Mon 24 Dec 07:46:41 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqy-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqy-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.6-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 07:46:46 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.6-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 754 and 0 Target number of residues in the AU: 754 Target solvent content: 0.5834 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 46.12 11704 reflections ( 98.35 % complete ) and 0 restraints for refining 8262 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3101 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2971 (Rfree = 0.000) for 8262 atoms. Found 53 (53 requested) and removed 77 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.12 3.16 Search for helices and strands: 0 residues in 0 chains, 8378 seeds are put forward NCS extension: 0 residues added, 8378 seeds are put forward Round 1: 337 peptides, 67 chains. Longest chain 11 peptides. Score 0.301 Round 2: 447 peptides, 74 chains. Longest chain 19 peptides. Score 0.436 Round 3: 480 peptides, 74 chains. Longest chain 15 peptides. Score 0.486 Round 4: 487 peptides, 70 chains. Longest chain 21 peptides. Score 0.521 Round 5: 523 peptides, 70 chains. Longest chain 24 peptides. Score 0.569 Taking the results from Round 5 Chains 70, Residues 453, Estimated correctness of the model 2.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 15106 restraints for refining 6727 atoms. 13364 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2523 (Rfree = 0.000) for 6727 atoms. Found 29 (43 requested) and removed 48 (21 requested) atoms. Cycle 2: After refmac, R = 0.2482 (Rfree = 0.000) for 6604 atoms. Found 43 (43 requested) and removed 47 (21 requested) atoms. Cycle 3: After refmac, R = 0.2372 (Rfree = 0.000) for 6559 atoms. Found 41 (42 requested) and removed 42 (21 requested) atoms. Cycle 4: After refmac, R = 0.2290 (Rfree = 0.000) for 6525 atoms. Found 41 (42 requested) and removed 39 (21 requested) atoms. Cycle 5: After refmac, R = 0.2273 (Rfree = 0.000) for 6503 atoms. Found 34 (41 requested) and removed 44 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.08 3.12 Search for helices and strands: 0 residues in 0 chains, 6738 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 6768 seeds are put forward Round 1: 446 peptides, 75 chains. Longest chain 16 peptides. Score 0.428 Round 2: 498 peptides, 73 chains. Longest chain 18 peptides. Score 0.518 Round 3: 497 peptides, 71 chains. Longest chain 18 peptides. Score 0.529 Round 4: 511 peptides, 69 chains. Longest chain 19 peptides. Score 0.560 Round 5: 497 peptides, 69 chains. Longest chain 20 peptides. Score 0.541 Taking the results from Round 4 Chains 74, Residues 442, Estimated correctness of the model 0.0 % 5 chains (55 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 14650 restraints for refining 6730 atoms. 12707 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2484 (Rfree = 0.000) for 6730 atoms. Found 39 (43 requested) and removed 59 (21 requested) atoms. Cycle 7: After refmac, R = 0.2323 (Rfree = 0.000) for 6657 atoms. Found 41 (43 requested) and removed 50 (21 requested) atoms. Cycle 8: After refmac, R = 0.2171 (Rfree = 0.000) for 6603 atoms. Found 31 (42 requested) and removed 48 (21 requested) atoms. Cycle 9: After refmac, R = 0.2126 (Rfree = 0.000) for 6562 atoms. Found 29 (42 requested) and removed 34 (21 requested) atoms. Cycle 10: After refmac, R = 0.2067 (Rfree = 0.000) for 6540 atoms. Found 37 (42 requested) and removed 36 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 6722 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 6747 seeds are put forward Round 1: 472 peptides, 80 chains. Longest chain 16 peptides. Score 0.435 Round 2: 535 peptides, 81 chains. Longest chain 21 peptides. Score 0.521 Round 3: 509 peptides, 76 chains. Longest chain 17 peptides. Score 0.515 Round 4: 498 peptides, 73 chains. Longest chain 17 peptides. Score 0.518 Round 5: 511 peptides, 71 chains. Longest chain 25 peptides. Score 0.548 Taking the results from Round 5 Chains 72, Residues 440, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 14815 restraints for refining 6729 atoms. 