Mon 24 Dec 01:01:11 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 1vm8-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.8-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/1vm8-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.8-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 ============================================================ Mon 24 Dec 01:01:16 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/1vm8-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.8-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 793 and 0 Target number of residues in the AU: 793 Target solvent content: 0.6542 Checking the provided sequence file Detected sequence length: 534 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1068 Adjusted target solvent content: 0.53 Input MTZ file: 1vm8-3.8-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: 4 Cell parameters: 80.094 73.402 107.132 90.000 99.827 90.000 Input sequence file: 1vm8-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8544 target number of atoms Had to go as low as 0.65 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: 105.560 3.800 Wilson plot Bfac: 80.80 12194 reflections ( 98.99 % complete ) and 0 restraints for refining 9439 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3291 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3228 (Rfree = 0.000) for 9439 atoms. Found 51 (51 requested) and removed 158 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.46 Search for helices and strands: 0 residues in 0 chains, 9476 seeds are put forward NCS extension: 0 residues added, 9476 seeds are put forward Round 1: 361 peptides, 75 chains. Longest chain 11 peptides. Score 0.265 Round 2: 440 peptides, 86 chains. Longest chain 13 peptides. Score 0.313 Round 3: 472 peptides, 84 chains. Longest chain 12 peptides. Score 0.369 Round 4: 506 peptides, 84 chains. Longest chain 15 peptides. Score 0.414 Round 5: 507 peptides, 87 chains. Longest chain 15 peptides. Score 0.398 Taking the results from Round 4 Chains 85, Residues 422, Estimated correctness of the model 0.0 % 5 chains (26 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 18415 restraints for refining 7726 atoms. 16746 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2492 (Rfree = 0.000) for 7726 atoms. Found 33 (42 requested) and removed 70 (21 requested) atoms. Cycle 2: After refmac, R = 0.2324 (Rfree = 0.000) for 7572 atoms. Found 25 (42 requested) and removed 71 (21 requested) atoms. Cycle 3: After refmac, R = 0.2004 (Rfree = 0.000) for 7481 atoms. Found 10 (41 requested) and removed 50 (20 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1977 (Rfree = 0.000) for 7415 atoms. Found 9 (40 requested) and removed 38 (20 requested) atoms. Cycle 5: After refmac, R = 0.1910 (Rfree = 0.000) for 7382 atoms. Found 9 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.50 Search for helices and strands: 0 residues in 0 chains, 7635 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 7660 seeds are put forward Round 1: 474 peptides, 89 chains. Longest chain 17 peptides. Score 0.343 Round 2: 546 peptides, 89 chains. Longest chain 18 peptides. Score 0.437 Round 3: 531 peptides, 80 chains. Longest chain 18 peptides. Score 0.466 Round 4: 545 peptides, 80 chains. Longest chain 19 peptides. Score 0.483 Round 5: 522 peptides, 76 chains. Longest chain 15 peptides. Score 0.477 Taking the results from Round 4 Chains 82, Residues 465, Estimated correctness of the model 0.0 % 8 chains (53 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 17633 restraints for refining 7727 atoms. 15678 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2253 (Rfree = 0.000) for 7727 atoms. Found 34 (42 requested) and removed 89 (21 requested) atoms. Cycle 7: After refmac, R = 0.2182 (Rfree = 0.000) for 7591 atoms. Found 35 (42 requested) and removed 57 (21 requested) atoms. Cycle 8: After refmac, R = 0.2147 (Rfree = 0.000) for 7525 atoms. Found 33 (41 requested) and removed 54 (20 requested) atoms. Cycle 9: After refmac, R = 0.2048 (Rfree = 0.000) for 7468 atoms. Found 24 (41 requested) and removed 37 (20 requested) atoms. Cycle 10: After refmac, R = 0.2124 (Rfree = 0.000) for 7426 atoms. Found 39 (40 requested) and removed 48 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.48 Search for helices and strands: 0 residues in 0 chains, 7641 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 7673 seeds are put forward Round 1: 436 peptides, 84 chains. Longest chain 12 peptides. Score 0.319 Round 2: 523 peptides, 88 chains. Longest chain 14 peptides. Score 0.413 Round 3: 521 peptides, 87 chains. Longest chain 13 peptides. Score 0.416 Round 4: 560 peptides, 82 chains. Longest chain 23 peptides. Score 0.490 Round 5: 557 peptides, 82 chains. Longest chain 21 peptides. Score 0.487 Taking the results from Round 4 Chains 84, Residues 478, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 17698 restraints for refining 7726 atoms. 