null Mon 24 Dec 07:37:25 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 1vkz-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.2-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/1vkz-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.2-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 07:37:29 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/1vkz-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.2-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 721 and 0 Target number of residues in the AU: 721 Target solvent content: 0.5393 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-3.2-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: 4 Cell parameters: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.55 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: 19.959 3.200 Wilson plot Bfac: 32.54 13478 reflections ( 96.64 % complete ) and 0 restraints for refining 7264 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.2919 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2383 (Rfree = 0.000) for 7264 atoms. Found 65 (65 requested) and removed 69 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.72 2.83 Search for helices and strands: 0 residues in 0 chains, 7389 seeds are put forward NCS extension: 0 residues added, 7389 seeds are put forward Round 1: 393 peptides, 73 chains. Longest chain 15 peptides. Score 0.377 Round 2: 481 peptides, 76 chains. Longest chain 17 peptides. Score 0.509 Round 3: 510 peptides, 73 chains. Longest chain 20 peptides. Score 0.573 Round 4: 539 peptides, 72 chains. Longest chain 24 peptides. Score 0.620 Round 5: 546 peptides, 69 chains. Longest chain 20 peptides. Score 0.646 Taking the results from Round 5 Chains 72, Residues 477, Estimated correctness of the model 52.9 % 12 chains (103 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12036 restraints for refining 6018 atoms. 9821 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2465 (Rfree = 0.000) for 6018 atoms. Found 54 (54 requested) and removed 50 (27 requested) atoms. Cycle 2: After refmac, R = 0.2294 (Rfree = 0.000) for 5925 atoms. Found 28 (54 requested) and removed 38 (27 requested) atoms. Cycle 3: After refmac, R = 0.2266 (Rfree = 0.000) for 5855 atoms. Found 36 (53 requested) and removed 34 (26 requested) atoms. Cycle 4: After refmac, R = 0.2194 (Rfree = 0.000) for 5831 atoms. Found 30 (52 requested) and removed 35 (26 requested) atoms. Cycle 5: After refmac, R = 0.2154 (Rfree = 0.000) for 5798 atoms. Found 23 (52 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.68 2.79 Search for helices and strands: 0 residues in 0 chains, 5961 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5984 seeds are put forward Round 1: 520 peptides, 66 chains. Longest chain 22 peptides. Score 0.630 Round 2: 555 peptides, 65 chains. Longest chain 33 peptides. Score 0.678 Round 3: 577 peptides, 62 chains. Longest chain 27 peptides. Score 0.717 Round 4: 573 peptides, 62 chains. Longest chain 26 peptides. Score 0.713 Round 5: 565 peptides, 63 chains. Longest chain 30 peptides. Score 0.700 Taking the results from Round 3 Chains 67, Residues 515, Estimated correctness of the model 68.7 % 11 chains (131 residues) have been docked in sequence Building loops using Loopy2018 67 chains (515 residues) following loop building 11 chains (131 residues) in sequence following loop building ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11672 restraints for refining 6015 atoms. 