null Sun 23 Dec 22:22:56 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 1vkz-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-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/1vkz-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-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 22:23:06 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/1vkz-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-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 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-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: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.4-parrot-hancs.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 7308 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.2867 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2835 (Rfree = 0.000) for 7308 atoms. Found 55 (55 requested) and removed 67 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.87 2.99 Search for helices and strands: 0 residues in 0 chains, 7408 seeds are put forward NCS extension: 0 residues added, 7408 seeds are put forward Round 1: 304 peptides, 65 chains. Longest chain 9 peptides. Score 0.265 Round 2: 423 peptides, 75 chains. Longest chain 14 peptides. Score 0.417 Round 3: 468 peptides, 74 chains. Longest chain 14 peptides. Score 0.502 Round 4: 475 peptides, 72 chains. Longest chain 18 peptides. Score 0.527 Round 5: 501 peptides, 69 chains. Longest chain 16 peptides. Score 0.586 Taking the results from Round 5 Chains 69, Residues 432, Estimated correctness of the model 24.0 % 11 chains (72 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12424 restraints for refining 5990 atoms. 10538 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2692 (Rfree = 0.000) for 5990 atoms. Found 45 (45 requested) and removed 55 (22 requested) atoms. Cycle 2: After refmac, R = 0.2430 (Rfree = 0.000) for 5883 atoms. Found 45 (45 requested) and removed 46 (22 requested) atoms. Cycle 3: After refmac, R = 0.2372 (Rfree = 0.000) for 5833 atoms. Found 32 (44 requested) and removed 37 (22 requested) atoms. Cycle 4: After refmac, R = 0.2343 (Rfree = 0.000) for 5794 atoms. Found 43 (44 requested) and removed 36 (22 requested) atoms. Cycle 5: After refmac, R = 0.2212 (Rfree = 0.000) for 5782 atoms. Found 39 (43 requested) and removed 37 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.89 3.01 Search for helices and strands: 0 residues in 0 chains, 5950 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5964 seeds are put forward Round 1: 445 peptides, 79 chains. Longest chain 13 peptides. Score 0.426 Round 2: 493 peptides, 66 chains. Longest chain 17 peptides. Score 0.593 Round 3: 523 peptides, 64 chains. Longest chain 25 peptides. Score 0.645 Round 4: 510 peptides, 66 chains. Longest chain 18 peptides. Score 0.617 Round 5: 524 peptides, 64 chains. Longest chain 25 peptides. Score 0.646 Taking the results from Round 5 Chains 68, Residues 460, Estimated correctness of the model 43.0 % 9 chains (57 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12823 restraints for refining 5994 atoms. 10878 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2450 (Rfree = 0.000) for 5994 atoms. Found 41 (45 requested) and removed 46 (22 requested) atoms. Cycle 7: After refmac, R = 0.2313 (Rfree = 0.000) for 5948 atoms. Found 26 (45 requested) and removed 46 (22 requested) atoms. Cycle 8: After refmac, R = 0.2252 (Rfree = 0.000) for 5901 atoms. Found 35 (44 requested) and removed 47 (22 requested) atoms. Cycle 9: After refmac, R = 0.2204 (Rfree = 0.000) for 5866 atoms. Found 34 (44 requested) and removed 38 (22 requested) atoms. Cycle 10: After refmac, R = 0.1948 (Rfree = 0.000) for 5843 atoms. Found 23 (44 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.94 3.06 Search for helices and strands: 0 residues in 0 chains, 6034 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6048 seeds are put forward Round 1: 444 peptides, 72 chains. Longest chain 19 peptides. Score 0.476 Round 2: 515 peptides, 68 chains. Longest chain 23 peptides. Score 0.611 Round 3: 496 peptides, 62 chains. Longest chain 26 peptides. Score 0.622 Round 4: 472 peptides, 56 chains. Longest chain 24 peptides. Score 0.626 Round 5: 513 peptides, 60 chains. Longest chain 26 peptides. Score 0.655 Taking the results from Round 5 Chains 61, Residues 453, Estimated correctness of the model 45.6 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12822 restraints for refining 5992 atoms. 