null Mon 24 Dec 07:56:26 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 1vkm-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.8-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/1vkm-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.8-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 07:56:30 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/1vkm-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.8-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 1136 and 0 Target number of residues in the AU: 1136 Target solvent content: 0.6344 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-3.8-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: 19 Cell parameters: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.60 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: 75.160 3.800 Wilson plot Bfac: 68.83 17186 reflections ( 99.97 % complete ) and 0 restraints for refining 15719 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3249 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3195 (Rfree = 0.000) for 15719 atoms. Found 86 (86 requested) and removed 146 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 16006 seeds are put forward NCS extension: 0 residues added, 16006 seeds are put forward Round 1: 517 peptides, 112 chains. Longest chain 9 peptides. Score 0.248 Round 2: 697 peptides, 132 chains. Longest chain 12 peptides. Score 0.349 Round 3: 795 peptides, 139 chains. Longest chain 16 peptides. Score 0.414 Round 4: 840 peptides, 146 chains. Longest chain 13 peptides. Score 0.428 Round 5: 847 peptides, 134 chains. Longest chain 18 peptides. Score 0.480 Taking the results from Round 5 Chains 134, Residues 713, Estimated correctness of the model 0.0 % 6 chains (24 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30918 restraints for refining 12886 atoms. 28150 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2911 (Rfree = 0.000) for 12886 atoms. Found 70 (70 requested) and removed 128 (35 requested) atoms. Cycle 2: After refmac, R = 0.2721 (Rfree = 0.000) for 12606 atoms. Found 70 (70 requested) and removed 103 (35 requested) atoms. Cycle 3: After refmac, R = 0.2624 (Rfree = 0.000) for 12409 atoms. Found 65 (69 requested) and removed 107 (34 requested) atoms. Cycle 4: After refmac, R = 0.2461 (Rfree = 0.000) for 12248 atoms. Found 57 (68 requested) and removed 87 (34 requested) atoms. Cycle 5: After refmac, R = 0.2317 (Rfree = 0.000) for 12153 atoms. Found 57 (67 requested) and removed 84 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.77 Search for helices and strands: 0 residues in 0 chains, 12589 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 12609 seeds are put forward Round 1: 631 peptides, 130 chains. Longest chain 12 peptides. Score 0.290 Round 2: 746 peptides, 132 chains. Longest chain 16 peptides. Score 0.397 Round 3: 764 peptides, 131 chains. Longest chain 13 peptides. Score 0.417 Round 4: 783 peptides, 132 chains. Longest chain 18 peptides. Score 0.431 Round 5: 789 peptides, 127 chains. Longest chain 19 peptides. Score 0.456 Taking the results from Round 5 Chains 129, Residues 662, Estimated correctness of the model 0.0 % 7 chains (48 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 27922 restraints for refining 12115 atoms. 25242 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2288 (Rfree = 0.000) for 12115 atoms. Found 47 (66 requested) and removed 121 (33 requested) atoms. Cycle 7: After refmac, R = 0.2121 (Rfree = 0.000) for 11956 atoms. Found 37 (66 requested) and removed 94 (33 requested) atoms. Cycle 8: After refmac, R = 0.1995 (Rfree = 0.000) for 11854 atoms. Found 28 (65 requested) and removed 78 (32 requested) atoms. Cycle 9: After refmac, R = 0.1906 (Rfree = 0.000) for 11770 atoms. Found 29 (64 requested) and removed 57 (32 requested) atoms. Cycle 10: After refmac, R = 0.1836 (Rfree = 0.000) for 11722 atoms. Found 26 (64 requested) and removed 51 (32 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.73 Search for helices and strands: 0 residues in 0 chains, 12142 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 12158 seeds are put forward Round 1: 699 peptides, 140 chains. Longest chain 9 peptides. Score 0.317 Round 2: 805 peptides, 130 chains. Longest chain 18 peptides. Score 0.458 Round 3: 804 peptides, 125 chains. Longest chain 17 peptides. Score 0.477 Round 4: 800 peptides, 122 chains. Longest chain 19 peptides. Score 0.484 Round 5: 813 peptides, 125 chains. Longest chain 21 peptides. Score 0.484 Taking the results from Round 5 Chains 125, Residues 688, Estimated correctness of the model 0.0 % 8 chains (31 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 29317 restraints for refining 12627 atoms. 