Sun 23 Dec 23:58:17 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 2pgc-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pgc-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pgc-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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/2pgc-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 ============================================================ Sun 23 Dec 23:58:21 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/2pgc-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 722 and 0 Target number of residues in the AU: 722 Target solvent content: 0.6654 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8280 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. 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: 98.043 3.800 Wilson plot Bfac: 88.94 12038 reflections ( 99.49 % complete ) and 0 restraints for refining 9166 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3414 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3246 (Rfree = 0.000) for 9166 atoms. Found 50 (50 requested) and removed 33 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 9373 seeds are put forward NCS extension: 0 residues added, 9373 seeds are put forward Round 1: 379 peptides, 74 chains. Longest chain 12 peptides. Score 0.304 Round 2: 514 peptides, 82 chains. Longest chain 16 peptides. Score 0.447 Round 3: 551 peptides, 77 chains. Longest chain 15 peptides. Score 0.520 Round 4: 564 peptides, 79 chains. Longest chain 16 peptides. Score 0.525 Round 5: 561 peptides, 74 chains. Longest chain 17 peptides. Score 0.547 Taking the results from Round 5 Chains 75, Residues 487, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17037 restraints for refining 7478 atoms. 15055 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2909 (Rfree = 0.000) for 7478 atoms. Found 34 (41 requested) and removed 48 (20 requested) atoms. Cycle 2: After refmac, R = 0.2576 (Rfree = 0.000) for 7315 atoms. Found 30 (41 requested) and removed 37 (20 requested) atoms. Cycle 3: After refmac, R = 0.2427 (Rfree = 0.000) for 7215 atoms. Found 31 (40 requested) and removed 28 (20 requested) atoms. Cycle 4: After refmac, R = 0.2039 (Rfree = 0.000) for 7151 atoms. Found 19 (39 requested) and removed 28 (19 requested) atoms. Cycle 5: After refmac, R = 0.2126 (Rfree = 0.000) for 7104 atoms. Found 19 (39 requested) and removed 29 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.53 Search for helices and strands: 0 residues in 0 chains, 7353 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 7368 seeds are put forward Round 1: 479 peptides, 93 chains. Longest chain 12 peptides. Score 0.334 Round 2: 537 peptides, 81 chains. Longest chain 19 peptides. Score 0.482 Round 3: 564 peptides, 86 chains. Longest chain 35 peptides. Score 0.488 Round 4: 567 peptides, 80 chains. Longest chain 35 peptides. Score 0.523 Round 5: 561 peptides, 78 chains. Longest chain 21 peptides. Score 0.527 Taking the results from Round 5 Chains 80, Residues 483, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 16994 restraints for refining 7489 atoms. 15059 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2482 (Rfree = 0.000) for 7489 atoms. Found 29 (41 requested) and removed 91 (20 requested) atoms. Cycle 7: After refmac, R = 0.2220 (Rfree = 0.000) for 7352 atoms. Found 32 (40 requested) and removed 47 (20 requested) atoms. Cycle 8: After refmac, R = 0.1951 (Rfree = 0.000) for 7279 atoms. Found 30 (40 requested) and removed 42 (20 requested) atoms. Cycle 9: After refmac, R = 0.1997 (Rfree = 0.000) for 7230 atoms. Found 31 (39 requested) and removed 25 (19 requested) atoms. Cycle 10: After refmac, R = 0.1899 (Rfree = 0.000) for 7217 atoms. Found 31 (39 requested) and removed 35 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.53 Search for helices and strands: 0 residues in 0 chains, 7561 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7578 seeds are put forward Round 1: 446 peptides, 87 chains. Longest chain 13 peptides. Score 0.322 Round 2: 500 peptides, 84 chains. Longest chain 19 peptides. Score 0.417 Round 3: 517 peptides, 83 chains. Longest chain 24 peptides. Score 0.445 Round 4: 522 peptides, 76 chains. Longest chain 19 peptides. Score 0.490 Round 5: 537 peptides, 76 chains. Longest chain 30 peptides. Score 0.509 Taking the results from Round 5 Chains 76, Residues 461, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17369 restraints for refining 7487 atoms. 