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 1vqy-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-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/1vqy-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-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/1vqy-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-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 703 and 0 Target number of residues in the AU: 703 Target solvent content: 0.6116 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 8 Adjusted target number of residues: 928 Adjusted target solvent content: 0.49 Input MTZ file: 1vqy-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: 19 Cell parameters: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 7424 target number of atoms Had to go as low as 0.65 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: 29.074 4.000 Wilson plot Bfac: 57.43 8602 reflections ( 98.34 % complete ) and 0 restraints for refining 8194 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.2946 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2882 (Rfree = 0.000) for 8194 atoms. Found 38 (38 requested) and removed 63 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 8346 seeds are put forward NCS extension: 0 residues added, 8346 seeds are put forward Round 1: 368 peptides, 70 chains. Longest chain 12 peptides. Score 0.334 Round 2: 456 peptides, 71 chains. Longest chain 17 peptides. Score 0.470 Round 3: 511 peptides, 68 chains. Longest chain 25 peptides. Score 0.566 Round 4: 532 peptides, 65 chains. Longest chain 19 peptides. Score 0.609 Round 5: 520 peptides, 72 chains. Longest chain 22 peptides. Score 0.554 Taking the results from Round 4 Chains 65, Residues 467, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15320 restraints for refining 6702 atoms. 13517 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2349 (Rfree = 0.000) for 6702 atoms. Found 18 (31 requested) and removed 59 (15 requested) atoms. Cycle 2: After refmac, R = 0.2374 (Rfree = 0.000) for 6565 atoms. Found 26 (31 requested) and removed 50 (15 requested) atoms. Cycle 3: After refmac, R = 0.2172 (Rfree = 0.000) for 6480 atoms. Found 20 (31 requested) and removed 47 (15 requested) atoms. Cycle 4: After refmac, R = 0.1753 (Rfree = 0.000) for 6426 atoms. Found 7 (30 requested) and removed 36 (15 requested) atoms. Cycle 5: After refmac, R = 0.1656 (Rfree = 0.000) for 6374 atoms. Found 4 (30 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 6617 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6636 seeds are put forward Round 1: 438 peptides, 76 chains. Longest chain 15 peptides. Score 0.408 Round 2: 487 peptides, 67 chains. Longest chain 20 peptides. Score 0.540 Round 3: 481 peptides, 64 chains. Longest chain 17 peptides. Score 0.550 Round 4: 495 peptides, 63 chains. Longest chain 21 peptides. Score 0.574 Round 5: 508 peptides, 64 chains. Longest chain 24 peptides. Score 0.585 Taking the results from Round 5 Chains 64, Residues 444, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15556 restraints for refining 6703 atoms. 13844 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2342 (Rfree = 0.000) for 6703 atoms. Found 22 (31 requested) and removed 65 (15 requested) atoms. Cycle 7: After refmac, R = 0.2220 (Rfree = 0.000) for 6604 atoms. Found 31 (31 requested) and removed 60 (15 requested) atoms. Cycle 8: After refmac, R = 0.2188 (Rfree = 0.000) for 6540 atoms. Found 31 (31 requested) and removed 48 (15 requested) atoms. Cycle 9: After refmac, R = 0.2102 (Rfree = 0.000) for 6488 atoms. Found 30 (30 requested) and removed 37 (15 requested) atoms. Cycle 10: After refmac, R = 0.1681 (Rfree = 0.000) for 6467 atoms. Found 10 (30 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 6696 seeds are put forward NCS extension: 13 residues added (9 deleted due to clashes), 6709 seeds are put forward Round 1: 447 peptides, 76 chains. Longest chain 16 peptides. Score 0.423 Round 2: 505 peptides, 71 chains. Longest chain 20 peptides. Score 0.540 Round 3: 496 peptides, 67 chains. Longest chain 18 peptides. Score 0.552 Round 4: 517 peptides, 67 chains. Longest chain 23 peptides. Score 0.579 Round 5: 510 peptides, 64 chains. Longest chain 22 peptides. Score 0.587 Taking the results from Round 5 Chains 64, Residues 446, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15296 restraints for refining 6703 atoms. 