9156 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2495 (Rfree = 0.000) for 6015 atoms. Found 54 (54 requested) and removed 72 (27 requested) atoms. Cycle 7: After refmac, R = 0.2238 (Rfree = 0.000) for 5944 atoms. Found 25 (52 requested) and removed 47 (26 requested) atoms. Cycle 8: After refmac, R = 0.2182 (Rfree = 0.000) for 5891 atoms. Found 21 (51 requested) and removed 34 (26 requested) atoms. Cycle 9: After refmac, R = 0.2181 (Rfree = 0.000) for 5856 atoms. Found 33 (49 requested) and removed 34 (26 requested) atoms. Cycle 10: After refmac, R = 0.2134 (Rfree = 0.000) for 5843 atoms. Found 27 (48 requested) and removed 35 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.64 2.75 Search for helices and strands: 0 residues in 0 chains, 5997 seeds are put forward NCS extension: 24 residues added (11 deleted due to clashes), 6021 seeds are put forward Round 1: 518 peptides, 67 chains. Longest chain 25 peptides. Score 0.621 Round 2: 555 peptides, 60 chains. Longest chain 30 peptides. Score 0.704 Round 3: 574 peptides, 64 chains. Longest chain 29 peptides. Score 0.704 Round 4: 566 peptides, 61 chains. Longest chain 27 peptides. Score 0.711 Round 5: 580 peptides, 59 chains. Longest chain 32 peptides. Score 0.734 Taking the results from Round 5 Chains 68, Residues 521, Estimated correctness of the model 72.1 % 13 chains (125 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 362 A and 372 A 67 chains (525 residues) following loop building 12 chains (134 residues) in sequence following loop building ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11696 restraints for refining 6017 atoms. 9220 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2515 (Rfree = 0.000) for 6017 atoms. Found 49 (49 requested) and removed 66 (27 requested) atoms. Cycle 12: After refmac, R = 0.2269 (Rfree = 0.000) for 5970 atoms. Found 21 (47 requested) and removed 35 (26 requested) atoms. Cycle 13: After refmac, R = 0.2360 (Rfree = 0.000) for 5926 atoms. Found 46 (46 requested) and removed 40 (26 requested) atoms. Cycle 14: After refmac, R = 0.2107 (Rfree = 0.000) for 5919 atoms. Found 26 (45 requested) and removed 35 (26 requested) atoms. Cycle 15: After refmac, R = 0.2098 (Rfree = 0.000) for 5891 atoms. Found 35 (43 requested) and removed 34 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.69 2.80 Search for helices and strands: 0 residues in 0 chains, 6059 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 6086 seeds are put forward Round 1: 491 peptides, 67 chains. Longest chain 25 peptides. Score 0.584 Round 2: 547 peptides, 58 chains. Longest chain 32 peptides. Score 0.705 Round 3: 561 peptides, 62 chains. Longest chain 28 peptides. Score 0.700 Round 4: 559 peptides, 61 chains. Longest chain 35 peptides. Score 0.703 Round 5: 550 peptides, 64 chains. Longest chain 31 peptides. Score 0.678 Taking the results from Round 2 Chains 62, Residues 489, Estimated correctness of the model 66.2 % 10 chains (95 residues) have been docked in sequence Building loops using Loopy2018 62 chains (489 residues) following loop building 10 chains (95 residues) in sequence following loop building ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12237 restraints for refining 6017 atoms. 9997 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2192 (Rfree = 0.000) for 6017 atoms. Found 40 (43 requested) and removed 44 (27 requested) atoms. Cycle 17: After refmac, R = 0.2039 (Rfree = 0.000) for 5986 atoms. Found 24 (41 requested) and removed 35 (26 requested) atoms. Cycle 18: After refmac, R = 0.1980 (Rfree = 0.000) for 5954 atoms. Found 25 (40 requested) and removed 31 (26 requested) atoms. Cycle 19: After refmac, R = 0.1926 (Rfree = 0.000) for 5943 atoms. Found 13 (39 requested) and removed 28 (26 requested) atoms. Cycle 20: After refmac, R = 0.1900 (Rfree = 0.000) for 5916 atoms. Found 18 (38 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.70 2.81 Search for helices and strands: 0 residues in 0 chains, 6039 seeds are put forward NCS extension: 14 residues added (14 deleted due to clashes), 6053 seeds are put forward Round 1: 476 peptides, 64 chains. Longest chain 17 peptides. Score 0.582 Round 2: 544 peptides, 68 chains. Longest chain 20 peptides. Score 0.649 Round 3: 546 peptides, 62 chains. Longest chain 28 peptides. Score 0.684 Round 4: 569 peptides, 65 chains. Longest chain 31 peptides. Score 0.694 Round 5: 553 peptides, 62 chains. Longest chain 40 peptides. Score 0.691 Taking the results from Round 4 Chains 72, Residues 504, Estimated correctness of the model 63.9 % 9 chains (98 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11919 restraints for refining 6016 atoms. 