26629 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2168 (Rfree = 0.000) for 12627 atoms. Found 50 (69 requested) and removed 133 (34 requested) atoms. Cycle 12: After refmac, R = 0.1950 (Rfree = 0.000) for 12444 atoms. Found 48 (68 requested) and removed 90 (34 requested) atoms. Cycle 13: After refmac, R = 0.2119 (Rfree = 0.000) for 12360 atoms. Found 68 (68 requested) and removed 90 (34 requested) atoms. Cycle 14: After refmac, R = 0.1946 (Rfree = 0.000) for 12311 atoms. Found 67 (67 requested) and removed 66 (33 requested) atoms. Cycle 15: After refmac, R = 0.1509 (Rfree = 0.000) for 12278 atoms. Found 14 (67 requested) and removed 42 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 12705 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 12736 seeds are put forward Round 1: 613 peptides, 127 chains. Longest chain 10 peptides. Score 0.284 Round 2: 695 peptides, 123 chains. Longest chain 21 peptides. Score 0.385 Round 3: 719 peptides, 123 chains. Longest chain 14 peptides. Score 0.408 Round 4: 753 peptides, 120 chains. Longest chain 19 peptides. Score 0.451 Round 5: 745 peptides, 114 chains. Longest chain 17 peptides. Score 0.467 Taking the results from Round 5 Chains 115, Residues 631, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 29632 restraints for refining 12696 atoms. 27147 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2160 (Rfree = 0.000) for 12696 atoms. Found 64 (69 requested) and removed 129 (34 requested) atoms. Cycle 17: After refmac, R = 0.1978 (Rfree = 0.000) for 12546 atoms. Found 68 (69 requested) and removed 94 (34 requested) atoms. Cycle 18: After refmac, R = 0.1578 (Rfree = 0.000) for 12485 atoms. Found 12 (68 requested) and removed 55 (34 requested) atoms. Cycle 19: After refmac, R = 0.1508 (Rfree = 0.000) for 12410 atoms. Found 7 (68 requested) and removed 50 (34 requested) atoms. Cycle 20: After refmac, R = 0.1451 (Rfree = 0.000) for 12359 atoms. Found 10 (68 requested) and removed 43 (34 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 12726 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 12744 seeds are put forward Round 1: 661 peptides, 134 chains. Longest chain 13 peptides. Score 0.304 Round 2: 721 peptides, 123 chains. Longest chain 14 peptides. Score 0.409 Round 3: 711 peptides, 124 chains. Longest chain 15 peptides. Score 0.396 Round 4: 714 peptides, 115 chains. Longest chain 14 peptides. Score 0.435 Round 5: 714 peptides, 114 chains. Longest chain 19 peptides. Score 0.439 Taking the results from Round 5 Chains 115, Residues 600, Estimated correctness of the model 0.0 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30107 restraints for refining 12894 atoms. 27666 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2202 (Rfree = 0.000) for 12894 atoms. Found 69 (70 requested) and removed 130 (35 requested) atoms. Cycle 22: After refmac, R = 0.1941 (Rfree = 0.000) for 12765 atoms. Found 50 (70 requested) and removed 96 (35 requested) atoms. Cycle 23: After refmac, R = 0.1643 (Rfree = 0.000) for 12682 atoms. Found 17 (69 requested) and removed 57 (34 requested) atoms. Cycle 24: After refmac, R = 0.1607 (Rfree = 0.000) for 12615 atoms. Found 9 (69 requested) and removed 51 (34 requested) atoms. Cycle 25: After refmac, R = 0.1612 (Rfree = 0.000) for 12566 atoms. Found 6 (69 requested) and removed 42 (34 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 12876 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 12895 seeds are put forward Round 1: 589 peptides, 123 chains. Longest chain 11 peptides. Score 0.276 Round 2: 682 peptides, 128 chains. Longest chain 13 peptides. Score 0.351 Round 3: 683 peptides, 120 chains. Longest chain 12 peptides. Score 0.385 Round 4: 659 peptides, 117 chains. Longest chain 12 peptides. Score 0.375 Round 5: 678 peptides, 120 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 3 Chains 120, Residues 563, Estimated correctness of the model 0.0 % 5 chains (20 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30466 restraints for refining 12895 atoms. 28299 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2036 (Rfree = 0.000) for 12895 atoms. Found 70 (70 requested) and removed 111 (35 requested) atoms. Cycle 27: After refmac, R = 0.2078 (Rfree = 0.000) for 12785 atoms. Found 70 (70 requested) and removed 104 (35 requested) atoms. Cycle 28: After refmac, R = 0.1963 (Rfree = 0.000) for 12709 atoms. Found 70 (70 requested) and removed 77 (35 requested) atoms. Cycle 29: After refmac, R = 0.1545 (Rfree = 0.000) for 12667 atoms. Found 24 (69 requested) and removed 50 (34 requested) atoms. Cycle 30: After refmac, R = 0.1443 (Rfree = 0.000) for 12612 atoms. Found 14 (69 requested) and removed 46 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 12906 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 12924 seeds are put forward Round 1: 561 peptides, 128 chains. Longest chain 8 peptides. Score 0.223 Round 2: 648 peptides, 122 chains. Longest chain 13 peptides. Score 0.342 Round 3: 640 peptides, 120 chains. Longest chain 12 peptides. Score 0.343 Round 4: 642 peptides, 123 chains. Longest chain 10 peptides. Score 0.332 Round 5: 632 peptides, 117 chains. Longest chain 14 peptides. Score 0.348 Taking the results from Round 5 Chains 117, Residues 515, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30710 restraints for refining 12893 atoms. 