10948 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2571 (Rfree = 0.000) for 5992 atoms. Found 45 (45 requested) and removed 48 (22 requested) atoms. Cycle 12: After refmac, R = 0.2328 (Rfree = 0.000) for 5936 atoms. Found 36 (45 requested) and removed 40 (22 requested) atoms. Cycle 13: After refmac, R = 0.2264 (Rfree = 0.000) for 5902 atoms. Found 31 (44 requested) and removed 35 (22 requested) atoms. Cycle 14: After refmac, R = 0.2257 (Rfree = 0.000) for 5873 atoms. Found 38 (44 requested) and removed 35 (22 requested) atoms. Cycle 15: After refmac, R = 0.1988 (Rfree = 0.000) for 5853 atoms. Found 31 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.89 3.01 Search for helices and strands: 0 residues in 0 chains, 6020 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 6048 seeds are put forward Round 1: 428 peptides, 70 chains. Longest chain 18 peptides. Score 0.464 Round 2: 482 peptides, 62 chains. Longest chain 22 peptides. Score 0.603 Round 3: 481 peptides, 64 chains. Longest chain 20 peptides. Score 0.589 Round 4: 489 peptides, 60 chains. Longest chain 25 peptides. Score 0.624 Round 5: 476 peptides, 61 chains. Longest chain 21 peptides. Score 0.601 Taking the results from Round 4 Chains 63, Residues 429, Estimated correctness of the model 36.3 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12965 restraints for refining 5992 atoms. 11148 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2382 (Rfree = 0.000) for 5992 atoms. Found 45 (45 requested) and removed 53 (22 requested) atoms. Cycle 17: After refmac, R = 0.2171 (Rfree = 0.000) for 5950 atoms. Found 36 (45 requested) and removed 36 (22 requested) atoms. Cycle 18: After refmac, R = 0.2110 (Rfree = 0.000) for 5931 atoms. Found 33 (44 requested) and removed 30 (22 requested) atoms. Cycle 19: After refmac, R = 0.2075 (Rfree = 0.000) for 5917 atoms. Found 38 (44 requested) and removed 28 (22 requested) atoms. Cycle 20: After refmac, R = 0.2046 (Rfree = 0.000) for 5907 atoms. Found 36 (44 requested) and removed 30 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.89 3.01 Search for helices and strands: 0 residues in 0 chains, 6059 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 6080 seeds are put forward Round 1: 415 peptides, 69 chains. Longest chain 13 peptides. Score 0.448 Round 2: 470 peptides, 67 chains. Longest chain 16 peptides. Score 0.553 Round 3: 486 peptides, 62 chains. Longest chain 19 peptides. Score 0.608 Round 4: 485 peptides, 65 chains. Longest chain 22 peptides. Score 0.588 Round 5: 498 peptides, 65 chains. Longest chain 27 peptides. Score 0.606 Taking the results from Round 3 Chains 66, Residues 424, Estimated correctness of the model 31.3 % 7 chains (65 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12490 restraints for refining 5993 atoms. 10605 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2472 (Rfree = 0.000) for 5993 atoms. Found 45 (45 requested) and removed 47 (22 requested) atoms. Cycle 22: After refmac, R = 0.2235 (Rfree = 0.000) for 5938 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. Cycle 23: After refmac, R = 0.2192 (Rfree = 0.000) for 5912 atoms. Found 44 (44 requested) and removed 35 (22 requested) atoms. Cycle 24: After refmac, R = 0.2107 (Rfree = 0.000) for 5897 atoms. Found 44 (44 requested) and removed 25 (22 requested) atoms. Cycle 25: After refmac, R = 0.1823 (Rfree = 0.000) for 5901 atoms. Found 22 (44 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.90 3.02 Search for helices and strands: 0 residues in 0 chains, 6021 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 6035 seeds are put forward Round 1: 395 peptides, 70 chains. Longest chain 17 peptides. Score 0.404 Round 2: 465 peptides, 65 chains. Longest chain 21 peptides. Score 0.559 Round 3: 482 peptides, 67 chains. Longest chain 22 peptides. Score 0.571 Round 4: 456 peptides, 64 chains. Longest chain 16 peptides. Score 0.552 Round 5: 467 peptides, 63 chains. Longest chain 26 peptides. Score 0.575 Taking the results from Round 5 Chains 66, Residues 404, Estimated correctness of the model 20.3 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12829 restraints for refining 5993 atoms. 11089 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2334 (Rfree = 0.000) for 5993 atoms. Found 45 (45 requested) and removed 54 (22 requested) atoms. Cycle 27: After refmac, R = 0.2245 (Rfree = 0.000) for 5943 atoms. Found 45 (45 requested) and removed 44 (22 requested) atoms. Cycle 28: After refmac, R = 0.1988 (Rfree = 0.000) for 5924 atoms. Found 34 (44 requested) and removed 33 (22 requested) atoms. Cycle 29: After refmac, R = 0.1971 (Rfree = 0.000) for 5913 atoms. Found 36 (44 requested) and removed 35 (22 requested) atoms. Cycle 30: After refmac, R = 0.1841 (Rfree = 0.000) for 5898 atoms. Found 27 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.85 2.97 Search for helices and strands: 0 residues in 0 chains, 6052 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6068 seeds are put forward Round 1: 405 peptides, 70 chains. Longest chain 13 peptides. Score 0.423 Round 2: 426 peptides, 64 chains. Longest chain 15 peptides. Score 0.504 Round 3: 460 peptides, 65 chains. Longest chain 15 peptides. Score 0.551 Round 4: 459 peptides, 64 chains. Longest chain 14 peptides. Score 0.556 Round 5: 458 peptides, 63 chains. Longest chain 17 peptides. Score 0.562 Taking the results from Round 5 Chains 65, Residues 395, Estimated correctness of the model 15.8 % 10 chains (54 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12838 restraints for refining 5994 atoms. 