Mon 24 Dec 07:28:22 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vqy-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqy-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqy-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.8-parrot-noncs ############### 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 07:28:27 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/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.8-parrot-noncs/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 721 and 0 Target number of residues in the AU: 721 Target solvent content: 0.6016 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-3.8-parrot-noncs.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-3.8-parrot-noncs.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 3.800 Wilson plot Bfac: 53.20 9994 reflections ( 98.35 % complete ) and 0 restraints for refining 8221 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3131 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2964 (Rfree = 0.000) for 8221 atoms. Found 45 (45 requested) and removed 63 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 8344 seeds are put forward NCS extension: 0 residues added, 8344 seeds are put forward Round 1: 322 peptides, 65 chains. Longest chain 12 peptides. Score 0.289 Round 2: 445 peptides, 76 chains. Longest chain 13 peptides. Score 0.419 Round 3: 488 peptides, 75 chains. Longest chain 16 peptides. Score 0.491 Round 4: 504 peptides, 76 chains. Longest chain 17 peptides. Score 0.508 Round 5: 520 peptides, 80 chains. Longest chain 17 peptides. Score 0.506 Taking the results from Round 4 Chains 77, Residues 428, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15293 restraints for refining 6712 atoms. 13568 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2970 (Rfree = 0.000) for 6712 atoms. Found 31 (36 requested) and removed 72 (18 requested) atoms. Cycle 2: After refmac, R = 0.2475 (Rfree = 0.000) for 6558 atoms. Found 36 (36 requested) and removed 53 (18 requested) atoms. Cycle 3: After refmac, R = 0.2402 (Rfree = 0.000) for 6483 atoms. Found 35 (35 requested) and removed 36 (17 requested) atoms. Cycle 4: After refmac, R = 0.1948 (Rfree = 0.000) for 6447 atoms. Found 15 (35 requested) and removed 31 (17 requested) atoms. Cycle 5: After refmac, R = 0.1809 (Rfree = 0.000) for 6402 atoms. Found 10 (35 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.36 Search for helices and strands: 0 residues in 0 chains, 6651 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6667 seeds are put forward Round 1: 411 peptides, 72 chains. Longest chain 12 peptides. Score 0.392 Round 2: 462 peptides, 72 chains. Longest chain 15 peptides. Score 0.472 Round 3: 473 peptides, 71 chains. Longest chain 18 peptides. Score 0.495 Round 4: 479 peptides, 68 chains. Longest chain 22 peptides. Score 0.522 Round 5: 492 peptides, 68 chains. Longest chain 19 peptides. Score 0.540 Taking the results from Round 5 Chains 68, Residues 424, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15483 restraints for refining 6678 atoms. 13855 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2362 (Rfree = 0.000) for 6678 atoms. Found 30 (36 requested) and removed 75 (18 requested) atoms. Cycle 7: After refmac, R = 0.2258 (Rfree = 0.000) for 6566 atoms. Found 36 (36 requested) and removed 51 (18 requested) atoms. Cycle 8: After refmac, R = 0.2193 (Rfree = 0.000) for 6521 atoms. Found 36 (36 requested) and removed 50 (18 requested) atoms. Cycle 9: After refmac, R = 0.1777 (Rfree = 0.000) for 6488 atoms. Found 9 (35 requested) and removed 28 (17 requested) atoms. Cycle 10: After refmac, R = 0.1676 (Rfree = 0.000) for 6460 atoms. Found 7 (35 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 6680 seeds are put forward NCS extension: 9 residues added (5 deleted due to clashes), 6689 seeds are put forward Round 1: 436 peptides, 79 chains. Longest chain 16 peptides. Score 0.384 Round 2: 496 peptides, 80 chains. Longest chain 18 peptides. Score 0.471 Round 3: 515 peptides, 81 chains. Longest chain 17 peptides. Score 0.493 Round 4: 491 peptides, 72 chains. Longest chain 24 peptides. Score 0.514 Round 5: 487 peptides, 68 chains. Longest chain 25 peptides. Score 0.533 Taking the results from Round 5 Chains 68, Residues 419, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15443 restraints for refining 6714 atoms. 