null Mon 24 Dec 07:58:10 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vlu-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-4.0-parrot-noncs ############### 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 07:58:15 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/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-4.0-parrot-noncs/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 909 and 0 Target number of residues in the AU: 909 Target solvent content: 0.6653 Checking the provided sequence file Detected sequence length: 468 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 936 Adjusted target solvent content: 0.66 Input MTZ file: 1vlu-4.0-parrot-noncs.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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.95 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: 44.569 4.000 Wilson plot Bfac: 88.66 12767 reflections ( 99.80 % complete ) and 0 restraints for refining 8325 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3464 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3369 (Rfree = 0.000) for 8325 atoms. Found 39 (39 requested) and removed 77 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.07 Search for helices and strands: 0 residues in 0 chains, 8455 seeds are put forward NCS extension: 0 residues added, 8455 seeds are put forward Round 1: 414 peptides, 68 chains. Longest chain 14 peptides. Score 0.360 Round 2: 486 peptides, 60 chains. Longest chain 19 peptides. Score 0.481 Round 3: 489 peptides, 57 chains. Longest chain 21 peptides. Score 0.498 Round 4: 498 peptides, 55 chains. Longest chain 30 peptides. Score 0.517 Round 5: 516 peptides, 52 chains. Longest chain 29 peptides. Score 0.548 Taking the results from Round 5 Chains 57, Residues 464, Estimated correctness of the model 0.0 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 15325 restraints for refining 6760 atoms. 13363 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2543 (Rfree = 0.000) for 6760 atoms. Found 32 (32 requested) and removed 60 (16 requested) atoms. Cycle 2: After refmac, R = 0.2451 (Rfree = 0.000) for 6553 atoms. Found 31 (31 requested) and removed 73 (15 requested) atoms. Cycle 3: After refmac, R = 0.2273 (Rfree = 0.000) for 6413 atoms. Found 30 (30 requested) and removed 59 (15 requested) atoms. Cycle 4: After refmac, R = 0.2172 (Rfree = 0.000) for 6328 atoms. Found 28 (30 requested) and removed 47 (15 requested) atoms. Cycle 5: After refmac, R = 0.2161 (Rfree = 0.000) for 6260 atoms. Found 29 (29 requested) and removed 39 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.01 Search for helices and strands: 0 residues in 0 chains, 6537 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 6562 seeds are put forward Round 1: 465 peptides, 64 chains. Longest chain 16 peptides. Score 0.439 Round 2: 509 peptides, 59 chains. Longest chain 20 peptides. Score 0.509 Round 3: 514 peptides, 57 chains. Longest chain 18 peptides. Score 0.523 Round 4: 505 peptides, 55 chains. Longest chain 20 peptides. Score 0.524 Round 5: 524 peptides, 53 chains. Longest chain 22 peptides. Score 0.551 Taking the results from Round 5 Chains 59, Residues 471, Estimated correctness of the model 0.0 % 7 chains (78 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14351 restraints for refining 6713 atoms. 12264 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2328 (Rfree = 0.000) for 6713 atoms. Found 31 (31 requested) and removed 90 (15 requested) atoms. Cycle 7: After refmac, R = 0.2307 (Rfree = 0.000) for 6550 atoms. Found 31 (31 requested) and removed 64 (15 requested) atoms. Cycle 8: After refmac, R = 0.2205 (Rfree = 0.000) for 6458 atoms. Found 30 (30 requested) and removed 36 (15 requested) atoms. Cycle 9: After refmac, R = 0.2111 (Rfree = 0.000) for 6402 atoms. Found 25 (30 requested) and removed 43 (15 requested) atoms. Cycle 10: After refmac, R = 0.2045 (Rfree = 0.000) for 6352 atoms. Found 21 (30 requested) and removed 40 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.01 Search for helices and strands: 0 residues in 0 chains, 6596 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 6623 seeds are put forward Round 1: 476 peptides, 64 chains. Longest chain 19 peptides. Score 0.451 Round 2: 506 peptides, 60 chains. Longest chain 28 peptides. Score 0.501 Round 3: 518 peptides, 56 chains. Longest chain 23 peptides. Score 0.532 Round 4: 507 peptides, 59 chains. Longest chain 21 peptides. Score 0.507 Round 5: 508 peptides, 55 chains. Longest chain 37 peptides. Score 0.527 Taking the results from Round 3 Chains 61, Residues 462, Estimated correctness of the model 0.0 % 10 chains (101 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14061 restraints for refining 6760 atoms. 