null Sun 23 Dec 22:23:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pg4-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:12 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/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.8-parrot-hancs/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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.6608 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 190 Adjusted target solvent content: 0.54 Input MTZ file: 2pg4-3.8-parrot-hancs.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: 90 Cell parameters: 109.840 109.840 36.760 90.000 90.000 90.000 Input sequence file: 2pg4-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.75 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. Conditional restraints will be used 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: 77.669 3.800 Wilson plot Bfac: 85.33 2456 reflections ( 99.47 % complete ) and 0 restraints for refining 1678 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3778 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3640 (Rfree = 0.000) for 1678 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 1715 seeds are put forward NCS extension: 0 residues added, 1715 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.290 Round 2: 97 peptides, 16 chains. Longest chain 23 peptides. Score 0.430 Round 3: 100 peptides, 16 chains. Longest chain 17 peptides. Score 0.451 Round 4: 107 peptides, 16 chains. Longest chain 20 peptides. Score 0.497 Round 5: 116 peptides, 14 chains. Longest chain 24 peptides. Score 0.603 Taking the results from Round 5 Chains 14, Residues 102, Estimated correctness of the model 0.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 3063 restraints for refining 1375 atoms. 2669 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2973 (Rfree = 0.000) for 1375 atoms. Found 3 (7 requested) and removed 14 (3 requested) atoms. Cycle 2: After refmac, R = 0.2594 (Rfree = 0.000) for 1334 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2589 (Rfree = 0.000) for 1324 atoms. Found 0 (7 requested) and removed 11 (3 requested) atoms. Cycle 4: After refmac, R = 0.2570 (Rfree = 0.000) for 1297 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.2343 (Rfree = 0.000) for 1287 atoms. Found 3 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 1357 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 1395 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 14 peptides. Score 0.365 Round 2: 96 peptides, 14 chains. Longest chain 18 peptides. Score 0.483 Round 3: 94 peptides, 12 chains. Longest chain 21 peptides. Score 0.528 Round 4: 94 peptides, 13 chains. Longest chain 16 peptides. Score 0.499 Round 5: 111 peptides, 14 chains. Longest chain 21 peptides. Score 0.575 Taking the results from Round 5 Chains 14, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 3043 restraints for refining 1371 atoms. 2669 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2831 (Rfree = 0.000) for 1371 atoms. Found 5 (7 requested) and removed 10 (3 requested) atoms. Cycle 7: After refmac, R = 0.2727 (Rfree = 0.000) for 1347 atoms. Found 4 (7 requested) and removed 16 (3 requested) atoms. Cycle 8: After refmac, R = 0.2630 (Rfree = 0.000) for 1313 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.2623 (Rfree = 0.000) for 1301 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 10: After refmac, R = 0.2433 (Rfree = 0.000) for 1286 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 1368 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 1392 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.287 Round 2: 90 peptides, 15 chains. Longest chain 13 peptides. Score 0.411 Round 3: 93 peptides, 15 chains. Longest chain 18 peptides. Score 0.432 Round 4: 89 peptides, 15 chains. Longest chain 12 peptides. Score 0.404 Round 5: 97 peptides, 16 chains. Longest chain 18 peptides. Score 0.430 Taking the results from Round 3 Chains 15, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2930 restraints for refining 1313 atoms. 2633 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3026 (Rfree = 0.000) for 1313 atoms. Found 6 (7 requested) and removed 10 (3 requested) atoms. Cycle 12: After refmac, R = 0.2720 (Rfree = 0.000) for 1298 atoms. Found 5 (7 requested) and removed 9 (3 requested) atoms. Cycle 13: After refmac, R = 0.2741 (Rfree = 0.000) for 1279 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.2973 (Rfree = 0.000) for 1267 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.2547 (Rfree = 0.000) for 1254 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 1321 seeds are put forward NCS extension: 0 residues added, 1321 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 9 peptides. Score 0.292 Round 2: 93 peptides, 16 chains. Longest chain 9 peptides. Score 0.401 Round 3: 96 peptides, 14 chains. Longest chain 14 peptides. Score 0.483 Round 4: 89 peptides, 13 chains. Longest chain 10 peptides. Score 0.466 Round 5: 90 peptides, 15 chains. Longest chain 10 peptides. Score 0.411 Taking the results from Round 3 Chains 14, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2652 restraints for refining 1262 atoms. 2338 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2637 (Rfree = 0.000) for 1262 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 17: After refmac, R = 0.2704 (Rfree = 0.000) for 1247 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 18: After refmac, R = 0.2595 (Rfree = 0.000) for 1241 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2288 (Rfree = 0.000) for 1240 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2455 (Rfree = 0.000) for 1231 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 1297 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1318 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.285 Round 2: 93 peptides, 15 chains. Longest chain 17 peptides. Score 0.432 Round 3: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.432 Round 4: 98 peptides, 15 chains. Longest chain 17 peptides. Score 0.467 Round 5: 90 peptides, 13 chains. Longest chain 16 peptides. Score 0.472 Taking the results from Round 5 Chains 13, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2913 restraints for refining 1314 atoms. 