null Sun 23 Dec 22:23:01 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkn-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-parrot-hancs ############### 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 22:23:11 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/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-parrot-hancs/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 943 and 0 Target number of residues in the AU: 943 Target solvent content: 0.6523 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1404 Adjusted target solvent content: 0.48 Input MTZ file: 1vkn-3.8-parrot-hancs.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: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 11232 target number of atoms Had to go as low as 0.75 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: 93.562 3.800 Wilson plot Bfac: 79.66 14292 reflections ( 98.94 % complete ) and 0 restraints for refining 12356 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3151 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2975 (Rfree = 0.000) for 12356 atoms. Found 67 (67 requested) and removed 77 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 12595 seeds are put forward NCS extension: 0 residues added, 12595 seeds are put forward Round 1: 529 peptides, 101 chains. Longest chain 11 peptides. Score 0.327 Round 2: 693 peptides, 107 chains. Longest chain 20 peptides. Score 0.477 Round 3: 730 peptides, 107 chains. Longest chain 19 peptides. Score 0.513 Round 4: 771 peptides, 95 chains. Longest chain 45 peptides. Score 0.596 Round 5: 787 peptides, 98 chains. Longest chain 26 peptides. Score 0.598 Taking the results from Round 5 Chains 101, Residues 689, Estimated correctness of the model 0.0 % 8 chains (82 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 22266 restraints for refining 10158 atoms. 19292 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2341 (Rfree = 0.000) for 10158 atoms. Found 48 (55 requested) and removed 77 (27 requested) atoms. Cycle 2: After refmac, R = 0.2107 (Rfree = 0.000) for 9935 atoms. Found 51 (55 requested) and removed 66 (27 requested) atoms. Cycle 3: After refmac, R = 0.1971 (Rfree = 0.000) for 9838 atoms. Found 54 (54 requested) and removed 58 (27 requested) atoms. Cycle 4: After refmac, R = 0.1910 (Rfree = 0.000) for 9778 atoms. Found 54 (54 requested) and removed 47 (27 requested) atoms. Cycle 5: After refmac, R = 0.1801 (Rfree = 0.000) for 9755 atoms. Found 35 (53 requested) and removed 42 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 10074 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 10093 seeds are put forward Round 1: 641 peptides, 108 chains. Longest chain 17 peptides. Score 0.419 Round 2: 732 peptides, 106 chains. Longest chain 17 peptides. Score 0.519 Round 3: 754 peptides, 101 chains. Longest chain 22 peptides. Score 0.559 Round 4: 767 peptides, 106 chains. Longest chain 23 peptides. Score 0.551 Round 5: 752 peptides, 97 chains. Longest chain 24 peptides. Score 0.573 Taking the results from Round 5 Chains 98, Residues 655, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23535 restraints for refining 10158 atoms. 20932 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2128 (Rfree = 0.000) for 10158 atoms. Found 54 (55 requested) and removed 97 (27 requested) atoms. Cycle 7: After refmac, R = 0.1909 (Rfree = 0.000) for 10031 atoms. Found 47 (55 requested) and removed 56 (27 requested) atoms. Cycle 8: After refmac, R = 0.1838 (Rfree = 0.000) for 9967 atoms. Found 38 (55 requested) and removed 55 (27 requested) atoms. Cycle 9: After refmac, R = 0.1742 (Rfree = 0.000) for 9931 atoms. Found 26 (54 requested) and removed 57 (27 requested) atoms. Cycle 10: After refmac, R = 0.1749 (Rfree = 0.000) for 9885 atoms. Found 35 (54 requested) and removed 43 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 10217 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 10232 seeds are put forward Round 1: 662 peptides, 119 chains. Longest chain 14 peptides. Score 0.391 Round 2: 725 peptides, 102 chains. Longest chain 19 peptides. Score 0.529 Round 3: 740 peptides, 103 chains. Longest chain 20 peptides. Score 0.538 Round 4: 758 peptides, 102 chains. Longest chain 27 peptides. Score 0.558 Round 5: 744 peptides, 102 chains. Longest chain 20 peptides. Score 0.546 Taking the results from Round 4 Chains 103, Residues 656, Estimated correctness of the model 0.0 % 7 chains (69 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 22553 restraints for refining 10158 atoms. 