9607 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2304 (Rfree = 0.000) for 6016 atoms. Found 38 (38 requested) and removed 49 (27 requested) atoms. Cycle 22: After refmac, R = 0.2078 (Rfree = 0.000) for 5984 atoms. Found 24 (37 requested) and removed 32 (26 requested) atoms. Cycle 23: After refmac, R = 0.2024 (Rfree = 0.000) for 5963 atoms. Found 20 (37 requested) and removed 32 (26 requested) atoms. Cycle 24: After refmac, R = 0.2055 (Rfree = 0.000) for 5944 atoms. Found 24 (37 requested) and removed 31 (26 requested) atoms. Cycle 25: After refmac, R = 0.1958 (Rfree = 0.000) for 5927 atoms. Found 24 (37 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.71 2.82 Search for helices and strands: 0 residues in 0 chains, 6063 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6084 seeds are put forward Round 1: 496 peptides, 65 chains. Longest chain 25 peptides. Score 0.604 Round 2: 513 peptides, 59 chains. Longest chain 32 peptides. Score 0.661 Round 3: 529 peptides, 64 chains. Longest chain 24 peptides. Score 0.653 Round 4: 520 peptides, 60 chains. Longest chain 27 peptides. Score 0.664 Round 5: 533 peptides, 66 chains. Longest chain 27 peptides. Score 0.646 Taking the results from Round 4 Chains 67, Residues 460, Estimated correctness of the model 57.2 % 9 chains (76 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12337 restraints for refining 6018 atoms. 10291 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2222 (Rfree = 0.000) for 6018 atoms. Found 38 (38 requested) and removed 41 (27 requested) atoms. Cycle 27: After refmac, R = 0.2087 (Rfree = 0.000) for 5994 atoms. Found 29 (37 requested) and removed 29 (26 requested) atoms. Cycle 28: After refmac, R = 0.2007 (Rfree = 0.000) for 5982 atoms. Found 24 (37 requested) and removed 30 (26 requested) atoms. Cycle 29: After refmac, R = 0.2020 (Rfree = 0.000) for 5962 atoms. Found 27 (37 requested) and removed 27 (26 requested) atoms. Cycle 30: After refmac, R = 0.1981 (Rfree = 0.000) for 5955 atoms. Found 21 (37 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.68 2.79 Search for helices and strands: 0 residues in 0 chains, 6066 seeds are put forward NCS extension: 16 residues added (7 deleted due to clashes), 6082 seeds are put forward Round 1: 441 peptides, 65 chains. Longest chain 19 peptides. Score 0.521 Round 2: 492 peptides, 56 chains. Longest chain 26 peptides. Score 0.652 Round 3: 490 peptides, 60 chains. Longest chain 25 peptides. Score 0.626 Round 4: 497 peptides, 55 chains. Longest chain 29 peptides. Score 0.664 Round 5: 499 peptides, 59 chains. Longest chain 20 peptides. Score 0.643 Taking the results from Round 4 Chains 58, Residues 442, Estimated correctness of the model 57.2 % 11 chains (113 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11936 restraints for refining 6018 atoms. 9796 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2194 (Rfree = 0.000) for 6018 atoms. Found 38 (38 requested) and removed 38 (27 requested) atoms. Cycle 32: After refmac, R = 0.2070 (Rfree = 0.000) for 5997 atoms. Found 35 (38 requested) and removed 33 (27 requested) atoms. Cycle 33: After refmac, R = 0.2002 (Rfree = 0.000) for 5987 atoms. Found 27 (37 requested) and removed 28 (26 requested) atoms. Cycle 34: After refmac, R = 0.1969 (Rfree = 0.000) for 5972 atoms. Found 29 (37 requested) and removed 31 (26 requested) atoms. Cycle 35: After refmac, R = 0.1941 (Rfree = 0.000) for 5955 atoms. Found 25 (37 requested) and removed 31 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.71 2.82 Search for helices and strands: 0 residues in 0 chains, 6056 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 6069 seeds are put forward Round 1: 439 peptides, 69 chains. Longest chain 16 peptides. Score 0.490 Round 2: 469 peptides, 63 chains. Longest chain 24 peptides. Score 0.578 Round 3: 498 peptides, 60 chains. Longest chain 21 peptides. Score 0.636 Round 4: 507 peptides, 62 chains. Longest chain 25 peptides. Score 0.636 Round 5: 528 peptides, 65 chains. Longest chain 22 peptides. Score 0.646 Taking the results from Round 5 Chains 67, Residues 463, Estimated correctness of the model 52.9 % 8 chains (67 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12207 restraints for refining 6016 atoms. 