2618 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2685 (Rfree = 0.000) for 1314 atoms. Found 5 (7 requested) and removed 17 (3 requested) atoms. Cycle 22: After refmac, R = 0.2696 (Rfree = 0.000) for 1300 atoms. Found 7 (7 requested) and removed 61 (3 requested) atoms. Cycle 23: After refmac, R = 0.2463 (Rfree = 0.000) for 1239 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 24: After refmac, R = 0.2823 (Rfree = 0.000) for 1235 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 25: After refmac, R = 0.2370 (Rfree = 0.000) for 1228 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.59 Search for helices and strands: 0 residues in 0 chains, 1298 seeds are put forward NCS extension: 0 residues added, 1298 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 8 peptides. Score 0.280 Round 2: 80 peptides, 14 chains. Longest chain 8 peptides. Score 0.369 Round 3: 86 peptides, 13 chains. Longest chain 15 peptides. Score 0.445 Round 4: 84 peptides, 12 chains. Longest chain 15 peptides. Score 0.462 Round 5: 89 peptides, 15 chains. Longest chain 15 peptides. Score 0.404 Taking the results from Round 4 Chains 12, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2894 restraints for refining 1298 atoms. 2618 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2688 (Rfree = 0.000) for 1298 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.2782 (Rfree = 0.000) for 1292 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2429 (Rfree = 0.000) for 1283 atoms. Found 2 (7 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.2636 (Rfree = 0.000) for 1268 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2494 (Rfree = 0.000) for 1265 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 1336 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1356 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 6 peptides. Score 0.221 Round 2: 80 peptides, 14 chains. Longest chain 11 peptides. Score 0.369 Round 3: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.357 Round 4: 86 peptides, 14 chains. Longest chain 14 peptides. Score 0.414 Round 5: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.374 Taking the results from Round 4 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2831 restraints for refining 1263 atoms. 2557 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2780 (Rfree = 0.000) for 1263 atoms. Found 2 (6 requested) and removed 13 (3 requested) atoms. Cycle 32: After refmac, R = 0.2671 (Rfree = 0.000) for 1240 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.2898 (Rfree = 0.000) for 1231 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2588 (Rfree = 0.000) for 1220 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.2725 (Rfree = 0.000) for 1215 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.91 3.71 Search for helices and strands: 0 residues in 0 chains, 1264 seeds are put forward NCS extension: 0 residues added, 1264 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 7 peptides. Score 0.263 Round 2: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.364 Round 3: 89 peptides, 14 chains. Longest chain 14 peptides. Score 0.435 Round 4: 82 peptides, 12 chains. Longest chain 12 peptides. Score 0.448 Round 5: 89 peptides, 14 chains. Longest chain 16 peptides. Score 0.435 Taking the results from Round 4 Chains 12, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2917 restraints for refining 1307 atoms. 2649 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2488 (Rfree = 0.000) for 1307 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.2851 (Rfree = 0.000) for 1299 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 38: After refmac, R = 0.2446 (Rfree = 0.000) for 1290 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.2597 (Rfree = 0.000) for 1290 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.2263 (Rfree = 0.000) for 1287 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 1341 seeds are put forward NCS extension: 0 residues added, 1341 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.320 Round 2: 81 peptides, 15 chains. Longest chain 11 peptides. Score 0.344 Round 3: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.350 Round 4: 89 peptides, 14 chains. Longest chain 14 peptides. Score 0.435 Round 5: 76 peptides, 12 chains. Longest chain 14 peptides. Score 0.405 Taking the results from Round 4 Chains 14, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2760 restraints for refining 1287 atoms. 2474 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2920 (Rfree = 0.000) for 1287 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 42: After refmac, R = 0.2403 (Rfree = 0.000) for 1265 atoms. Found 2 (7 requested) and removed 9 (3 requested) atoms. Cycle 43: After refmac, R = 0.2282 (Rfree = 0.000) for 1250 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.2239 (Rfree = 0.000) for 1249 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.2137 (Rfree = 0.000) for 1245 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 1294 seeds are put forward NCS extension: 0 residues added, 1294 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 5 peptides. Score 0.219 Round 2: 78 peptides, 15 chains. Longest chain 7 peptides. Score 0.320 Round 3: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.328 Round 4: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.336 Round 5: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.288 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pg4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2456 reflections ( 99.47 % complete ) and 2962 restraints for refining 1298 atoms. 2717 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3166 (Rfree = 0.000) for 1298 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2530 (Rfree = 0.000) for 1291 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2617 (Rfree = 0.000) for 1283 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2430 (Rfree = 0.000) for 1273 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:43 GMT 2018 Job finished. TimeTaking 28.69 Used memory is bytes: 5366640