null Sun 23 Dec 22:22:41 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-4.0-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 22:22:50 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-4.0-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 918 and 0 Target number of residues in the AU: 918 Target solvent content: 0.6615 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 11232 target number of atoms Had to go as low as 0.80 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 4.000 Wilson plot Bfac: 85.81 12267 reflections ( 98.92 % complete ) and 0 restraints for refining 12470 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3203 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2944 (Rfree = 0.000) for 12470 atoms. Found 59 (59 requested) and removed 84 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 12651 seeds are put forward NCS extension: 0 residues added, 12651 seeds are put forward Round 1: 489 peptides, 96 chains. Longest chain 10 peptides. Score 0.304 Round 2: 624 peptides, 103 chains. Longest chain 16 peptides. Score 0.424 Round 3: 659 peptides, 98 chains. Longest chain 18 peptides. Score 0.482 Round 4: 712 peptides, 105 chains. Longest chain 20 peptides. Score 0.504 Round 5: 733 peptides, 107 chains. Longest chain 19 peptides. Score 0.516 Taking the results from Round 5 Chains 109, Residues 626, Estimated correctness of the model 0.0 % 6 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23457 restraints for refining 10141 atoms. 20966 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2332 (Rfree = 0.000) for 10141 atoms. Found 37 (48 requested) and removed 111 (24 requested) atoms. Cycle 2: After refmac, R = 0.2118 (Rfree = 0.000) for 9879 atoms. Found 47 (47 requested) and removed 38 (23 requested) atoms. Cycle 3: After refmac, R = 0.2030 (Rfree = 0.000) for 9809 atoms. Found 46 (46 requested) and removed 47 (23 requested) atoms. Cycle 4: After refmac, R = 0.1601 (Rfree = 0.000) for 9723 atoms. Found 8 (46 requested) and removed 47 (23 requested) atoms. Cycle 5: After refmac, R = 0.1529 (Rfree = 0.000) for 9650 atoms. Found 15 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 3.88 Search for helices and strands: 0 residues in 0 chains, 9953 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 9984 seeds are put forward Round 1: 590 peptides, 113 chains. Longest chain 14 peptides. Score 0.339 Round 2: 684 peptides, 112 chains. Longest chain 21 peptides. Score 0.446 Round 3: 725 peptides, 113 chains. Longest chain 20 peptides. Score 0.483 Round 4: 701 peptides, 108 chains. Longest chain 17 peptides. Score 0.481 Round 5: 698 peptides, 98 chains. Longest chain 28 peptides. Score 0.520 Taking the results from Round 5 Chains 99, Residues 600, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23091 restraints for refining 9976 atoms. 20694 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2030 (Rfree = 0.000) for 9976 atoms. Found 40 (47 requested) and removed 76 (23 requested) atoms. Cycle 7: After refmac, R = 0.1884 (Rfree = 0.000) for 9834 atoms. Found 47 (47 requested) and removed 52 (23 requested) atoms. Cycle 8: After refmac, R = 0.1834 (Rfree = 0.000) for 9776 atoms. Found 46 (46 requested) and removed 45 (23 requested) atoms. Cycle 9: After refmac, R = 0.1391 (Rfree = 0.000) for 9736 atoms. Found 10 (46 requested) and removed 34 (23 requested) atoms. Cycle 10: After refmac, R = 0.1333 (Rfree = 0.000) for 9688 atoms. Found 16 (46 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 10003 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 10016 seeds are put forward Round 1: 580 peptides, 107 chains. Longest chain 13 peptides. Score 0.356 Round 2: 677 peptides, 106 chains. Longest chain 15 peptides. Score 0.465 Round 3: 687 peptides, 106 chains. Longest chain 13 peptides. Score 0.475 Round 4: 686 peptides, 97 chains. Longest chain 34 peptides. Score 0.513 Round 5: 696 peptides, 103 chains. Longest chain 17 peptides. Score 0.497 Taking the results from Round 4 Chains 100, Residues 589, Estimated correctness of the model 0.0 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23164 restraints for refining 10143 atoms. 