15601 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2375 (Rfree = 0.000) for 7487 atoms. Found 41 (41 requested) and removed 39 (20 requested) atoms. Cycle 12: After refmac, R = 0.2202 (Rfree = 0.000) for 7410 atoms. Found 41 (41 requested) and removed 41 (20 requested) atoms. Cycle 13: After refmac, R = 0.2010 (Rfree = 0.000) for 7374 atoms. Found 35 (40 requested) and removed 33 (20 requested) atoms. Cycle 14: After refmac, R = 0.1980 (Rfree = 0.000) for 7350 atoms. Found 40 (40 requested) and removed 31 (20 requested) atoms. Cycle 15: After refmac, R = 0.2092 (Rfree = 0.000) for 7337 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 7673 seeds are put forward NCS extension: 38 residues added (3 deleted due to clashes), 7711 seeds are put forward Round 1: 428 peptides, 84 chains. Longest chain 12 peptides. Score 0.314 Round 2: 495 peptides, 86 chains. Longest chain 13 peptides. Score 0.398 Round 3: 500 peptides, 81 chains. Longest chain 15 peptides. Score 0.434 Round 4: 512 peptides, 81 chains. Longest chain 17 peptides. Score 0.450 Round 5: 498 peptides, 79 chains. Longest chain 18 peptides. Score 0.443 Taking the results from Round 4 Chains 83, Residues 431, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12038 reflections ( 99.49 % complete ) and 17115 restraints for refining 7488 atoms. 15413 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2330 (Rfree = 0.000) for 7488 atoms. Found 41 (41 requested) and removed 49 (20 requested) atoms. Cycle 17: After refmac, R = 0.2151 (Rfree = 0.000) for 7433 atoms. Found 41 (41 requested) and removed 35 (20 requested) atoms. Cycle 18: After refmac, R = 0.2027 (Rfree = 0.000) for 7400 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. Cycle 19: After refmac, R = 0.1902 (Rfree = 0.000) for 7360 atoms. Found 33 (40 requested) and removed 30 (20 requested) atoms. Cycle 20: After refmac, R = 0.1879 (Rfree = 0.000) for 7340 atoms. Found 38 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 7637 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7651 seeds are put forward Round 1: 366 peptides, 73 chains. Longest chain 11 peptides. Score 0.291 Round 2: 461 peptides, 80 chains. Longest chain 14 peptides. Score 0.387 Round 3: 464 peptides, 83 chains. Longest chain 11 peptides. Score 0.373 Round 4: 468 peptides, 81 chains. Longest chain 11 peptides. Score 0.391 Round 5: 478 peptides, 78 chains. Longest chain 19 peptides. Score 0.422 Taking the results from Round 5 Chains 78, Residues 400, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17465 restraints for refining 7489 atoms. 15913 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2384 (Rfree = 0.000) for 7489 atoms. Found 41 (41 requested) and removed 44 (20 requested) atoms. Cycle 22: After refmac, R = 0.2435 (Rfree = 0.000) for 7426 atoms. Found 41 (41 requested) and removed 50 (20 requested) atoms. Cycle 23: After refmac, R = 0.2283 (Rfree = 0.000) for 7373 atoms. Found 40 (40 requested) and removed 31 (20 requested) atoms. Cycle 24: After refmac, R = 0.2433 (Rfree = 0.000) for 7337 atoms. Found 40 (40 requested) and removed 39 (20 requested) atoms. Cycle 25: After refmac, R = 0.2374 (Rfree = 0.000) for 7281 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 7625 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 7640 seeds are put forward Round 1: 331 peptides, 70 chains. Longest chain 9 peptides. Score 0.255 Round 2: 395 peptides, 75 chains. Longest chain 11 peptides. Score 0.322 Round 3: 421 peptides, 69 chains. Longest chain 18 peptides. Score 0.398 Round 4: 402 peptides, 70 chains. Longest chain 13 peptides. Score 0.365 Round 5: 424 peptides, 66 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 5 Chains 66, Residues 358, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17131 restraints for refining 7486 atoms. 15728 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2403 (Rfree = 0.000) for 7486 atoms. Found 41 (41 requested) and removed 56 (20 requested) atoms. Cycle 27: After refmac, R = 0.2152 (Rfree = 0.000) for 7399 atoms. Found 41 (41 requested) and removed 33 (20 requested) atoms. Cycle 28: After refmac, R = 0.1951 (Rfree = 0.000) for 7354 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2045 (Rfree = 0.000) for 7343 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 30: After refmac, R = 0.1557 (Rfree = 0.000) for 7330 atoms. Found 14 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 7531 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 7550 seeds are put forward Round 1: 308 peptides, 68 chains. Longest chain 8 peptides. Score 0.230 Round 2: 390 peptides, 75 chains. Longest chain 9 peptides. Score 0.315 Round 3: 404 peptides, 74 chains. Longest chain 12 peptides. Score 0.342 Round 4: 410 peptides, 69 chains. Longest chain 15 peptides. Score 0.382 Round 5: 406 peptides, 73 chains. Longest chain 11 peptides. Score 0.351 Taking the results from Round 4 Chains 69, Residues 341, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17348 restraints for refining 7465 atoms. 