Mon 24 Dec 00:33:36 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkz-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-parrot-mrncs ############### 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 00:33:41 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-parrot-mrncs/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 683 and 0 Target number of residues in the AU: 683 Target solvent content: 0.5635 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-3.4-parrot-mrncs.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-3.4-parrot-mrncs.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 3.400 Wilson plot Bfac: 39.52 11256 reflections ( 96.76 % complete ) and 0 restraints for refining 7339 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.2863 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2759 (Rfree = 0.000) for 7339 atoms. Found 55 (55 requested) and removed 90 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.91 3.03 Search for helices and strands: 0 residues in 0 chains, 7419 seeds are put forward NCS extension: 0 residues added, 7419 seeds are put forward Round 1: 327 peptides, 63 chains. Longest chain 11 peptides. Score 0.330 Round 2: 441 peptides, 74 chains. Longest chain 12 peptides. Score 0.456 Round 3: 491 peptides, 74 chains. Longest chain 15 peptides. Score 0.538 Round 4: 477 peptides, 64 chains. Longest chain 17 peptides. Score 0.583 Round 5: 499 peptides, 67 chains. Longest chain 22 peptides. Score 0.595 Taking the results from Round 5 Chains 69, Residues 432, Estimated correctness of the model 27.0 % 9 chains (76 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12436 restraints for refining 5990 atoms. 10538 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2502 (Rfree = 0.000) for 5990 atoms. Found 40 (45 requested) and removed 46 (22 requested) atoms. Cycle 2: After refmac, R = 0.2330 (Rfree = 0.000) for 5870 atoms. Found 45 (45 requested) and removed 40 (22 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2161 (Rfree = 0.000) for 5826 atoms. Found 24 (44 requested) and removed 35 (22 requested) atoms. Cycle 4: After refmac, R = 0.2118 (Rfree = 0.000) for 5795 atoms. Found 19 (43 requested) and removed 30 (21 requested) atoms. Cycle 5: After refmac, R = 0.2065 (Rfree = 0.000) for 5772 atoms. Found 22 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.90 3.02 Search for helices and strands: 0 residues in 0 chains, 5949 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 5965 seeds are put forward Round 1: 462 peptides, 77 chains. Longest chain 23 peptides. Score 0.470 Round 2: 514 peptides, 72 chains. Longest chain 24 peptides. Score 0.585 Round 3: 523 peptides, 73 chains. Longest chain 24 peptides. Score 0.592 Round 4: 529 peptides, 71 chains. Longest chain 19 peptides. Score 0.612 Round 5: 513 peptides, 67 chains. Longest chain 17 peptides. Score 0.615 Taking the results from Round 5 Chains 71, Residues 446, Estimated correctness of the model 33.5 % 10 chains (75 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12795 restraints for refining 5992 atoms. 10838 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2544 (Rfree = 0.000) for 5992 atoms. Found 45 (45 requested) and removed 59 (22 requested) atoms. Cycle 7: After refmac, R = 0.2369 (Rfree = 0.000) for 5903 atoms. Found 42 (45 requested) and removed 45 (22 requested) atoms. Cycle 8: After refmac, R = 0.2317 (Rfree = 0.000) for 5857 atoms. Found 44 (44 requested) and removed 41 (22 requested) atoms. Cycle 9: After refmac, R = 0.2238 (Rfree = 0.000) for 5824 atoms. Found 38 (44 requested) and removed 36 (22 requested) atoms. Cycle 10: After refmac, R = 0.1945 (Rfree = 0.000) for 5796 atoms. Found 26 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.87 2.99 Search for helices and strands: 0 residues in 0 chains, 5939 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 5953 seeds are put forward Round 1: 447 peptides, 74 chains. Longest chain 15 peptides. Score 0.467 Round 2: 491 peptides, 72 chains. Longest chain 15 peptides. Score 0.552 Round 3: 504 peptides, 70 chains. Longest chain 21 peptides. Score 0.584 Round 4: 487 peptides, 69 chains. Longest chain 25 peptides. Score 0.565 Round 5: 491 peptides, 70 chains. Longest chain 18 peptides. Score 0.565 Taking the results from Round 3 Chains 72, Residues 434, Estimated correctness of the model 23.4 % 6 chains (60 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12617 restraints for refining 5914 atoms. 