20711 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1903 (Rfree = 0.000) for 10143 atoms. Found 48 (48 requested) and removed 81 (24 requested) atoms. Cycle 12: After refmac, R = 0.1834 (Rfree = 0.000) for 10024 atoms. Found 48 (48 requested) and removed 65 (24 requested) atoms. Cycle 13: After refmac, R = 0.1778 (Rfree = 0.000) for 9956 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 14: After refmac, R = 0.1678 (Rfree = 0.000) for 9917 atoms. Found 47 (47 requested) and removed 58 (23 requested) atoms. Cycle 15: After refmac, R = 0.1656 (Rfree = 0.000) for 9873 atoms. Found 47 (47 requested) and removed 45 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 10179 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 10198 seeds are put forward Round 1: 557 peptides, 99 chains. Longest chain 15 peptides. Score 0.369 Round 2: 635 peptides, 96 chains. Longest chain 16 peptides. Score 0.467 Round 3: 650 peptides, 96 chains. Longest chain 20 peptides. Score 0.482 Round 4: 647 peptides, 96 chains. Longest chain 19 peptides. Score 0.479 Round 5: 664 peptides, 99 chains. Longest chain 19 peptides. Score 0.483 Taking the results from Round 5 Chains 99, Residues 565, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23688 restraints for refining 10141 atoms. 21507 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1978 (Rfree = 0.000) for 10141 atoms. Found 48 (48 requested) and removed 60 (24 requested) atoms. Cycle 17: After refmac, R = 0.1829 (Rfree = 0.000) for 10059 atoms. Found 48 (48 requested) and removed 48 (24 requested) atoms. Cycle 18: After refmac, R = 0.1817 (Rfree = 0.000) for 10004 atoms. Found 47 (47 requested) and removed 53 (23 requested) atoms. Cycle 19: After refmac, R = 0.1833 (Rfree = 0.000) for 9960 atoms. Found 47 (47 requested) and removed 60 (23 requested) atoms. Cycle 20: After refmac, R = 0.1380 (Rfree = 0.000) for 9910 atoms. Found 14 (47 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 10174 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 10189 seeds are put forward Round 1: 551 peptides, 106 chains. Longest chain 9 peptides. Score 0.328 Round 2: 639 peptides, 108 chains. Longest chain 14 peptides. Score 0.417 Round 3: 627 peptides, 98 chains. Longest chain 14 peptides. Score 0.450 Round 4: 635 peptides, 101 chains. Longest chain 16 peptides. Score 0.445 Round 5: 643 peptides, 98 chains. Longest chain 17 peptides. Score 0.466 Taking the results from Round 5 Chains 98, Residues 545, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23696 restraints for refining 10143 atoms. 21560 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1933 (Rfree = 0.000) for 10143 atoms. Found 48 (48 requested) and removed 59 (24 requested) atoms. Cycle 22: After refmac, R = 0.1905 (Rfree = 0.000) for 10056 atoms. Found 48 (48 requested) and removed 54 (24 requested) atoms. Cycle 23: After refmac, R = 0.1885 (Rfree = 0.000) for 9994 atoms. Found 47 (47 requested) and removed 47 (23 requested) atoms. Cycle 24: After refmac, R = 0.1672 (Rfree = 0.000) for 9943 atoms. Found 47 (47 requested) and removed 38 (23 requested) atoms. Cycle 25: After refmac, R = 0.1814 (Rfree = 0.000) for 9921 atoms. Found 47 (47 requested) and removed 41 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 10278 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 10299 seeds are put forward Round 1: 467 peptides, 94 chains. Longest chain 12 peptides. Score 0.287 Round 2: 567 peptides, 97 chains. Longest chain 16 peptides. Score 0.390 Round 3: 589 peptides, 95 chains. Longest chain 14 peptides. Score 0.424 Round 4: 594 peptides, 88 chains. Longest chain 15 peptides. Score 0.462 Round 5: 570 peptides, 87 chains. Longest chain 17 peptides. Score 0.441 Taking the results from Round 4 Chains 88, Residues 506, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23428 restraints for refining 10037 atoms. 21492 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1809 (Rfree = 0.000) for 10037 atoms. Found 47 (47 requested) and removed 65 (23 requested) atoms. Cycle 27: After refmac, R = 0.1770 (Rfree = 0.000) for 9967 atoms. Found 47 (47 requested) and removed 46 (23 requested) atoms. Cycle 28: After refmac, R = 0.1750 (Rfree = 0.000) for 9931 atoms. Found 47 (47 requested) and removed 48 (23 requested) atoms. Cycle 29: After refmac, R = 0.1646 (Rfree = 0.000) for 9901 atoms. Found 47 (47 requested) and removed 47 (23 requested) atoms. Cycle 30: After refmac, R = 0.1111 (Rfree = 0.000) for 9876 atoms. Found 17 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 10121 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 10144 seeds are put forward Round 1: 440 peptides, 93 chains. Longest chain 9 peptides. Score 0.259 Round 2: 496 peptides, 88 chains. Longest chain 11 peptides. Score 0.354 Round 3: 528 peptides, 90 chains. Longest chain 13 peptides. Score 0.381 Round 4: 568 peptides, 95 chains. Longest chain 18 peptides. Score 0.401 Round 5: 583 peptides, 95 chains. Longest chain 19 peptides. Score 0.417 Taking the results from Round 5 Chains 95, Residues 488, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 24042 restraints for refining 10141 atoms. 