null Mon 24 Dec 00:09:58 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 1vqy-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqy-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqy-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-4.0-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/1vqy-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-4.0-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 00:10:03 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/1vqy-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-4.0-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 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-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: 19 Cell parameters: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-4.0-parrot-mrncs.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 8193 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.2985 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2953 (Rfree = 0.000) for 8193 atoms. Found 38 (38 requested) and removed 54 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 8347 seeds are put forward NCS extension: 0 residues added, 8347 seeds are put forward Round 1: 341 peptides, 66 chains. Longest chain 10 peptides. Score 0.316 Round 2: 473 peptides, 71 chains. Longest chain 19 peptides. Score 0.495 Round 3: 529 peptides, 69 chains. Longest chain 18 peptides. Score 0.583 Round 4: 515 peptides, 69 chains. Longest chain 23 peptides. Score 0.565 Round 5: 501 peptides, 63 chains. Longest chain 20 peptides. Score 0.582 Taking the results from Round 3 Chains 69, Residues 460, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15124 restraints for refining 6701 atoms. 13290 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2475 (Rfree = 0.000) for 6701 atoms. Found 25 (31 requested) and removed 52 (15 requested) atoms. Cycle 2: After refmac, R = 0.2249 (Rfree = 0.000) for 6576 atoms. Found 15 (31 requested) and removed 47 (15 requested) atoms. Cycle 3: After refmac, R = 0.2294 (Rfree = 0.000) for 6488 atoms. Found 18 (31 requested) and removed 61 (15 requested) atoms. Cycle 4: After refmac, R = 0.2125 (Rfree = 0.000) for 6421 atoms. Found 22 (30 requested) and removed 51 (15 requested) atoms. Cycle 5: After refmac, R = 0.1999 (Rfree = 0.000) for 6380 atoms. Found 18 (30 requested) and removed 47 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 6564 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 6575 seeds are put forward Round 1: 438 peptides, 77 chains. Longest chain 15 peptides. Score 0.401 Round 2: 489 peptides, 66 chains. Longest chain 23 peptides. Score 0.548 Round 3: 512 peptides, 71 chains. Longest chain 23 peptides. Score 0.549 Round 4: 512 peptides, 71 chains. Longest chain 25 peptides. Score 0.549 Round 5: 527 peptides, 68 chains. Longest chain 21 peptides. Score 0.586 Taking the results from Round 5 Chains 69, Residues 459, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15069 restraints for refining 6705 atoms. 13218 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2201 (Rfree = 0.000) for 6705 atoms. Found 23 (31 requested) and removed 48 (15 requested) atoms. Cycle 7: After refmac, R = 0.2182 (Rfree = 0.000) for 6635 atoms. Found 31 (31 requested) and removed 41 (15 requested) atoms. Cycle 8: After refmac, R = 0.2122 (Rfree = 0.000) for 6584 atoms. Found 31 (31 requested) and removed 70 (15 requested) atoms. Cycle 9: After refmac, R = 0.1684 (Rfree = 0.000) for 6528 atoms. Found 8 (31 requested) and removed 33 (15 requested) atoms. Cycle 10: After refmac, R = 0.1673 (Rfree = 0.000) for 6496 atoms. Found 7 (30 requested) and removed 37 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 6703 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6729 seeds are put forward Round 1: 458 peptides, 81 chains. Longest chain 16 peptides. Score 0.406 Round 2: 478 peptides, 73 chains. Longest chain 26 peptides. Score 0.490 Round 3: 469 peptides, 68 chains. Longest chain 23 peptides. Score 0.508 Round 4: 504 peptides, 74 chains. Longest chain 18 peptides. Score 0.520 Round 5: 511 peptides, 72 chains. Longest chain 23 peptides. Score 0.542 Taking the results from Round 5 Chains 72, Residues 439, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15492 restraints for refining 6705 atoms. 