16033 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2105 (Rfree = 0.000) for 7465 atoms. Found 41 (41 requested) and removed 43 (20 requested) atoms. Cycle 32: After refmac, R = 0.2057 (Rfree = 0.000) for 7430 atoms. Found 41 (41 requested) and removed 38 (20 requested) atoms. Cycle 33: After refmac, R = 0.1883 (Rfree = 0.000) for 7411 atoms. Found 31 (40 requested) and removed 31 (20 requested) atoms. Cycle 34: After refmac, R = 0.1877 (Rfree = 0.000) for 7391 atoms. Found 40 (40 requested) and removed 24 (20 requested) atoms. Cycle 35: After refmac, R = 0.1580 (Rfree = 0.000) for 7391 atoms. Found 11 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 7591 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 7605 seeds are put forward Round 1: 315 peptides, 69 chains. Longest chain 8 peptides. Score 0.235 Round 2: 381 peptides, 72 chains. Longest chain 14 peptides. Score 0.320 Round 3: 385 peptides, 72 chains. Longest chain 11 peptides. Score 0.327 Round 4: 399 peptides, 72 chains. Longest chain 15 peptides. Score 0.347 Round 5: 407 peptides, 71 chains. Longest chain 14 peptides. Score 0.365 Taking the results from Round 5 Chains 71, Residues 336, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17651 restraints for refining 7489 atoms. 16359 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2084 (Rfree = 0.000) for 7489 atoms. Found 41 (41 requested) and removed 24 (20 requested) atoms. Cycle 37: After refmac, R = 0.2041 (Rfree = 0.000) for 7465 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. Cycle 38: After refmac, R = 0.1798 (Rfree = 0.000) for 7456 atoms. Found 26 (41 requested) and removed 27 (20 requested) atoms. Cycle 39: After refmac, R = 0.1723 (Rfree = 0.000) for 7436 atoms. Found 29 (40 requested) and removed 23 (20 requested) atoms. Cycle 40: After refmac, R = 0.1456 (Rfree = 0.000) for 7425 atoms. Found 14 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 7597 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 7618 seeds are put forward Round 1: 268 peptides, 58 chains. Longest chain 10 peptides. Score 0.233 Round 2: 322 peptides, 60 chains. Longest chain 14 peptides. Score 0.309 Round 3: 332 peptides, 62 chains. Longest chain 12 peptides. Score 0.311 Round 4: 337 peptides, 59 chains. Longest chain 13 peptides. Score 0.339 Round 5: 334 peptides, 61 chains. Longest chain 13 peptides. Score 0.321 Taking the results from Round 4 Chains 59, Residues 278, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12038 reflections ( 99.49 % complete ) and 17537 restraints for refining 7437 atoms. 16484 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1924 (Rfree = 0.000) for 7437 atoms. Found 39 (40 requested) and removed 40 (20 requested) atoms. Cycle 42: After refmac, R = 0.1943 (Rfree = 0.000) for 7402 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. Cycle 43: After refmac, R = 0.1794 (Rfree = 0.000) for 7388 atoms. Found 40 (40 requested) and removed 29 (20 requested) atoms. Cycle 44: After refmac, R = 0.1660 (Rfree = 0.000) for 7383 atoms. Found 28 (40 requested) and removed 24 (20 requested) atoms. Cycle 45: After refmac, R = 0.1406 (Rfree = 0.000) for 7370 atoms. Found 10 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 7542 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 7565 seeds are put forward Round 1: 281 peptides, 60 chains. Longest chain 11 peptides. Score 0.241 Round 2: 339 peptides, 65 chains. Longest chain 11 peptides. Score 0.302 Round 3: 344 peptides, 64 chains. Longest chain 12 peptides. Score 0.316 Round 4: 361 peptides, 66 chains. Longest chain 9 peptides. Score 0.329 Round 5: 326 peptides, 61 chains. Longest chain 12 peptides. Score 0.309 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 295, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2pgc-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (295 residues) following loop building 3 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12038 reflections ( 99.49 % complete ) and 17146 restraints for refining 7485 atoms. 16014 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1852 (Rfree = 0.000) for 7485 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1685 (Rfree = 0.000) for 7443 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.1742 (Rfree = 0.000) for 7407 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1766 (Rfree = 0.000) for 7375 atoms. TimeTaking 77.88