13576 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2404 (Rfree = 0.000) for 6703 atoms. Found 31 (31 requested) and removed 69 (15 requested) atoms. Cycle 12: After refmac, R = 0.2316 (Rfree = 0.000) for 6629 atoms. Found 31 (31 requested) and removed 53 (15 requested) atoms. Cycle 13: After refmac, R = 0.2157 (Rfree = 0.000) for 6568 atoms. Found 31 (31 requested) and removed 43 (15 requested) atoms. Cycle 14: After refmac, R = 0.1774 (Rfree = 0.000) for 6529 atoms. Found 7 (31 requested) and removed 38 (15 requested) atoms. Cycle 15: After refmac, R = 0.1998 (Rfree = 0.000) for 6483 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 6718 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6738 seeds are put forward Round 1: 439 peptides, 77 chains. Longest chain 14 peptides. Score 0.403 Round 2: 478 peptides, 73 chains. Longest chain 25 peptides. Score 0.490 Round 3: 485 peptides, 73 chains. Longest chain 17 peptides. Score 0.500 Round 4: 476 peptides, 66 chains. Longest chain 20 peptides. Score 0.531 Round 5: 497 peptides, 74 chains. Longest chain 15 peptides. Score 0.511 Taking the results from Round 4 Chains 66, Residues 410, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15714 restraints for refining 6704 atoms. 14140 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2398 (Rfree = 0.000) for 6704 atoms. Found 31 (31 requested) and removed 51 (15 requested) atoms. Cycle 17: After refmac, R = 0.2315 (Rfree = 0.000) for 6644 atoms. Found 31 (31 requested) and removed 51 (15 requested) atoms. Cycle 18: After refmac, R = 0.1929 (Rfree = 0.000) for 6598 atoms. Found 13 (31 requested) and removed 30 (15 requested) atoms. Cycle 19: After refmac, R = 0.1836 (Rfree = 0.000) for 6573 atoms. Found 2 (31 requested) and removed 32 (15 requested) atoms. Cycle 20: After refmac, R = 0.1816 (Rfree = 0.000) for 6538 atoms. Found 4 (31 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 6729 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 6740 seeds are put forward Round 1: 401 peptides, 77 chains. Longest chain 14 peptides. Score 0.340 Round 2: 464 peptides, 75 chains. Longest chain 16 peptides. Score 0.456 Round 3: 462 peptides, 71 chains. Longest chain 14 peptides. Score 0.479 Round 4: 463 peptides, 67 chains. Longest chain 16 peptides. Score 0.506 Round 5: 483 peptides, 67 chains. Longest chain 18 peptides. Score 0.534 Taking the results from Round 5 Chains 69, Residues 416, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15519 restraints for refining 6703 atoms. 13881 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2314 (Rfree = 0.000) for 6703 atoms. Found 31 (31 requested) and removed 47 (15 requested) atoms. Cycle 22: After refmac, R = 0.2234 (Rfree = 0.000) for 6653 atoms. Found 31 (31 requested) and removed 52 (15 requested) atoms. Cycle 23: After refmac, R = 0.2163 (Rfree = 0.000) for 6614 atoms. Found 31 (31 requested) and removed 48 (15 requested) atoms. Cycle 24: After refmac, R = 0.1810 (Rfree = 0.000) for 6582 atoms. Found 13 (31 requested) and removed 31 (15 requested) atoms. Cycle 25: After refmac, R = 0.1737 (Rfree = 0.000) for 6556 atoms. Found 7 (31 requested) and removed 40 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 6737 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 6762 seeds are put forward Round 1: 384 peptides, 72 chains. Longest chain 11 peptides. Score 0.347 Round 2: 430 peptides, 64 chains. Longest chain 16 peptides. Score 0.477 Round 3: 436 peptides, 62 chains. Longest chain 21 peptides. Score 0.499 Round 4: 424 peptides, 61 chains. Longest chain 20 peptides. Score 0.488 Round 5: 438 peptides, 62 chains. Longest chain 29 peptides. Score 0.502 Taking the results from Round 5 Chains 62, Residues 376, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15688 restraints for refining 6705 atoms. 14189 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2290 (Rfree = 0.000) for 6705 atoms. Found 31 (31 requested) and removed 58 (15 requested) atoms. Cycle 27: After refmac, R = 0.2169 (Rfree = 0.000) for 6656 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 28: After refmac, R = 0.2098 (Rfree = 0.000) for 6623 atoms. Found 31 (31 requested) and removed 51 (15 requested) atoms. Cycle 29: After refmac, R = 0.2045 (Rfree = 0.000) for 6590 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 30: After refmac, R = 0.1968 (Rfree = 0.000) for 6584 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 6762 seeds are put forward NCS extension: 34 residues added (4 deleted due to clashes), 6796 seeds are put forward Round 1: 367 peptides, 70 chains. Longest chain 15 peptides. Score 0.332 Round 2: 402 peptides, 67 chains. Longest chain 19 peptides. Score 0.413 Round 3: 407 peptides, 60 chains. Longest chain 17 peptides. Score 0.469 Round 4: 417 peptides, 62 chains. Longest chain 15 peptides. Score 0.471 Round 5: 407 peptides, 55 chains. Longest chain 18 peptides. Score 0.503 Taking the results from Round 5 Chains 55, Residues 352, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15851 restraints for refining 6705 atoms. 