46 peptides. Score 0.482 Taking the results from Round 2 Chains 148, Residues 1275, Estimated correctness of the model 0.0 % 16 chains (272 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 6230 restraints for refining 16051 atoms. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2197 (Rfree = 0.000) for 16051 atoms. Found 121 (121 requested) and removed 74 (60 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2075 (Rfree = 0.000) for 16098 atoms. Found 111 (121 requested) and removed 68 (60 requested) atoms. Cycle 38: After refmac, R = 0.2014 (Rfree = 0.000) for 16141 atoms. Found 68 (121 requested) and removed 65 (60 requested) atoms. Cycle 39: After refmac, R = 0.1991 (Rfree = 0.000) for 16144 atoms. Found 67 (121 requested) and removed 66 (60 requested) atoms. Cycle 40: After refmac, R = 0.1984 (Rfree = 0.000) for 16145 atoms. Found 58 (121 requested) and removed 66 (60 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 1.91 Search for helices and strands: 0 residues in 0 chains, 16607 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 16626 seeds are put forward Round 1: 1315 peptides, 151 chains. Longest chain 33 peptides. Score 0.435 Round 2: 1388 peptides, 146 chains. Longest chain 34 peptides. Score 0.464 Round 3: 1397 peptides, 144 chains. Longest chain 50 peptides. Score 0.469 Round 4: 1377 peptides, 138 chains. Longest chain 38 peptides. Score 0.472 Round 5: 1388 peptides, 146 chains. Longest chain 40 peptides. Score 0.464 Taking the results from Round 4 Chains 156, Residues 1239, Estimated correctness of the model 0.0 % 15 chains (242 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5868 restraints for refining 16191 atoms. Observations/parameters ratio is 1.17 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2253 (Rfree = 0.000) for 16191 atoms. Found 122 (122 requested) and removed 70 (61 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2089 (Rfree = 0.000) for 16243 atoms. Found 113 (122 requested) and removed 66 (61 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2061 (Rfree = 0.000) for 16290 atoms. Found 86 (122 requested) and removed 67 (61 requested) atoms. Cycle 44: After refmac, R = 0.2046 (Rfree = 0.000) for 16309 atoms. Found 79 (123 requested) and removed 69 (61 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Cycle 45: After refmac, R = 0.2016 (Rfree = 0.000) for 16319 atoms. Found 77 (123 requested) and removed 64 (61 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 1.91 Search for helices and strands: 0 residues in 0 chains, 16866 seeds are put forward NCS extension: 14 residues added (10 deleted due to clashes), 16880 seeds are put forward Round 1: 1293 peptides, 150 chains. Longest chain 27 peptides. Score 0.430 Round 2: 1355 peptides, 146 chains. Longest chain 29 peptides. Score 0.454 Round 3: 1356 peptides, 137 chains. Longest chain 33 peptides. Score 0.467 Round 4: 1365 peptides, 132 chains. Longest chain 51 peptides. Score 0.477 Round 5: 1356 peptides, 127 chains. Longest chain 45 peptides. Score 0.482 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 137, Residues 1229, Estimated correctness of the model 0.0 % 12 chains (187 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2aam-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 153 A and 163 A 137 chains (1231 residues) following loop building 11 chains (196 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 75788 reflections ( 99.05 % complete ) and 5525 restraints for refining 16071 atoms. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2275 (Rfree = 0.000) for 16071 atoms. Found 0 (121 requested) and removed 56 (60 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2184 (Rfree = 0.000) for 16015 atoms. Found 0 (120 requested) and removed 22 (60 requested) atoms. Cycle 48: After refmac, R = 0.2166 (Rfree = 0.000) for 15993 atoms. Found 0 (120 requested) and removed 29 (60 requested) atoms. Cycle 49: After refmac, R = 0.2114 (Rfree = 0.000) for 15964 atoms. TimeTaking 213.47