19783 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2055 (Rfree = 0.000) for 10158 atoms. Found 50 (55 requested) and removed 59 (27 requested) atoms. Cycle 12: After refmac, R = 0.1887 (Rfree = 0.000) for 10075 atoms. Found 47 (55 requested) and removed 57 (27 requested) atoms. Cycle 13: After refmac, R = 0.1815 (Rfree = 0.000) for 10016 atoms. Found 38 (55 requested) and removed 37 (27 requested) atoms. Cycle 14: After refmac, R = 0.1766 (Rfree = 0.000) for 9990 atoms. Found 55 (55 requested) and removed 41 (27 requested) atoms. Cycle 15: After refmac, R = 0.1785 (Rfree = 0.000) for 9990 atoms. Found 55 (55 requested) and removed 38 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 10328 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 10342 seeds are put forward Round 1: 603 peptides, 115 chains. Longest chain 19 peptides. Score 0.344 Round 2: 668 peptides, 106 chains. Longest chain 19 peptides. Score 0.456 Round 3: 692 peptides, 104 chains. Longest chain 16 peptides. Score 0.489 Round 4: 692 peptides, 103 chains. Longest chain 16 peptides. Score 0.493 Round 5: 681 peptides, 91 chains. Longest chain 18 peptides. Score 0.533 Taking the results from Round 5 Chains 92, Residues 590, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23950 restraints for refining 10159 atoms. 21615 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2018 (Rfree = 0.000) for 10159 atoms. Found 55 (55 requested) and removed 60 (27 requested) atoms. Cycle 17: After refmac, R = 0.2007 (Rfree = 0.000) for 10082 atoms. Found 55 (55 requested) and removed 41 (27 requested) atoms. Cycle 18: After refmac, R = 0.1925 (Rfree = 0.000) for 10064 atoms. Found 55 (55 requested) and removed 47 (27 requested) atoms. Cycle 19: After refmac, R = 0.1449 (Rfree = 0.000) for 10043 atoms. Found 18 (55 requested) and removed 38 (27 requested) atoms. Cycle 20: After refmac, R = 0.1331 (Rfree = 0.000) for 10008 atoms. Found 13 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 10319 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 10335 seeds are put forward Round 1: 578 peptides, 111 chains. Longest chain 17 peptides. Score 0.335 Round 2: 639 peptides, 103 chains. Longest chain 18 peptides. Score 0.440 Round 3: 653 peptides, 102 chains. Longest chain 18 peptides. Score 0.459 Round 4: 671 peptides, 102 chains. Longest chain 18 peptides. Score 0.477 Round 5: 668 peptides, 100 chains. Longest chain 18 peptides. Score 0.483 Taking the results from Round 5 Chains 100, Residues 568, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23763 restraints for refining 10160 atoms. 21512 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1830 (Rfree = 0.000) for 10160 atoms. Found 40 (55 requested) and removed 43 (27 requested) atoms. Cycle 22: After refmac, R = 0.1832 (Rfree = 0.000) for 10097 atoms. Found 38 (55 requested) and removed 46 (27 requested) atoms. Cycle 23: After refmac, R = 0.1775 (Rfree = 0.000) for 10055 atoms. Found 35 (55 requested) and removed 36 (27 requested) atoms. Cycle 24: After refmac, R = 0.1680 (Rfree = 0.000) for 10031 atoms. Found 41 (55 requested) and removed 36 (27 requested) atoms. Cycle 25: After refmac, R = 0.1687 (Rfree = 0.000) for 10019 atoms. Found 33 (55 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 10320 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 10341 seeds are put forward Round 1: 494 peptides, 93 chains. Longest chain 15 peptides. Score 0.326 Round 2: 608 peptides, 99 chains. Longest chain 23 peptides. Score 0.425 Round 3: 597 peptides, 99 chains. Longest chain 21 peptides. Score 0.414 Round 4: 604 peptides, 101 chains. Longest chain 14 peptides. Score 0.412 Round 5: 584 peptides, 89 chains. Longest chain 26 peptides. Score 0.447 Taking the results from Round 5 Chains 89, Residues 495, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 24189 restraints for refining 10160 atoms. 22271 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1946 (Rfree = 0.000) for 10160 atoms. Found 55 (55 requested) and removed 44 (27 requested) atoms. Cycle 27: After refmac, R = 0.1890 (Rfree = 0.000) for 10110 atoms. Found 55 (55 requested) and removed 42 (27 requested) atoms. Cycle 28: After refmac, R = 0.1491 (Rfree = 0.000) for 10099 atoms. Found 27 (55 requested) and removed 31 (27 requested) atoms. Cycle 29: After refmac, R = 0.1651 (Rfree = 0.000) for 10083 atoms. Found 47 (55 requested) and removed 35 (27 requested) atoms. Cycle 30: After refmac, R = 0.1825 (Rfree = 0.000) for 10081 atoms. Found 55 (55 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 10391 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 10418 seeds are put forward Round 1: 479 peptides, 101 chains. Longest chain 11 peptides. Score 0.266 Round 2: 562 peptides, 103 chains. Longest chain 21 peptides. Score 0.355 Round 3: 580 peptides, 102 chains. Longest chain 15 peptides. Score 0.381 Round 4: 568 peptides, 92 chains. Longest chain 13 peptides. Score 0.415 Round 5: 547 peptides, 85 chains. Longest chain 20 peptides. Score 0.426 Taking the results from Round 5 Chains 88, Residues 462, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 24280 restraints for refining 10158 atoms. 