11942 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2392 (Rfree = 0.000) for 6760 atoms. Found 32 (32 requested) and removed 92 (16 requested) atoms. Cycle 12: After refmac, R = 0.2251 (Rfree = 0.000) for 6595 atoms. Found 31 (31 requested) and removed 60 (15 requested) atoms. Cycle 13: After refmac, R = 0.2132 (Rfree = 0.000) for 6516 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 14: After refmac, R = 0.2121 (Rfree = 0.000) for 6466 atoms. Found 30 (30 requested) and removed 63 (15 requested) atoms. Cycle 15: After refmac, R = 0.2013 (Rfree = 0.000) for 6402 atoms. Found 12 (30 requested) and removed 46 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.04 Search for helices and strands: 0 residues in 0 chains, 6621 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6645 seeds are put forward Round 1: 468 peptides, 69 chains. Longest chain 16 peptides. Score 0.417 Round 2: 514 peptides, 59 chains. Longest chain 21 peptides. Score 0.514 Round 3: 505 peptides, 53 chains. Longest chain 29 peptides. Score 0.533 Round 4: 524 peptides, 61 chains. Longest chain 17 peptides. Score 0.515 Round 5: 521 peptides, 56 chains. Longest chain 26 peptides. Score 0.534 Taking the results from Round 5 Chains 60, Residues 465, Estimated correctness of the model 0.0 % 6 chains (52 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14536 restraints for refining 6762 atoms. 12558 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2413 (Rfree = 0.000) for 6762 atoms. Found 32 (32 requested) and removed 82 (16 requested) atoms. Cycle 17: After refmac, R = 0.2283 (Rfree = 0.000) for 6616 atoms. Found 31 (31 requested) and removed 46 (15 requested) atoms. Cycle 18: After refmac, R = 0.2165 (Rfree = 0.000) for 6542 atoms. Found 31 (31 requested) and removed 41 (15 requested) atoms. Cycle 19: After refmac, R = 0.2110 (Rfree = 0.000) for 6493 atoms. Found 23 (31 requested) and removed 35 (15 requested) atoms. Cycle 20: After refmac, R = 0.2027 (Rfree = 0.000) for 6455 atoms. Found 13 (30 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.79 3.04 Search for helices and strands: 0 residues in 0 chains, 6691 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 6708 seeds are put forward Round 1: 459 peptides, 68 chains. Longest chain 17 peptides. Score 0.413 Round 2: 495 peptides, 64 chains. Longest chain 18 peptides. Score 0.471 Round 3: 522 peptides, 59 chains. Longest chain 30 peptides. Score 0.522 Round 4: 509 peptides, 65 chains. Longest chain 18 peptides. Score 0.481 Round 5: 493 peptides, 63 chains. Longest chain 19 peptides. Score 0.474 Taking the results from Round 3 Chains 63, Residues 463, Estimated correctness of the model 0.0 % 5 chains (62 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14420 restraints for refining 6760 atoms. 12435 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2413 (Rfree = 0.000) for 6760 atoms. Found 32 (32 requested) and removed 72 (16 requested) atoms. Cycle 22: After refmac, R = 0.2319 (Rfree = 0.000) for 6635 atoms. Found 31 (31 requested) and removed 59 (15 requested) atoms. Cycle 23: After refmac, R = 0.2273 (Rfree = 0.000) for 6579 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 24: After refmac, R = 0.2158 (Rfree = 0.000) for 6530 atoms. Found 31 (31 requested) and removed 38 (15 requested) atoms. Cycle 25: After refmac, R = 0.2233 (Rfree = 0.000) for 6501 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.02 Search for helices and strands: 0 residues in 0 chains, 6778 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6796 seeds are put forward Round 1: 456 peptides, 74 chains. Longest chain 18 peptides. Score 0.378 Round 2: 485 peptides, 64 chains. Longest chain 23 peptides. Score 0.461 Round 3: 496 peptides, 60 chains. Longest chain 24 peptides. Score 0.491 Round 4: 502 peptides, 59 chains. Longest chain 22 peptides. Score 0.502 Round 5: 498 peptides, 58 chains. Longest chain 20 peptides. Score 0.503 Taking the results from Round 5 Chains 62, Residues 440, Estimated correctness of the model 0.0 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 15016 restraints for refining 6761 atoms. 13214 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2546 (Rfree = 0.000) for 6761 atoms. Found 32 (32 requested) and removed 66 (16 requested) atoms. Cycle 27: After refmac, R = 0.2475 (Rfree = 0.000) for 6620 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 28: After refmac, R = 0.2302 (Rfree = 0.000) for 6555 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 29: After refmac, R = 0.2247 (Rfree = 0.000) for 6503 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. Cycle 30: After refmac, R = 0.2208 (Rfree = 0.000) for 6469 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.04 Search for helices and strands: 0 residues in 0 chains, 6715 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 6729 seeds are put forward Round 1: 445 peptides, 69 chains. Longest chain 18 peptides. Score 0.391 Round 2: 460 peptides, 57 chains. Longest chain 24 peptides. Score 0.469 Round 3: 474 peptides, 55 chains. Longest chain 33 peptides. Score 0.493 Round 4: 481 peptides, 55 chains. Longest chain 21 peptides. Score 0.500 Round 5: 487 peptides, 57 chains. Longest chain 21 peptides. Score 0.496 Taking the results from Round 4 Chains 60, Residues 426, Estimated correctness of the model 0.0 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14785 restraints for refining 6761 atoms. 