11173 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2308 (Rfree = 0.000) for 5994 atoms. Found 45 (45 requested) and removed 36 (22 requested) atoms. Cycle 32: After refmac, R = 0.2073 (Rfree = 0.000) for 5971 atoms. Found 39 (45 requested) and removed 37 (22 requested) atoms. Cycle 33: After refmac, R = 0.1967 (Rfree = 0.000) for 5962 atoms. Found 43 (45 requested) and removed 44 (22 requested) atoms. Cycle 34: After refmac, R = 0.1747 (Rfree = 0.000) for 5947 atoms. Found 26 (45 requested) and removed 32 (22 requested) atoms. Cycle 35: After refmac, R = 0.1706 (Rfree = 0.000) for 5936 atoms. Found 26 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.87 2.99 Search for helices and strands: 0 residues in 0 chains, 6054 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6069 seeds are put forward Round 1: 369 peptides, 63 chains. Longest chain 15 peptides. Score 0.412 Round 2: 414 peptides, 62 chains. Longest chain 15 peptides. Score 0.499 Round 3: 428 peptides, 64 chains. Longest chain 22 peptides. Score 0.507 Round 4: 411 peptides, 61 chains. Longest chain 15 peptides. Score 0.501 Round 5: 417 peptides, 64 chains. Longest chain 15 peptides. Score 0.489 Taking the results from Round 3 Chains 64, Residues 364, Estimated correctness of the model 0.0 % 10 chains (51 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12948 restraints for refining 5994 atoms. 11411 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2053 (Rfree = 0.000) for 5994 atoms. Found 45 (45 requested) and removed 45 (22 requested) atoms. Cycle 37: After refmac, R = 0.1905 (Rfree = 0.000) for 5980 atoms. Found 42 (45 requested) and removed 32 (22 requested) atoms. Cycle 38: After refmac, R = 0.1801 (Rfree = 0.000) for 5971 atoms. Found 32 (45 requested) and removed 30 (22 requested) atoms. Cycle 39: After refmac, R = 0.1758 (Rfree = 0.000) for 5966 atoms. Found 22 (45 requested) and removed 31 (22 requested) atoms. Cycle 40: After refmac, R = 0.1700 (Rfree = 0.000) for 5946 atoms. Found 32 (44 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.86 2.98 Search for helices and strands: 0 residues in 0 chains, 6062 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 6092 seeds are put forward Round 1: 357 peptides, 70 chains. Longest chain 12 peptides. Score 0.331 Round 2: 403 peptides, 64 chains. Longest chain 18 peptides. Score 0.465 Round 3: 406 peptides, 64 chains. Longest chain 18 peptides. Score 0.470 Round 4: 417 peptides, 70 chains. Longest chain 18 peptides. Score 0.444 Round 5: 409 peptides, 66 chains. Longest chain 14 peptides. Score 0.461 Taking the results from Round 3 Chains 65, Residues 342, Estimated correctness of the model 0.0 % 5 chains (26 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 13360 restraints for refining 5993 atoms. 11989 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1919 (Rfree = 0.000) for 5993 atoms. Found 45 (45 requested) and removed 25 (22 requested) atoms. Cycle 42: After refmac, R = 0.1834 (Rfree = 0.000) for 5994 atoms. Found 43 (45 requested) and removed 26 (22 requested) atoms. Cycle 43: After refmac, R = 0.1694 (Rfree = 0.000) for 6000 atoms. Found 29 (45 requested) and removed 29 (22 requested) atoms. Cycle 44: After refmac, R = 0.1613 (Rfree = 0.000) for 5995 atoms. Found 26 (45 requested) and removed 27 (22 requested) atoms. Cycle 45: After refmac, R = 0.1571 (Rfree = 0.000) for 5992 atoms. Found 26 (45 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.93 3.05 Search for helices and strands: 0 residues in 0 chains, 6109 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 6132 seeds are put forward Round 1: 351 peptides, 69 chains. Longest chain 12 peptides. Score 0.328 Round 2: 375 peptides, 68 chains. Longest chain 16 peptides. Score 0.383 Round 3: 402 peptides, 66 chains. Longest chain 20 peptides. Score 0.448 Round 4: 393 peptides, 66 chains. Longest chain 13 peptides. Score 0.432 Round 5: 377 peptides, 61 chains. Longest chain 17 peptides. Score 0.442 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 336, Estimated correctness of the model 0.0 % 5 chains (20 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (336 residues) following loop building 5 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11256 reflections ( 96.76 % complete ) and 13432 restraints for refining 5992 atoms. 12102 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1881 (Rfree = 0.000) for 5992 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.1851 (Rfree = 0.000) for 5947 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.1786 (Rfree = 0.000) for 5921 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.1709 (Rfree = 0.000) for 5895 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:39:53 GMT 2018 Job finished. TimeTaking 76.96 Used memory is bytes: 16143296