15768 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2155 (Rfree = 0.000) for 7726 atoms. Found 31 (42 requested) and removed 60 (21 requested) atoms. Cycle 12: After refmac, R = 0.2038 (Rfree = 0.000) for 7640 atoms. Found 23 (42 requested) and removed 47 (21 requested) atoms. Cycle 13: After refmac, R = 0.2052 (Rfree = 0.000) for 7585 atoms. Found 29 (41 requested) and removed 46 (20 requested) atoms. Cycle 14: After refmac, R = 0.2013 (Rfree = 0.000) for 7552 atoms. Found 33 (41 requested) and removed 41 (20 requested) atoms. Cycle 15: After refmac, R = 0.1696 (Rfree = 0.000) for 7517 atoms. Found 13 (41 requested) and removed 40 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.48 Search for helices and strands: 0 residues in 0 chains, 7747 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 7771 seeds are put forward Round 1: 496 peptides, 94 chains. Longest chain 12 peptides. Score 0.344 Round 2: 526 peptides, 87 chains. Longest chain 19 peptides. Score 0.422 Round 3: 543 peptides, 85 chains. Longest chain 18 peptides. Score 0.454 Round 4: 550 peptides, 79 chains. Longest chain 19 peptides. Score 0.494 Round 5: 538 peptides, 73 chains. Longest chain 22 peptides. Score 0.511 Taking the results from Round 5 Chains 79, Residues 465, Estimated correctness of the model 0.0 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 17363 restraints for refining 7727 atoms. 15393 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2237 (Rfree = 0.000) for 7727 atoms. Found 42 (42 requested) and removed 61 (21 requested) atoms. Cycle 17: After refmac, R = 0.1987 (Rfree = 0.000) for 7642 atoms. Found 35 (42 requested) and removed 40 (21 requested) atoms. Cycle 18: After refmac, R = 0.1927 (Rfree = 0.000) for 7581 atoms. Found 38 (41 requested) and removed 40 (20 requested) atoms. Cycle 19: After refmac, R = 0.1645 (Rfree = 0.000) for 7551 atoms. Found 9 (41 requested) and removed 27 (20 requested) atoms. Cycle 20: After refmac, R = 0.1560 (Rfree = 0.000) for 7523 atoms. Found 2 (41 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.49 Search for helices and strands: 0 residues in 0 chains, 7716 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7734 seeds are put forward Round 1: 454 peptides, 86 chains. Longest chain 11 peptides. Score 0.333 Round 2: 528 peptides, 86 chains. Longest chain 13 peptides. Score 0.430 Round 3: 515 peptides, 82 chains. Longest chain 16 peptides. Score 0.436 Round 4: 526 peptides, 78 chains. Longest chain 22 peptides. Score 0.471 Round 5: 509 peptides, 77 chains. Longest chain 15 peptides. Score 0.456 Taking the results from Round 4 Chains 80, Residues 448, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 17671 restraints for refining 7728 atoms. 15818 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2138 (Rfree = 0.000) for 7728 atoms. Found 42 (42 requested) and removed 61 (21 requested) atoms. Cycle 22: After refmac, R = 0.1997 (Rfree = 0.000) for 7652 atoms. Found 42 (42 requested) and removed 42 (21 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1975 (Rfree = 0.000) for 7614 atoms. Found 42 (42 requested) and removed 50 (21 requested) atoms. Cycle 24: After refmac, R = 0.1878 (Rfree = 0.000) for 7585 atoms. Found 41 (41 requested) and removed 37 (20 requested) atoms. Cycle 25: After refmac, R = 0.1868 (Rfree = 0.000) for 7567 atoms. Found 41 (41 requested) and removed 36 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 7810 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 7848 seeds are put forward Round 1: 445 peptides, 85 chains. Longest chain 12 peptides. Score 0.326 Round 2: 488 peptides, 77 chains. Longest chain 24 peptides. Score 0.430 Round 3: 511 peptides, 88 chains. Longest chain 14 peptides. Score 0.398 Round 4: 489 peptides, 74 chains. Longest chain 16 peptides. Score 0.447 Round 5: 507 peptides, 82 chains. Longest chain 17 peptides. Score 0.426 Taking the results from Round 4 Chains 75, Residues 415, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12194 reflections ( 98.99 % complete ) and 17980 restraints for refining 7726 atoms. 16311 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2145 (Rfree = 0.000) for 7726 atoms. Found 42 (42 requested) and removed 49 (21 requested) atoms. Cycle 27: After refmac, R = 0.2112 (Rfree = 0.000) for 7658 atoms. Found 42 (42 requested) and removed 44 (21 requested) atoms. Cycle 28: After refmac, R = 0.1940 (Rfree = 0.000) for 7624 atoms. Found 42 (42 requested) and removed 33 (21 requested) atoms. Cycle 29: After refmac, R = 0.1991 (Rfree = 0.000) for 7607 atoms. Found 41 (41 requested) and removed 34 (20 requested) atoms. Cycle 30: After refmac, R = 0.1889 (Rfree = 0.000) for 7588 atoms. Found 41 (41 requested) and removed 37 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.49 Search for helices and strands: 0 residues in 0 chains, 7808 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 7828 seeds are put forward Round 1: 404 peptides, 83 chains. Longest chain 10 peptides. Score 0.279 Round 2: 475 peptides, 85 chains. Longest chain 12 peptides. Score 0.367 Round 3: 485 peptides, 80 chains. Longest chain 15 peptides. Score 0.409 Round 4: 466 peptides, 77 chains. Longest chain 17 peptides. Score 0.401 Round 5: 459 peptides, 76 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 3 Chains 81, Residues 405, Estimated correctness of the model 0.0 % 7 chains (43 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 18091 restraints for refining 7721 atoms. 