13835 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2209 (Rfree = 0.000) for 6714 atoms. Found 36 (36 requested) and removed 45 (18 requested) atoms. Cycle 12: After refmac, R = 0.2048 (Rfree = 0.000) for 6661 atoms. Found 36 (36 requested) and removed 38 (18 requested) atoms. Cycle 13: After refmac, R = 0.1937 (Rfree = 0.000) for 6640 atoms. Found 36 (36 requested) and removed 33 (18 requested) atoms. Cycle 14: After refmac, R = 0.1606 (Rfree = 0.000) for 6630 atoms. Found 11 (36 requested) and removed 25 (18 requested) atoms. Cycle 15: After refmac, R = 0.1566 (Rfree = 0.000) for 6605 atoms. Found 2 (36 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.35 Search for helices and strands: 0 residues in 0 chains, 6822 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6838 seeds are put forward Round 1: 421 peptides, 76 chains. Longest chain 22 peptides. Score 0.381 Round 2: 460 peptides, 70 chains. Longest chain 24 peptides. Score 0.482 Round 3: 477 peptides, 67 chains. Longest chain 24 peptides. Score 0.526 Round 4: 455 peptides, 68 chains. Longest chain 22 peptides. Score 0.488 Round 5: 477 peptides, 65 chains. Longest chain 21 peptides. Score 0.538 Taking the results from Round 5 Chains 67, Residues 412, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15229 restraints for refining 6714 atoms. 13592 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2183 (Rfree = 0.000) for 6714 atoms. Found 25 (36 requested) and removed 46 (18 requested) atoms. Cycle 17: After refmac, R = 0.2114 (Rfree = 0.000) for 6666 atoms. Found 36 (36 requested) and removed 41 (18 requested) atoms. Cycle 18: After refmac, R = 0.2051 (Rfree = 0.000) for 6637 atoms. Found 36 (36 requested) and removed 36 (18 requested) atoms. Cycle 19: After refmac, R = 0.1981 (Rfree = 0.000) for 6623 atoms. Found 36 (36 requested) and removed 35 (18 requested) atoms. Cycle 20: After refmac, R = 0.1975 (Rfree = 0.000) for 6607 atoms. Found 33 (36 requested) and removed 37 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 6785 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6798 seeds are put forward Round 1: 375 peptides, 71 chains. Longest chain 16 peptides. Score 0.339 Round 2: 443 peptides, 71 chains. Longest chain 16 peptides. Score 0.450 Round 3: 442 peptides, 68 chains. Longest chain 16 peptides. Score 0.469 Round 4: 450 peptides, 69 chains. Longest chain 14 peptides. Score 0.474 Round 5: 453 peptides, 69 chains. Longest chain 16 peptides. Score 0.479 Taking the results from Round 5 Chains 69, Residues 384, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15845 restraints for refining 6715 atoms. 14378 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2271 (Rfree = 0.000) for 6715 atoms. Found 36 (36 requested) and removed 45 (18 requested) atoms. Cycle 22: After refmac, R = 0.2063 (Rfree = 0.000) for 6675 atoms. Found 34 (36 requested) and removed 37 (18 requested) atoms. Cycle 23: After refmac, R = 0.1757 (Rfree = 0.000) for 6660 atoms. Found 6 (36 requested) and removed 30 (18 requested) atoms. Cycle 24: After refmac, R = 0.1695 (Rfree = 0.000) for 6629 atoms. Found 10 (36 requested) and removed 23 (18 requested) atoms. Cycle 25: After refmac, R = 0.1691 (Rfree = 0.000) for 6615 atoms. Found 5 (36 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.30 Search for helices and strands: 0 residues in 0 chains, 6813 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6833 seeds are put forward Round 1: 360 peptides, 72 chains. Longest chain 9 peptides. Score 0.305 Round 2: 442 peptides, 72 chains. Longest chain 15 peptides. Score 0.442 Round 3: 441 peptides, 74 chains. Longest chain 13 peptides. Score 0.427 Round 4: 431 peptides, 67 chains. Longest chain 15 peptides. Score 0.459 Round 5: 450 peptides, 68 chains. Longest chain 15 peptides. Score 0.481 Taking the results from Round 5 Chains 68, Residues 382, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15713 restraints for refining 6715 atoms. 14253 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2284 (Rfree = 0.000) for 6715 atoms. Found 34 (36 requested) and removed 38 (18 requested) atoms. Cycle 27: After refmac, R = 0.2239 (Rfree = 0.000) for 6673 atoms. Found 36 (36 requested) and removed 36 (18 requested) atoms. Cycle 28: After refmac, R = 0.2173 (Rfree = 0.000) for 6653 atoms. Found 36 (36 requested) and removed 43 (18 requested) atoms. Cycle 29: After refmac, R = 0.2142 (Rfree = 0.000) for 6635 atoms. Found 36 (36 requested) and removed 28 (18 requested) atoms. Cycle 30: After refmac, R = 0.2064 (Rfree = 0.000) for 6631 atoms. Found 36 (36 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 6814 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6828 seeds are put forward Round 1: 350 peptides, 68 chains. Longest chain 14 peptides. Score 0.317 Round 2: 406 peptides, 73 chains. Longest chain 17 peptides. Score 0.377 Round 3: 431 peptides, 72 chains. Longest chain 15 peptides. Score 0.425 Round 4: 426 peptides, 73 chains. Longest chain 17 peptides. Score 0.410 Round 5: 436 peptides, 67 chains. Longest chain 17 peptides. Score 0.466 Taking the results from Round 5 Chains 67, Residues 369, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15716 restraints for refining 6714 atoms. 