13758 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2161 (Rfree = 0.000) for 6705 atoms. Found 29 (31 requested) and removed 62 (15 requested) atoms. Cycle 12: After refmac, R = 0.1960 (Rfree = 0.000) for 6629 atoms. Found 19 (31 requested) and removed 41 (15 requested) atoms. Cycle 13: After refmac, R = 0.1937 (Rfree = 0.000) for 6578 atoms. Found 27 (31 requested) and removed 33 (15 requested) atoms. Cycle 14: After refmac, R = 0.1626 (Rfree = 0.000) for 6561 atoms. Found 5 (31 requested) and removed 33 (15 requested) atoms. Cycle 15: After refmac, R = 0.1636 (Rfree = 0.000) for 6524 atoms. Found 13 (31 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 6756 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 6775 seeds are put forward Round 1: 417 peptides, 78 chains. Longest chain 12 peptides. Score 0.360 Round 2: 445 peptides, 72 chains. Longest chain 13 peptides. Score 0.447 Round 3: 465 peptides, 69 chains. Longest chain 16 peptides. Score 0.496 Round 4: 464 peptides, 69 chains. Longest chain 16 peptides. Score 0.495 Round 5: 483 peptides, 71 chains. Longest chain 18 peptides. Score 0.509 Taking the results from Round 5 Chains 71, Residues 412, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15645 restraints for refining 6705 atoms. 14068 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2091 (Rfree = 0.000) for 6705 atoms. Found 25 (31 requested) and removed 67 (15 requested) atoms. Cycle 17: After refmac, R = 0.2004 (Rfree = 0.000) for 6609 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 18: After refmac, R = 0.1653 (Rfree = 0.000) for 6568 atoms. Found 13 (31 requested) and removed 27 (15 requested) atoms. Cycle 19: After refmac, R = 0.1755 (Rfree = 0.000) for 6535 atoms. Found 13 (31 requested) and removed 30 (15 requested) atoms. Cycle 20: After refmac, R = 0.1518 (Rfree = 0.000) for 6508 atoms. Found 7 (30 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 6719 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6734 seeds are put forward Round 1: 401 peptides, 80 chains. Longest chain 9 peptides. Score 0.318 Round 2: 453 peptides, 74 chains. Longest chain 15 peptides. Score 0.446 Round 3: 424 peptides, 70 chains. Longest chain 13 peptides. Score 0.427 Round 4: 456 peptides, 70 chains. Longest chain 15 peptides. Score 0.476 Round 5: 452 peptides, 72 chains. Longest chain 16 peptides. Score 0.457 Taking the results from Round 4 Chains 71, Residues 386, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15592 restraints for refining 6703 atoms. 14076 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2294 (Rfree = 0.000) for 6703 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 22: After refmac, R = 0.2212 (Rfree = 0.000) for 6649 atoms. Found 31 (31 requested) and removed 50 (15 requested) atoms. Cycle 23: After refmac, R = 0.2142 (Rfree = 0.000) for 6601 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 24: After refmac, R = 0.1720 (Rfree = 0.000) for 6579 atoms. Found 12 (31 requested) and removed 20 (15 requested) atoms. Cycle 25: After refmac, R = 0.1653 (Rfree = 0.000) for 6560 atoms. Found 7 (31 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 6743 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 6767 seeds are put forward Round 1: 376 peptides, 74 chains. Longest chain 10 peptides. Score 0.318 Round 2: 441 peptides, 75 chains. Longest chain 13 peptides. Score 0.420 Round 3: 439 peptides, 74 chains. Longest chain 14 peptides. Score 0.424 Round 4: 442 peptides, 70 chains. Longest chain 15 peptides. Score 0.455 Round 5: 463 peptides, 68 chains. Longest chain 18 peptides. Score 0.500 Taking the results from Round 5 Chains 68, Residues 395, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15591 restraints for refining 6704 atoms. 14036 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2153 (Rfree = 0.000) for 6704 atoms. Found 28 (31 requested) and removed 34 (15 requested) atoms. Cycle 27: After refmac, R = 0.2153 (Rfree = 0.000) for 6662 atoms. Found 31 (31 requested) and removed 47 (15 requested) atoms. Cycle 28: After refmac, R = 0.1696 (Rfree = 0.000) for 6624 atoms. Found 13 (31 requested) and removed 24 (15 requested) atoms. Cycle 29: After refmac, R = 0.1634 (Rfree = 0.000) for 6593 atoms. Found 7 (31 requested) and removed 23 (15 requested) atoms. Cycle 30: After refmac, R = 0.1938 (Rfree = 0.000) for 6569 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 6778 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6795 seeds are put forward Round 1: 350 peptides, 76 chains. Longest chain 9 peptides. Score 0.256 Round 2: 399 peptides, 63 chains. Longest chain 17 peptides. Score 0.436 Round 3: 405 peptides, 62 chains. Longest chain 20 peptides. Score 0.452 Round 4: 404 peptides, 61 chains. Longest chain 21 peptides. Score 0.458 Round 5: 418 peptides, 60 chains. Longest chain 17 peptides. Score 0.486 Taking the results from Round 5 Chains 60, Residues 358, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15766 restraints for refining 6703 atoms. 