22442 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1980 (Rfree = 0.000) for 10158 atoms. Found 55 (55 requested) and removed 48 (27 requested) atoms. Cycle 32: After refmac, R = 0.1956 (Rfree = 0.000) for 10111 atoms. Found 55 (55 requested) and removed 41 (27 requested) atoms. Cycle 33: After refmac, R = 0.1811 (Rfree = 0.000) for 10086 atoms. Found 55 (55 requested) and removed 33 (27 requested) atoms. Cycle 34: After refmac, R = 0.1448 (Rfree = 0.000) for 10080 atoms. Found 22 (55 requested) and removed 33 (27 requested) atoms. Cycle 35: After refmac, R = 0.1384 (Rfree = 0.000) for 10051 atoms. Found 12 (55 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 10311 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 10324 seeds are put forward Round 1: 462 peptides, 97 chains. Longest chain 11 peptides. Score 0.265 Round 2: 540 peptides, 101 chains. Longest chain 12 peptides. Score 0.340 Round 3: 524 peptides, 91 chains. Longest chain 14 peptides. Score 0.371 Round 4: 556 peptides, 93 chains. Longest chain 20 peptides. Score 0.397 Round 5: 534 peptides, 88 chains. Longest chain 20 peptides. Score 0.397 Taking the results from Round 5 Chains 88, Residues 446, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 24491 restraints for refining 10159 atoms. 22771 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1956 (Rfree = 0.000) for 10159 atoms. Found 55 (55 requested) and removed 62 (27 requested) atoms. Cycle 37: After refmac, R = 0.1815 (Rfree = 0.000) for 10120 atoms. Found 55 (55 requested) and removed 49 (27 requested) atoms. Cycle 38: After refmac, R = 0.1855 (Rfree = 0.000) for 10112 atoms. Found 55 (55 requested) and removed 38 (27 requested) atoms. Cycle 39: After refmac, R = 0.1788 (Rfree = 0.000) for 10111 atoms. Found 55 (55 requested) and removed 41 (27 requested) atoms. Cycle 40: After refmac, R = 0.1404 (Rfree = 0.000) for 10103 atoms. Found 18 (55 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 10321 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 10348 seeds are put forward Round 1: 393 peptides, 84 chains. Longest chain 11 peptides. Score 0.246 Round 2: 479 peptides, 90 chains. Longest chain 12 peptides. Score 0.323 Round 3: 492 peptides, 89 chains. Longest chain 16 peptides. Score 0.344 Round 4: 483 peptides, 82 chains. Longest chain 14 peptides. Score 0.369 Round 5: 479 peptides, 81 chains. Longest chain 14 peptides. Score 0.369 Taking the results from Round 5 Chains 83, Residues 398, Estimated correctness of the model 0.0 % 6 chains (33 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 24486 restraints for refining 10159 atoms. 22879 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1944 (Rfree = 0.000) for 10159 atoms. Found 55 (55 requested) and removed 50 (27 requested) atoms. Cycle 42: After refmac, R = 0.1875 (Rfree = 0.000) for 10123 atoms. Found 55 (55 requested) and removed 44 (27 requested) atoms. Cycle 43: After refmac, R = 0.1812 (Rfree = 0.000) for 10110 atoms. Found 55 (55 requested) and removed 36 (27 requested) atoms. Cycle 44: After refmac, R = 0.1341 (Rfree = 0.000) for 10102 atoms. Found 19 (55 requested) and removed 32 (27 requested) atoms. Cycle 45: After refmac, R = 0.1247 (Rfree = 0.000) for 10075 atoms. Found 11 (55 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 10345 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 10362 seeds are put forward Round 1: 412 peptides, 89 chains. Longest chain 9 peptides. Score 0.244 Round 2: 451 peptides, 82 chains. Longest chain 18 peptides. Score 0.331 Round 3: 457 peptides, 84 chains. Longest chain 19 peptides. Score 0.328 Round 4: 480 peptides, 80 chains. Longest chain 19 peptides. Score 0.376 Round 5: 473 peptides, 79 chains. Longest chain 19 peptides. Score 0.373 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 400, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input Building loops using Loopy2018 80 chains (400 residues) following loop building 2 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14292 reflections ( 98.94 % complete ) and 24412 restraints for refining 10136 atoms. 22812 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1776 (Rfree = 0.000) for 10136 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.1844 (Rfree = 0.000) for 10072 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1715 (Rfree = 0.000) for 10021 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1280 (Rfree = 0.000) for 9983 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:22:06 GMT 2018 Job finished. TimeTaking 119.08 Used memory is bytes: 13599808