14307 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2172 (Rfree = 0.000) for 6714 atoms. Found 28 (36 requested) and removed 42 (18 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2148 (Rfree = 0.000) for 6670 atoms. Found 36 (36 requested) and removed 31 (18 requested) atoms. Cycle 33: After refmac, R = 0.2003 (Rfree = 0.000) for 6651 atoms. Found 36 (36 requested) and removed 27 (18 requested) atoms. Cycle 34: After refmac, R = 0.1988 (Rfree = 0.000) for 6640 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. Cycle 35: After refmac, R = 0.1974 (Rfree = 0.000) for 6627 atoms. Found 36 (36 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 6820 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6832 seeds are put forward Round 1: 355 peptides, 77 chains. Longest chain 11 peptides. Score 0.257 Round 2: 395 peptides, 72 chains. Longest chain 14 peptides. Score 0.366 Round 3: 408 peptides, 67 chains. Longest chain 16 peptides. Score 0.423 Round 4: 405 peptides, 67 chains. Longest chain 13 peptides. Score 0.418 Round 5: 421 peptides, 67 chains. Longest chain 14 peptides. Score 0.443 Taking the results from Round 5 Chains 67, Residues 354, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15937 restraints for refining 6715 atoms. 14588 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2168 (Rfree = 0.000) for 6715 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Cycle 37: After refmac, R = 0.2149 (Rfree = 0.000) for 6687 atoms. Found 36 (36 requested) and removed 38 (18 requested) atoms. Cycle 38: After refmac, R = 0.2053 (Rfree = 0.000) for 6670 atoms. Found 36 (36 requested) and removed 34 (18 requested) atoms. Cycle 39: After refmac, R = 0.2137 (Rfree = 0.000) for 6657 atoms. Found 36 (36 requested) and removed 30 (18 requested) atoms. Cycle 40: After refmac, R = 0.2030 (Rfree = 0.000) for 6655 atoms. Found 36 (36 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.30 Search for helices and strands: 0 residues in 0 chains, 6829 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6846 seeds are put forward Round 1: 350 peptides, 71 chains. Longest chain 12 peptides. Score 0.294 Round 2: 376 peptides, 64 chains. Longest chain 16 peptides. Score 0.392 Round 3: 372 peptides, 67 chains. Longest chain 15 peptides. Score 0.363 Round 4: 387 peptides, 65 chains. Longest chain 14 peptides. Score 0.403 Round 5: 392 peptides, 63 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 5 Chains 63, Residues 329, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15421 restraints for refining 6715 atoms. 14066 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2222 (Rfree = 0.000) for 6715 atoms. Found 36 (36 requested) and removed 36 (18 requested) atoms. Cycle 42: After refmac, R = 0.2123 (Rfree = 0.000) for 6674 atoms. Found 36 (36 requested) and removed 30 (18 requested) atoms. Cycle 43: After refmac, R = 0.2028 (Rfree = 0.000) for 6656 atoms. Found 36 (36 requested) and removed 35 (18 requested) atoms. Cycle 44: After refmac, R = 0.1964 (Rfree = 0.000) for 6641 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. Cycle 45: After refmac, R = 0.1952 (Rfree = 0.000) for 6628 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 6806 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 6816 seeds are put forward Round 1: 284 peptides, 59 chains. Longest chain 10 peptides. Score 0.265 Round 2: 344 peptides, 63 chains. Longest chain 11 peptides. Score 0.344 Round 3: 361 peptides, 62 chains. Longest chain 13 peptides. Score 0.381 Round 4: 363 peptides, 62 chains. Longest chain 12 peptides. Score 0.384 Round 5: 359 peptides, 61 chains. Longest chain 13 peptides. Score 0.385 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 298, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9994 reflections ( 98.35 % complete ) and 15797 restraints for refining 6691 atoms. 14666 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2299 (Rfree = 0.000) for 6691 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2173 (Rfree = 0.000) for 6632 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2067 (Rfree = 0.000) for 6589 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2043 (Rfree = 0.000) for 6556 atoms. TimeTaking 65.97