10779 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2466 (Rfree = 0.000) for 5914 atoms. Found 44 (44 requested) and removed 53 (22 requested) atoms. Cycle 12: After refmac, R = 0.2336 (Rfree = 0.000) for 5863 atoms. Found 44 (44 requested) and removed 44 (22 requested) atoms. Cycle 13: After refmac, R = 0.1935 (Rfree = 0.000) for 5843 atoms. Found 23 (44 requested) and removed 27 (22 requested) atoms. Cycle 14: After refmac, R = 0.1866 (Rfree = 0.000) for 5824 atoms. Found 13 (44 requested) and removed 34 (22 requested) atoms. Cycle 15: After refmac, R = 0.1807 (Rfree = 0.000) for 5791 atoms. Found 15 (43 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.88 3.00 Search for helices and strands: 0 residues in 0 chains, 5924 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 5936 seeds are put forward Round 1: 451 peptides, 79 chains. Longest chain 16 peptides. Score 0.436 Round 2: 473 peptides, 70 chains. Longest chain 19 peptides. Score 0.537 Round 3: 480 peptides, 74 chains. Longest chain 16 peptides. Score 0.521 Round 4: 494 peptides, 71 chains. Longest chain 19 peptides. Score 0.563 Round 5: 496 peptides, 72 chains. Longest chain 27 peptides. Score 0.559 Taking the results from Round 4 Chains 76, Residues 423, Estimated correctness of the model 16.1 % 8 chains (65 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12880 restraints for refining 5994 atoms. 11051 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2189 (Rfree = 0.000) for 5994 atoms. Found 44 (45 requested) and removed 50 (22 requested) atoms. Cycle 17: After refmac, R = 0.2065 (Rfree = 0.000) for 5954 atoms. Found 22 (45 requested) and removed 37 (22 requested) atoms. Cycle 18: After refmac, R = 0.1957 (Rfree = 0.000) for 5908 atoms. Found 27 (44 requested) and removed 29 (22 requested) atoms. Cycle 19: After refmac, R = 0.1907 (Rfree = 0.000) for 5891 atoms. Found 18 (44 requested) and removed 29 (22 requested) atoms. Cycle 20: After refmac, R = 0.1864 (Rfree = 0.000) for 5859 atoms. Found 22 (44 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.91 3.03 Search for helices and strands: 0 residues in 0 chains, 5999 seeds are put forward NCS extension: 12 residues added (6 deleted due to clashes), 6011 seeds are put forward Round 1: 463 peptides, 81 chains. Longest chain 18 peptides. Score 0.443 Round 2: 508 peptides, 73 chains. Longest chain 20 peptides. Score 0.570 Round 3: 520 peptides, 74 chains. Longest chain 20 peptides. Score 0.581 Round 4: 514 peptides, 70 chains. Longest chain 20 peptides. Score 0.598 Round 5: 482 peptides, 61 chains. Longest chain 20 peptides. Score 0.609 Taking the results from Round 5 Chains 66, Residues 421, Estimated correctness of the model 31.6 % 10 chains (93 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12198 restraints for refining 5991 atoms. 10218 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2402 (Rfree = 0.000) for 5991 atoms. Found 45 (45 requested) and removed 51 (22 requested) atoms. Cycle 22: After refmac, R = 0.2305 (Rfree = 0.000) for 5948 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. Cycle 23: After refmac, R = 0.2021 (Rfree = 0.000) for 5923 atoms. Found 27 (44 requested) and removed 29 (22 requested) atoms. Cycle 24: After refmac, R = 0.2010 (Rfree = 0.000) for 5908 atoms. Found 19 (44 requested) and removed 32 (22 requested) atoms. Cycle 25: After refmac, R = 0.1878 (Rfree = 0.000) for 5879 atoms. Found 18 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.88 3.00 Search for helices and strands: 0 residues in 0 chains, 6013 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 6027 seeds are put forward Round 1: 408 peptides, 71 chains. Longest chain 18 peptides. Score 0.420 Round 2: 468 peptides, 65 chains. Longest chain 20 peptides. Score 0.563 Round 3: 456 peptides, 66 chains. Longest chain 21 peptides. Score 0.538 Round 4: 470 peptides, 65 chains. Longest chain 20 peptides. Score 0.566 Round 5: 471 peptides, 69 chains. Longest chain 19 peptides. Score 0.541 Taking the results from Round 4 Chains 73, Residues 405, Estimated correctness of the model 17.2 % 11 chains (93 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12449 restraints for refining 5994 atoms. 10567 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2222 (Rfree = 0.000) for 5994 atoms. Found 37 (45 requested) and removed 46 (22 requested) atoms. Cycle 27: After refmac, R = 0.2086 (Rfree = 0.000) for 5961 atoms. Found 30 (45 requested) and removed 33 (22 requested) atoms. Cycle 28: After refmac, R = 0.1943 (Rfree = 0.000) for 5939 atoms. Found 25 (44 requested) and removed 33 (22 requested) atoms. Cycle 29: After refmac, R = 0.1878 (Rfree = 0.000) for 5919 atoms. Found 26 (44 requested) and removed 28 (22 requested) atoms. Cycle 30: After refmac, R = 0.1773 (Rfree = 0.000) for 5905 atoms. Found 19 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.94 3.06 Search for helices and strands: 0 residues in 0 chains, 6054 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 6081 seeds are put forward Round 1: 376 peptides, 66 chains. Longest chain 17 peptides. Score 0.401 Round 2: 438 peptides, 67 chains. Longest chain 18 peptides. Score 0.502 Round 3: 474 peptides, 67 chains. Longest chain 19 peptides. Score 0.559 Round 4: 476 peptides, 68 chains. Longest chain 20 peptides. Score 0.555 Round 5: 475 peptides, 66 chains. Longest chain 17 peptides. Score 0.567 Taking the results from Round 5 Chains 70, Residues 409, Estimated correctness of the model 17.5 % 8 chains (67 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12608 restraints for refining 5994 atoms. 