28740 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2195 (Rfree = 0.000) for 12893 atoms. Found 70 (70 requested) and removed 121 (35 requested) atoms. Cycle 32: After refmac, R = 0.2051 (Rfree = 0.000) for 12784 atoms. Found 70 (70 requested) and removed 81 (35 requested) atoms. Cycle 33: After refmac, R = 0.2058 (Rfree = 0.000) for 12727 atoms. Found 70 (70 requested) and removed 71 (35 requested) atoms. Cycle 34: After refmac, R = 0.1999 (Rfree = 0.000) for 12690 atoms. Found 69 (69 requested) and removed 61 (34 requested) atoms. Cycle 35: After refmac, R = 0.1911 (Rfree = 0.000) for 12659 atoms. Found 69 (69 requested) and removed 61 (34 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.80 Search for helices and strands: 0 residues in 0 chains, 13016 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 13030 seeds are put forward Round 1: 449 peptides, 100 chains. Longest chain 10 peptides. Score 0.227 Round 2: 581 peptides, 121 chains. Longest chain 11 peptides. Score 0.277 Round 3: 564 peptides, 110 chains. Longest chain 12 peptides. Score 0.308 Round 4: 590 peptides, 113 chains. Longest chain 11 peptides. Score 0.322 Round 5: 598 peptides, 108 chains. Longest chain 13 peptides. Score 0.352 Taking the results from Round 5 Chains 108, Residues 490, Estimated correctness of the model 0.0 % 5 chains (21 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30030 restraints for refining 12673 atoms. 28131 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2122 (Rfree = 0.000) for 12673 atoms. Found 69 (69 requested) and removed 95 (34 requested) atoms. Cycle 37: After refmac, R = 0.1997 (Rfree = 0.000) for 12593 atoms. Found 69 (69 requested) and removed 78 (34 requested) atoms. Cycle 38: After refmac, R = 0.2046 (Rfree = 0.000) for 12552 atoms. Found 69 (69 requested) and removed 64 (34 requested) atoms. Cycle 39: After refmac, R = 0.1938 (Rfree = 0.000) for 12535 atoms. Found 69 (69 requested) and removed 59 (34 requested) atoms. Cycle 40: After refmac, R = 0.1539 (Rfree = 0.000) for 12520 atoms. Found 21 (68 requested) and removed 40 (34 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.81 Search for helices and strands: 0 residues in 0 chains, 12825 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 12844 seeds are put forward Round 1: 432 peptides, 99 chains. Longest chain 7 peptides. Score 0.211 Round 2: 503 peptides, 102 chains. Longest chain 11 peptides. Score 0.279 Round 3: 532 peptides, 104 chains. Longest chain 14 peptides. Score 0.301 Round 4: 548 peptides, 107 chains. Longest chain 12 peptides. Score 0.305 Round 5: 556 peptides, 104 chains. Longest chain 13 peptides. Score 0.327 Taking the results from Round 5 Chains 104, Residues 452, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 29601 restraints for refining 12492 atoms. 27866 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2011 (Rfree = 0.000) for 12492 atoms. Found 68 (68 requested) and removed 96 (34 requested) atoms. Cycle 42: After refmac, R = 0.1966 (Rfree = 0.000) for 12427 atoms. Found 68 (68 requested) and removed 73 (34 requested) atoms. Cycle 43: After refmac, R = 0.1947 (Rfree = 0.000) for 12391 atoms. Found 68 (68 requested) and removed 64 (34 requested) atoms. Cycle 44: After refmac, R = 0.1843 (Rfree = 0.000) for 12373 atoms. Found 68 (68 requested) and removed 57 (34 requested) atoms. Cycle 45: After refmac, R = 0.1472 (Rfree = 0.000) for 12361 atoms. Found 17 (68 requested) and removed 40 (34 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.80 Search for helices and strands: 0 residues in 0 chains, 12631 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 12648 seeds are put forward Round 1: 437 peptides, 97 chains. Longest chain 10 peptides. Score 0.227 Round 2: 469 peptides, 89 chains. Longest chain 11 peptides. Score 0.302 Round 3: 487 peptides, 93 chains. Longest chain 11 peptides. Score 0.303 Round 4: 487 peptides, 90 chains. Longest chain 13 peptides. Score 0.317 Round 5: 503 peptides, 90 chains. Longest chain 17 peptides. Score 0.335 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 90, Residues 413, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 90 chains (413 residues) following loop building 3 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17186 reflections ( 99.97 % complete ) and 29115 restraints for refining 12341 atoms. 27534 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1935 (Rfree = 0.000) for 12341 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Cycle 47: After refmac, R = 0.1867 (Rfree = 0.000) for 12267 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Cycle 48: After refmac, R = 0.1862 (Rfree = 0.000) for 12219 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Cycle 49: After refmac, R = 0.1848 (Rfree = 0.000) for 12170 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:56:37 GMT 2018 Job finished. TimeTaking 120.18 Used memory is bytes: 6956400