12975 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2501 (Rfree = 0.000) for 6761 atoms. Found 32 (32 requested) and removed 75 (16 requested) atoms. Cycle 32: After refmac, R = 0.2391 (Rfree = 0.000) for 6619 atoms. Found 31 (31 requested) and removed 51 (15 requested) atoms. Cycle 33: After refmac, R = 0.2379 (Rfree = 0.000) for 6560 atoms. Found 31 (31 requested) and removed 48 (15 requested) atoms. Cycle 34: After refmac, R = 0.2299 (Rfree = 0.000) for 6512 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 35: After refmac, R = 0.2323 (Rfree = 0.000) for 6486 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.04 Search for helices and strands: 0 residues in 0 chains, 6737 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6757 seeds are put forward Round 1: 443 peptides, 71 chains. Longest chain 14 peptides. Score 0.379 Round 2: 468 peptides, 58 chains. Longest chain 36 peptides. Score 0.472 Round 3: 493 peptides, 58 chains. Longest chain 26 peptides. Score 0.498 Round 4: 494 peptides, 59 chains. Longest chain 18 peptides. Score 0.494 Round 5: 482 peptides, 56 chains. Longest chain 34 peptides. Score 0.496 Taking the results from Round 3 Chains 60, Residues 435, Estimated correctness of the model 0.0 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14797 restraints for refining 6761 atoms. 12966 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2528 (Rfree = 0.000) for 6761 atoms. Found 32 (32 requested) and removed 72 (16 requested) atoms. Cycle 37: After refmac, R = 0.2311 (Rfree = 0.000) for 6657 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 38: After refmac, R = 0.2194 (Rfree = 0.000) for 6613 atoms. Found 28 (31 requested) and removed 34 (15 requested) atoms. Cycle 39: After refmac, R = 0.2146 (Rfree = 0.000) for 6580 atoms. Found 21 (31 requested) and removed 33 (15 requested) atoms. Cycle 40: After refmac, R = 0.2130 (Rfree = 0.000) for 6551 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.84 3.08 Search for helices and strands: 0 residues in 0 chains, 6798 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 6830 seeds are put forward Round 1: 400 peptides, 60 chains. Longest chain 18 peptides. Score 0.387 Round 2: 452 peptides, 67 chains. Longest chain 16 peptides. Score 0.410 Round 3: 477 peptides, 57 chains. Longest chain 20 peptides. Score 0.486 Round 4: 466 peptides, 59 chains. Longest chain 19 peptides. Score 0.465 Round 5: 480 peptides, 59 chains. Longest chain 21 peptides. Score 0.480 Taking the results from Round 3 Chains 59, Residues 420, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14851 restraints for refining 6760 atoms. 13114 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2358 (Rfree = 0.000) for 6760 atoms. Found 32 (32 requested) and removed 56 (16 requested) atoms. Cycle 42: After refmac, R = 0.2336 (Rfree = 0.000) for 6683 atoms. Found 32 (32 requested) and removed 50 (16 requested) atoms. Cycle 43: After refmac, R = 0.2247 (Rfree = 0.000) for 6637 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 44: After refmac, R = 0.2167 (Rfree = 0.000) for 6611 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 45: After refmac, R = 0.2246 (Rfree = 0.000) for 6581 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.01 Search for helices and strands: 0 residues in 0 chains, 6837 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6858 seeds are put forward Round 1: 391 peptides, 66 chains. Longest chain 15 peptides. Score 0.343 Round 2: 453 peptides, 64 chains. Longest chain 23 peptides. Score 0.426 Round 3: 446 peptides, 64 chains. Longest chain 19 peptides. Score 0.418 Round 4: 451 peptides, 64 chains. Longest chain 15 peptides. Score 0.424 Round 5: 450 peptides, 66 chains. Longest chain 16 peptides. Score 0.413 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 389, Estimated correctness of the model 0.0 % 6 chains (56 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 1vlu-4_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (389 residues) following loop building 6 chains (56 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12767 reflections ( 99.80 % complete ) and 14582 restraints for refining 6760 atoms. 12871 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2425 (Rfree = 0.000) for 6760 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2319 (Rfree = 0.000) for 6687 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2301 (Rfree = 0.000) for 6638 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1929 (Rfree = 0.000) for 6591 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:04:47 GMT 2018 Job finished. TimeTaking 66.62 Used memory is bytes: 6449736