22165 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1798 (Rfree = 0.000) for 10141 atoms. Found 48 (48 requested) and removed 73 (24 requested) atoms. Cycle 32: After refmac, R = 0.1795 (Rfree = 0.000) for 10061 atoms. Found 48 (48 requested) and removed 59 (24 requested) atoms. Cycle 33: After refmac, R = 0.1685 (Rfree = 0.000) for 10010 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 34: After refmac, R = 0.1560 (Rfree = 0.000) for 9992 atoms. Found 47 (47 requested) and removed 42 (23 requested) atoms. Cycle 35: After refmac, R = 0.1165 (Rfree = 0.000) for 9971 atoms. Found 17 (47 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 10215 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 10235 seeds are put forward Round 1: 462 peptides, 97 chains. Longest chain 11 peptides. Score 0.265 Round 2: 540 peptides, 100 chains. Longest chain 14 peptides. Score 0.345 Round 3: 520 peptides, 96 chains. Longest chain 13 peptides. Score 0.341 Round 4: 516 peptides, 94 chains. Longest chain 12 peptides. Score 0.347 Round 5: 527 peptides, 96 chains. Longest chain 13 peptides. Score 0.350 Taking the results from Round 5 Chains 96, Residues 431, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 24449 restraints for refining 10143 atoms. 22807 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1930 (Rfree = 0.000) for 10143 atoms. Found 48 (48 requested) and removed 61 (24 requested) atoms. Cycle 37: After refmac, R = 0.1771 (Rfree = 0.000) for 10073 atoms. Found 48 (48 requested) and removed 56 (24 requested) atoms. Cycle 38: After refmac, R = 0.1262 (Rfree = 0.000) for 10035 atoms. Found 22 (47 requested) and removed 35 (23 requested) atoms. Cycle 39: After refmac, R = 0.1169 (Rfree = 0.000) for 9993 atoms. Found 13 (47 requested) and removed 32 (23 requested) atoms. Cycle 40: After refmac, R = 0.1135 (Rfree = 0.000) for 9962 atoms. Found 8 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 10195 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 10210 seeds are put forward Round 1: 361 peptides, 79 chains. Longest chain 8 peptides. Score 0.231 Round 2: 417 peptides, 84 chains. Longest chain 9 peptides. Score 0.278 Round 3: 437 peptides, 81 chains. Longest chain 10 peptides. Score 0.319 Round 4: 429 peptides, 79 chains. Longest chain 11 peptides. Score 0.320 Round 5: 416 peptides, 75 chains. Longest chain 11 peptides. Score 0.325 Taking the results from Round 5 Chains 75, Residues 341, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 25050 restraints for refining 10142 atoms. 23731 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1802 (Rfree = 0.000) for 10142 atoms. Found 48 (48 requested) and removed 55 (24 requested) atoms. Cycle 42: After refmac, R = 0.1793 (Rfree = 0.000) for 10096 atoms. Found 48 (48 requested) and removed 48 (24 requested) atoms. Cycle 43: After refmac, R = 0.1211 (Rfree = 0.000) for 10059 atoms. Found 22 (47 requested) and removed 36 (23 requested) atoms. Cycle 44: After refmac, R = 0.1104 (Rfree = 0.000) for 10029 atoms. Found 18 (47 requested) and removed 29 (23 requested) atoms. Cycle 45: After refmac, R = 0.1078 (Rfree = 0.000) for 10012 atoms. Found 18 (47 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 10265 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 10277 seeds are put forward Round 1: 329 peptides, 72 chains. Longest chain 9 peptides. Score 0.227 Round 2: 375 peptides, 77 chains. Longest chain 10 peptides. Score 0.262 Round 3: 407 peptides, 75 chains. Longest chain 11 peptides. Score 0.314 Round 4: 423 peptides, 80 chains. Longest chain 11 peptides. Score 0.307 Round 5: 411 peptides, 74 chains. Longest chain 11 peptides. Score 0.325 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 74, Residues 337, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vkn-4_warpNtrace.pdb as input Building loops using Loopy2018 74 chains (337 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12267 reflections ( 98.92 % complete ) and 24697 restraints for refining 10122 atoms. 23399 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1699 (Rfree = 0.000) for 10122 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.1802 (Rfree = 0.000) for 10065 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.1726 (Rfree = 0.000) for 10015 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1703 (Rfree = 0.000) for 9962 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:22:19 GMT 2018 Job finished. TimeTaking 119.64 Used memory is bytes: 26596472