14498 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2172 (Rfree = 0.000) for 6705 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 32: After refmac, R = 0.2169 (Rfree = 0.000) for 6657 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 33: After refmac, R = 0.1693 (Rfree = 0.000) for 6619 atoms. Found 22 (31 requested) and removed 31 (15 requested) atoms. Cycle 34: After refmac, R = 0.1585 (Rfree = 0.000) for 6591 atoms. Found 4 (31 requested) and removed 22 (15 requested) atoms. Cycle 35: After refmac, R = 0.1569 (Rfree = 0.000) for 6566 atoms. Found 6 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.45 Search for helices and strands: 0 residues in 0 chains, 6728 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6744 seeds are put forward Round 1: 319 peptides, 62 chains. Longest chain 19 peptides. Score 0.307 Round 2: 373 peptides, 63 chains. Longest chain 21 peptides. Score 0.394 Round 3: 397 peptides, 63 chains. Longest chain 19 peptides. Score 0.433 Round 4: 400 peptides, 63 chains. Longest chain 17 peptides. Score 0.438 Round 5: 397 peptides, 64 chains. Longest chain 15 peptides. Score 0.426 Taking the results from Round 4 Chains 63, Residues 337, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15966 restraints for refining 6705 atoms. 14681 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2137 (Rfree = 0.000) for 6705 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 37: After refmac, R = 0.2102 (Rfree = 0.000) for 6655 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 38: After refmac, R = 0.1961 (Rfree = 0.000) for 6628 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. Cycle 39: After refmac, R = 0.1504 (Rfree = 0.000) for 6603 atoms. Found 13 (31 requested) and removed 25 (15 requested) atoms. Cycle 40: After refmac, R = 0.1420 (Rfree = 0.000) for 6583 atoms. Found 8 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 6726 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 6755 seeds are put forward Round 1: 309 peptides, 66 chains. Longest chain 8 peptides. Score 0.257 Round 2: 342 peptides, 62 chains. Longest chain 12 peptides. Score 0.348 Round 3: 344 peptides, 63 chains. Longest chain 11 peptides. Score 0.344 Round 4: 359 peptides, 60 chains. Longest chain 12 peptides. Score 0.392 Round 5: 374 peptides, 62 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 5 Chains 62, Residues 312, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 16171 restraints for refining 6705 atoms. 14985 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2063 (Rfree = 0.000) for 6705 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 42: After refmac, R = 0.2021 (Rfree = 0.000) for 6657 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 43: After refmac, R = 0.1491 (Rfree = 0.000) for 6628 atoms. Found 12 (31 requested) and removed 32 (15 requested) atoms. Cycle 44: After refmac, R = 0.1348 (Rfree = 0.000) for 6600 atoms. Found 5 (31 requested) and removed 28 (15 requested) atoms. Cycle 45: After refmac, R = 0.1325 (Rfree = 0.000) for 6569 atoms. Found 5 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 6723 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6737 seeds are put forward Round 1: 307 peptides, 67 chains. Longest chain 9 peptides. Score 0.245 Round 2: 344 peptides, 59 chains. Longest chain 12 peptides. Score 0.374 Round 3: 354 peptides, 58 chains. Longest chain 13 peptides. Score 0.399 Round 4: 365 peptides, 60 chains. Longest chain 14 peptides. Score 0.402 Round 5: 366 peptides, 63 chains. Longest chain 15 peptides. Score 0.382 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 305, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vqy-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8602 reflections ( 98.34 % complete ) and 16018 restraints for refining 6705 atoms. 14858 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2044 (Rfree = 0.000) for 6705 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2072 (Rfree = 0.000) for 6666 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1898 (Rfree = 0.000) for 6631 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1420 (Rfree = 0.000) for 6608 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:48:04 GMT 2018 Job finished. TimeTaking 85.38 Used memory is bytes: 19207776