10807 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2249 (Rfree = 0.000) for 5994 atoms. Found 39 (45 requested) and removed 40 (22 requested) atoms. Cycle 32: After refmac, R = 0.2069 (Rfree = 0.000) for 5965 atoms. Found 42 (45 requested) and removed 32 (22 requested) atoms. Cycle 33: After refmac, R = 0.1956 (Rfree = 0.000) for 5954 atoms. Found 34 (45 requested) and removed 26 (22 requested) atoms. Cycle 34: After refmac, R = 0.1878 (Rfree = 0.000) for 5950 atoms. Found 21 (45 requested) and removed 26 (22 requested) atoms. Cycle 35: After refmac, R = 0.1781 (Rfree = 0.000) for 5935 atoms. Found 23 (44 requested) and removed 30 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.92 3.04 Search for helices and strands: 0 residues in 0 chains, 6058 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6083 seeds are put forward Round 1: 413 peptides, 73 chains. Longest chain 14 peptides. Score 0.414 Round 2: 461 peptides, 70 chains. Longest chain 15 peptides. Score 0.518 Round 3: 459 peptides, 72 chains. Longest chain 13 peptides. Score 0.501 Round 4: 436 peptides, 67 chains. Longest chain 26 peptides. Score 0.499 Round 5: 447 peptides, 67 chains. Longest chain 22 peptides. Score 0.517 Taking the results from Round 2 Chains 71, Residues 391, Estimated correctness of the model 0.0 % 10 chains (58 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12784 restraints for refining 5994 atoms. 11093 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2021 (Rfree = 0.000) for 5994 atoms. Found 35 (45 requested) and removed 33 (22 requested) atoms. Cycle 37: After refmac, R = 0.1904 (Rfree = 0.000) for 5969 atoms. Found 22 (45 requested) and removed 28 (22 requested) atoms. Cycle 38: After refmac, R = 0.1821 (Rfree = 0.000) for 5946 atoms. Found 37 (45 requested) and removed 31 (22 requested) atoms. Cycle 39: After refmac, R = 0.1770 (Rfree = 0.000) for 5948 atoms. Found 31 (44 requested) and removed 23 (22 requested) atoms. Cycle 40: After refmac, R = 0.1727 (Rfree = 0.000) for 5944 atoms. Found 28 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.92 3.04 Search for helices and strands: 0 residues in 0 chains, 6075 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6093 seeds are put forward Round 1: 347 peptides, 65 chains. Longest chain 15 peptides. Score 0.353 Round 2: 406 peptides, 68 chains. Longest chain 18 peptides. Score 0.440 Round 3: 416 peptides, 61 chains. Longest chain 19 peptides. Score 0.509 Round 4: 407 peptides, 60 chains. Longest chain 16 peptides. Score 0.502 Round 5: 395 peptides, 62 chains. Longest chain 19 peptides. Score 0.467 Taking the results from Round 3 Chains 62, Residues 355, Estimated correctness of the model 0.0 % 10 chains (51 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 13085 restraints for refining 5993 atoms. 11557 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2011 (Rfree = 0.000) for 5993 atoms. Found 41 (45 requested) and removed 38 (22 requested) atoms. Cycle 42: After refmac, R = 0.1811 (Rfree = 0.000) for 5976 atoms. Found 27 (45 requested) and removed 24 (22 requested) atoms. Cycle 43: After refmac, R = 0.1745 (Rfree = 0.000) for 5971 atoms. Found 20 (45 requested) and removed 25 (22 requested) atoms. Cycle 44: After refmac, R = 0.1648 (Rfree = 0.000) for 5959 atoms. Found 17 (45 requested) and removed 23 (22 requested) atoms. Cycle 45: After refmac, R = 0.1641 (Rfree = 0.000) for 5951 atoms. Found 24 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.90 3.02 Search for helices and strands: 0 residues in 0 chains, 6081 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6099 seeds are put forward Round 1: 347 peptides, 65 chains. Longest chain 14 peptides. Score 0.353 Round 2: 379 peptides, 62 chains. Longest chain 19 peptides. Score 0.438 Round 3: 372 peptides, 57 chains. Longest chain 25 peptides. Score 0.464 Round 4: 348 peptides, 56 chains. Longest chain 19 peptides. Score 0.429 Round 5: 337 peptides, 55 chains. Longest chain 26 peptides. Score 0.417 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 59, Residues 315, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 59 chains (315 residues) following loop building 5 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11256 reflections ( 96.76 % complete ) and 13419 restraints for refining 5994 atoms. 12102 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1859 (Rfree = 0.000) for 5994 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.1774 (Rfree = 0.000) for 5959 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.1759 (Rfree = 0.000) for 5933 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.1688 (Rfree = 0.000) for 5907 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Writing output files ... TimeTaking 68.17