12994 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2408 (Rfree = 0.000) for 6729 atoms. Found 40 (43 requested) and removed 62 (21 requested) atoms. Cycle 12: After refmac, R = 0.2260 (Rfree = 0.000) for 6671 atoms. Found 31 (43 requested) and removed 51 (21 requested) atoms. Cycle 13: After refmac, R = 0.2182 (Rfree = 0.000) for 6622 atoms. Found 31 (42 requested) and removed 38 (21 requested) atoms. Cycle 14: After refmac, R = 0.1935 (Rfree = 0.000) for 6599 atoms. Found 17 (42 requested) and removed 34 (21 requested) atoms. Cycle 15: After refmac, R = 0.1852 (Rfree = 0.000) for 6574 atoms. Found 14 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 6763 seeds are put forward NCS extension: 46 residues added (3 deleted due to clashes), 6809 seeds are put forward Round 1: 454 peptides, 75 chains. Longest chain 14 peptides. Score 0.440 Round 2: 506 peptides, 76 chains. Longest chain 19 peptides. Score 0.511 Round 3: 506 peptides, 76 chains. Longest chain 22 peptides. Score 0.511 Round 4: 525 peptides, 75 chains. Longest chain 26 peptides. Score 0.543 Round 5: 511 peptides, 68 chains. Longest chain 32 peptides. Score 0.566 Taking the results from Round 5 Chains 69, Residues 443, Estimated correctness of the model 0.9 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 14941 restraints for refining 6729 atoms. 13134 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2342 (Rfree = 0.000) for 6729 atoms. Found 34 (43 requested) and removed 47 (21 requested) atoms. Cycle 17: After refmac, R = 0.2261 (Rfree = 0.000) for 6666 atoms. Found 42 (43 requested) and removed 58 (21 requested) atoms. Cycle 18: After refmac, R = 0.2282 (Rfree = 0.000) for 6623 atoms. Found 42 (42 requested) and removed 41 (21 requested) atoms. Cycle 19: After refmac, R = 0.2188 (Rfree = 0.000) for 6609 atoms. Found 42 (42 requested) and removed 49 (21 requested) atoms. Cycle 20: After refmac, R = 0.1852 (Rfree = 0.000) for 6582 atoms. Found 29 (42 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 6767 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 6797 seeds are put forward Round 1: 409 peptides, 73 chains. Longest chain 19 peptides. Score 0.382 Round 2: 465 peptides, 69 chains. Longest chain 19 peptides. Score 0.496 Round 3: 494 peptides, 73 chains. Longest chain 18 peptides. Score 0.513 Round 4: 464 peptides, 65 chains. Longest chain 19 peptides. Score 0.520 Round 5: 485 peptides, 70 chains. Longest chain 23 peptides. Score 0.518 Taking the results from Round 4 Chains 65, Residues 399, Estimated correctness of the model 0.0 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 14997 restraints for refining 6730 atoms. 13290 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2456 (Rfree = 0.000) for 6730 atoms. Found 43 (43 requested) and removed 58 (21 requested) atoms. Cycle 22: After refmac, R = 0.2144 (Rfree = 0.000) for 6683 atoms. Found 35 (43 requested) and removed 46 (21 requested) atoms. Cycle 23: After refmac, R = 0.2121 (Rfree = 0.000) for 6647 atoms. Found 35 (42 requested) and removed 38 (21 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1960 (Rfree = 0.000) for 6630 atoms. Found 42 (42 requested) and removed 32 (21 requested) atoms. Cycle 25: After refmac, R = 0.1949 (Rfree = 0.000) for 6624 atoms. Found 42 (42 requested) and removed 30 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.12 Search for helices and strands: 0 residues in 0 chains, 6793 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6815 seeds are put forward Round 1: 418 peptides, 74 chains. Longest chain 13 peptides. Score 0.390 Round 2: 450 peptides, 74 chains. Longest chain 15 peptides. Score 0.441 Round 3: 468 peptides, 69 chains. Longest chain 29 peptides. Score 0.501 Round 4: 464 peptides, 72 chains. Longest chain 19 peptides. Score 0.475 Round 5: 457 peptides, 68 chains. Longest chain 26 peptides. Score 0.491 Taking the results from Round 3 Chains 69, Residues 399, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11704 reflections ( 98.35 % complete ) and 15234 restraints for refining 6730 atoms. 13707 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2068 (Rfree = 0.000) for 6730 atoms. Found 26 (43 requested) and removed 40 (21 requested) atoms. Cycle 27: After refmac, R = 0.1945 (Rfree = 0.000) for 6693 atoms. Found 34 (43 requested) and removed 34 (21 requested) atoms. Cycle 28: After refmac, R = 0.1885 (Rfree = 0.000) for 6679 atoms. Found 34 (42 requested) and removed 29 (21 requested) atoms. Cycle 29: After refmac, R = 0.1861 (Rfree = 0.000) for 6678 atoms. Found 42 (42 requested) and removed 34 (21 requested) atoms. Cycle 30: After refmac, R = 0.1871 (Rfree = 0.000) for 6680 atoms. Found 42 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 6892 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 6917 seeds are put forward Round 1: 369 peptides, 72 chains. Longest chain 17 peptides. Score 0.321 Round 2: 426 peptides, 69 chains. Longest chain 14 peptides. Score 0.437 Round 3: 450 peptides, 71 chains. Longest chain 23 peptides. Score 0.461 Round 4: 431 peptides, 70 chains. Longest chain 16 peptides. Score 0.438 Round 5: 432 peptides, 68 chains. Longest chain 22 peptides. Score 0.453 Taking the results from Round 3 Chains 71, Residues 379, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 15424 restraints for refining 6728 atoms. 