16423 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1983 (Rfree = 0.000) for 7721 atoms. Found 42 (42 requested) and removed 61 (21 requested) atoms. Cycle 32: After refmac, R = 0.1861 (Rfree = 0.000) for 7657 atoms. Found 34 (42 requested) and removed 38 (21 requested) atoms. Cycle 33: After refmac, R = 0.1881 (Rfree = 0.000) for 7633 atoms. Found 41 (42 requested) and removed 35 (21 requested) atoms. Cycle 34: After refmac, R = 0.1792 (Rfree = 0.000) for 7625 atoms. Found 34 (42 requested) and removed 34 (21 requested) atoms. Cycle 35: After refmac, R = 0.1824 (Rfree = 0.000) for 7603 atoms. Found 41 (41 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 7827 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7845 seeds are put forward Round 1: 376 peptides, 74 chains. Longest chain 12 peptides. Score 0.294 Round 2: 386 peptides, 65 chains. Longest chain 14 peptides. Score 0.364 Round 3: 405 peptides, 66 chains. Longest chain 12 peptides. Score 0.384 Round 4: 431 peptides, 66 chains. Longest chain 24 peptides. Score 0.419 Round 5: 436 peptides, 69 chains. Longest chain 24 peptides. Score 0.408 Taking the results from Round 4 Chains 68, Residues 365, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 18216 restraints for refining 7728 atoms. 16776 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1876 (Rfree = 0.000) for 7728 atoms. Found 36 (42 requested) and removed 48 (21 requested) atoms. Cycle 37: After refmac, R = 0.1862 (Rfree = 0.000) for 7699 atoms. Found 34 (42 requested) and removed 36 (21 requested) atoms. Cycle 38: After refmac, R = 0.1873 (Rfree = 0.000) for 7677 atoms. Found 42 (42 requested) and removed 48 (21 requested) atoms. Cycle 39: After refmac, R = 0.1909 (Rfree = 0.000) for 7650 atoms. Found 42 (42 requested) and removed 44 (21 requested) atoms. Cycle 40: After refmac, R = 0.1491 (Rfree = 0.000) for 7630 atoms. Found 14 (42 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 7799 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 7824 seeds are put forward Round 1: 331 peptides, 67 chains. Longest chain 12 peptides. Score 0.271 Round 2: 385 peptides, 69 chains. Longest chain 13 peptides. Score 0.338 Round 3: 404 peptides, 66 chains. Longest chain 15 peptides. Score 0.383 Round 4: 410 peptides, 69 chains. Longest chain 13 peptides. Score 0.373 Round 5: 434 peptides, 64 chains. Longest chain 29 peptides. Score 0.434 Taking the results from Round 5 Chains 64, Residues 370, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 17823 restraints for refining 7726 atoms. 16379 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1985 (Rfree = 0.000) for 7726 atoms. Found 42 (42 requested) and removed 46 (21 requested) atoms. Cycle 42: After refmac, R = 0.1861 (Rfree = 0.000) for 7690 atoms. Found 42 (42 requested) and removed 37 (21 requested) atoms. Cycle 43: After refmac, R = 0.1911 (Rfree = 0.000) for 7666 atoms. Found 42 (42 requested) and removed 39 (21 requested) atoms. Cycle 44: After refmac, R = 0.1742 (Rfree = 0.000) for 7654 atoms. Found 42 (42 requested) and removed 38 (21 requested) atoms. Cycle 45: After refmac, R = 0.1381 (Rfree = 0.000) for 7643 atoms. Found 6 (42 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 7855 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7872 seeds are put forward Round 1: 323 peptides, 69 chains. Longest chain 9 peptides. Score 0.245 Round 2: 393 peptides, 72 chains. Longest chain 12 peptides. Score 0.331 Round 3: 407 peptides, 69 chains. Longest chain 14 peptides. Score 0.369 Round 4: 392 peptides, 65 chains. Longest chain 15 peptides. Score 0.373 Round 5: 394 peptides, 64 chains. Longest chain 17 peptides. Score 0.382 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 330, Estimated correctness of the model 0.0 % 8 chains (60 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 1vm8-3_warpNtrace.pdb as input Building loops using Loopy2018 65 chains (330 residues) following loop building 8 chains (60 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12194 reflections ( 98.99 % complete ) and 17834 restraints for refining 7728 atoms. 16377 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1839 (Rfree = 0.000) for 7728 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.1829 (Rfree = 0.000) for 7684 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.1832 (Rfree = 0.000) for 7640 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.1739 (Rfree = 0.000) for 7598 atoms. TimeTaking 86.85