14379 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2234 (Rfree = 0.000) for 6703 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 32: After refmac, R = 0.2150 (Rfree = 0.000) for 6656 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 33: After refmac, R = 0.1682 (Rfree = 0.000) for 6621 atoms. Found 15 (31 requested) and removed 26 (15 requested) atoms. Cycle 34: After refmac, R = 0.1608 (Rfree = 0.000) for 6593 atoms. Found 8 (31 requested) and removed 18 (15 requested) atoms. Cycle 35: After refmac, R = 0.1625 (Rfree = 0.000) for 6576 atoms. Found 3 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 6761 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 6787 seeds are put forward Round 1: 303 peptides, 65 chains. Longest chain 10 peptides. Score 0.253 Round 2: 379 peptides, 66 chains. Longest chain 12 peptides. Score 0.382 Round 3: 363 peptides, 62 chains. Longest chain 13 peptides. Score 0.384 Round 4: 379 peptides, 65 chains. Longest chain 12 peptides. Score 0.389 Round 5: 361 peptides, 59 chains. Longest chain 12 peptides. Score 0.403 Taking the results from Round 5 Chains 59, Residues 302, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 16290 restraints for refining 6704 atoms. 15141 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2067 (Rfree = 0.000) for 6704 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 37: After refmac, R = 0.2166 (Rfree = 0.000) for 6675 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 38: After refmac, R = 0.2061 (Rfree = 0.000) for 6651 atoms. Found 31 (31 requested) and removed 43 (15 requested) atoms. Cycle 39: After refmac, R = 0.1614 (Rfree = 0.000) for 6623 atoms. Found 11 (31 requested) and removed 23 (15 requested) atoms. Cycle 40: After refmac, R = 0.1551 (Rfree = 0.000) for 6602 atoms. Found 9 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 6774 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 6785 seeds are put forward Round 1: 299 peptides, 65 chains. Longest chain 10 peptides. Score 0.245 Round 2: 331 peptides, 60 chains. Longest chain 12 peptides. Score 0.344 Round 3: 334 peptides, 59 chains. Longest chain 12 peptides. Score 0.357 Round 4: 328 peptides, 56 chains. Longest chain 13 peptides. Score 0.369 Round 5: 338 peptides, 56 chains. Longest chain 15 peptides. Score 0.386 Taking the results from Round 5 Chains 56, Residues 282, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 16399 restraints for refining 6705 atoms. 15327 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2162 (Rfree = 0.000) for 6705 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 42: After refmac, R = 0.2249 (Rfree = 0.000) for 6673 atoms. Found 31 (31 requested) and removed 44 (15 requested) atoms. Cycle 43: After refmac, R = 0.2223 (Rfree = 0.000) for 6641 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 44: After refmac, R = 0.2124 (Rfree = 0.000) for 6621 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 45: After refmac, R = 0.1675 (Rfree = 0.000) for 6607 atoms. Found 14 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.51 Search for helices and strands: 0 residues in 0 chains, 6803 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6822 seeds are put forward Round 1: 263 peptides, 57 chains. Longest chain 8 peptides. Score 0.240 Round 2: 314 peptides, 58 chains. Longest chain 13 peptides. Score 0.329 Round 3: 321 peptides, 57 chains. Longest chain 11 peptides. Score 0.349 Round 4: 322 peptides, 55 chains. Longest chain 12 peptides. Score 0.366 Round 5: 330 peptides, 54 chains. Longest chain 12 peptides. Score 0.388 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 276, 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 16257 restraints for refining 6705 atoms. 15207 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2098 (Rfree = 0.000) for 6705 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2137 (Rfree = 0.000) for 6666 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1683 (Rfree = 0.000) for 6641 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1596 (Rfree = 0.000) for 6617 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:27:18 GMT 2018 Job finished. TimeTaking 77.34 Used memory is bytes: 6087584