13979 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2146 (Rfree = 0.000) for 6728 atoms. Found 40 (43 requested) and removed 30 (21 requested) atoms. Cycle 32: After refmac, R = 0.2032 (Rfree = 0.000) for 6715 atoms. Found 33 (43 requested) and removed 31 (21 requested) atoms. Cycle 33: After refmac, R = 0.1936 (Rfree = 0.000) for 6701 atoms. Found 34 (43 requested) and removed 27 (21 requested) atoms. Cycle 34: After refmac, R = 0.1911 (Rfree = 0.000) for 6699 atoms. Found 34 (43 requested) and removed 26 (21 requested) atoms. Cycle 35: After refmac, R = 0.1680 (Rfree = 0.000) for 6692 atoms. Found 14 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.07 3.11 Search for helices and strands: 0 residues in 0 chains, 6839 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 6876 seeds are put forward Round 1: 332 peptides, 68 chains. Longest chain 15 peptides. Score 0.284 Round 2: 433 peptides, 68 chains. Longest chain 15 peptides. Score 0.455 Round 3: 441 peptides, 73 chains. Longest chain 16 peptides. Score 0.434 Round 4: 442 peptides, 72 chains. Longest chain 16 peptides. Score 0.442 Round 5: 428 peptides, 69 chains. Longest chain 15 peptides. Score 0.440 Taking the results from Round 2 Chains 68, Residues 365, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 15396 restraints for refining 6720 atoms. 13976 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1966 (Rfree = 0.000) for 6720 atoms. Found 31 (43 requested) and removed 38 (21 requested) atoms. Cycle 37: After refmac, R = 0.1961 (Rfree = 0.000) for 6698 atoms. Found 34 (43 requested) and removed 31 (21 requested) atoms. Cycle 38: After refmac, R = 0.1944 (Rfree = 0.000) for 6692 atoms. Found 35 (42 requested) and removed 31 (21 requested) atoms. Cycle 39: After refmac, R = 0.1895 (Rfree = 0.000) for 6690 atoms. Found 40 (42 requested) and removed 26 (21 requested) atoms. Cycle 40: After refmac, R = 0.1862 (Rfree = 0.000) for 6701 atoms. Found 24 (43 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 6854 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6869 seeds are put forward Round 1: 335 peptides, 65 chains. Longest chain 11 peptides. Score 0.313 Round 2: 401 peptides, 65 chains. Longest chain 19 peptides. Score 0.425 Round 3: 411 peptides, 71 chains. Longest chain 13 peptides. Score 0.399 Round 4: 400 peptides, 62 chains. Longest chain 21 peptides. Score 0.445 Round 5: 407 peptides, 62 chains. Longest chain 28 peptides. Score 0.455 Taking the results from Round 5 Chains 62, Residues 345, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 15565 restraints for refining 6730 atoms. 14221 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2116 (Rfree = 0.000) for 6730 atoms. Found 40 (43 requested) and removed 36 (21 requested) atoms. Cycle 42: After refmac, R = 0.1898 (Rfree = 0.000) for 6715 atoms. Found 24 (43 requested) and removed 28 (21 requested) atoms. Cycle 43: After refmac, R = 0.1847 (Rfree = 0.000) for 6705 atoms. Found 23 (43 requested) and removed 31 (21 requested) atoms. Cycle 44: After refmac, R = 0.1951 (Rfree = 0.000) for 6689 atoms. Found 37 (42 requested) and removed 32 (21 requested) atoms. Cycle 45: After refmac, R = 0.1860 (Rfree = 0.000) for 6687 atoms. Found 33 (42 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 6902 seeds are put forward NCS extension: 43 residues added (2 deleted due to clashes), 6945 seeds are put forward Round 1: 333 peptides, 68 chains. Longest chain 10 peptides. Score 0.286 Round 2: 402 peptides, 69 chains. Longest chain 21 peptides. Score 0.399 Round 3: 382 peptides, 63 chains. Longest chain 15 peptides. Score 0.409 Round 4: 392 peptides, 63 chains. Longest chain 18 peptides. Score 0.425 Round 5: 405 peptides, 65 chains. Longest chain 20 peptides. Score 0.432 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 340, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vqy-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11704 reflections ( 98.35 % complete ) and 15649 restraints for refining 6730 atoms. 14302 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2054 (Rfree = 0.000) for 6730 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.1989 (Rfree = 0.000) for 6699 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.1929 (Rfree = 0.000) for 6658 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2010 (Rfree = 0.000) for 6627 atoms. TimeTaking 64.97