10169 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2300 (Rfree = 0.000) for 6016 atoms. Found 38 (38 requested) and removed 35 (27 requested) atoms. Cycle 37: After refmac, R = 0.2163 (Rfree = 0.000) for 5991 atoms. Found 33 (38 requested) and removed 29 (27 requested) atoms. Cycle 38: After refmac, R = 0.2124 (Rfree = 0.000) for 5978 atoms. Found 29 (37 requested) and removed 27 (26 requested) atoms. Cycle 39: After refmac, R = 0.2047 (Rfree = 0.000) for 5965 atoms. Found 30 (37 requested) and removed 29 (26 requested) atoms. Cycle 40: After refmac, R = 0.2007 (Rfree = 0.000) for 5952 atoms. Found 25 (37 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.69 2.80 Search for helices and strands: 0 residues in 0 chains, 6072 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 6084 seeds are put forward Round 1: 415 peptides, 64 chains. Longest chain 16 peptides. Score 0.486 Round 2: 464 peptides, 56 chains. Longest chain 29 peptides. Score 0.615 Round 3: 457 peptides, 57 chains. Longest chain 21 peptides. Score 0.599 Round 4: 448 peptides, 56 chains. Longest chain 19 peptides. Score 0.593 Round 5: 463 peptides, 59 chains. Longest chain 19 peptides. Score 0.595 Taking the results from Round 2 Chains 59, Residues 408, Estimated correctness of the model 45.0 % 10 chains (73 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12474 restraints for refining 6006 atoms. 10644 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2116 (Rfree = 0.000) for 6006 atoms. Found 37 (37 requested) and removed 37 (26 requested) atoms. Cycle 42: After refmac, R = 0.2043 (Rfree = 0.000) for 5991 atoms. Found 30 (37 requested) and removed 30 (26 requested) atoms. Cycle 43: After refmac, R = 0.2015 (Rfree = 0.000) for 5984 atoms. Found 35 (37 requested) and removed 27 (26 requested) atoms. Cycle 44: After refmac, R = 0.1950 (Rfree = 0.000) for 5983 atoms. Found 24 (37 requested) and removed 31 (26 requested) atoms. Cycle 45: After refmac, R = 0.1932 (Rfree = 0.000) for 5968 atoms. Found 18 (37 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.72 2.83 Search for helices and strands: 0 residues in 0 chains, 6043 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 6063 seeds are put forward Round 1: 437 peptides, 64 chains. Longest chain 18 peptides. Score 0.522 Round 2: 446 peptides, 54 chains. Longest chain 27 peptides. Score 0.603 Round 3: 482 peptides, 52 chains. Longest chain 23 peptides. Score 0.662 Round 4: 466 peptides, 54 chains. Longest chain 27 peptides. Score 0.630 Round 5: 459 peptides, 54 chains. Longest chain 19 peptides. Score 0.621 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 430, Estimated correctness of the model 56.7 % 12 chains (117 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 25 A and 37 A 56 chains (438 residues) following loop building 11 chains (128 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13478 reflections ( 96.64 % complete ) and 11698 restraints for refining 6018 atoms. 9520 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2238 (Rfree = 0.000) for 6018 atoms. Found 0 (38 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2178 (Rfree = 0.000) for 5958 atoms. Found 0 (37 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2128 (Rfree = 0.000) for 5922 atoms. Found 0 (37 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.2085 (Rfree = 0.000) for 5886 atoms. Found 0 (36 requested) and removed 26 (26 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:46:04 GMT 2018 Job finished. TimeTaking 68.66 Used memory is bytes: 12200688