Mon 24 Dec 00:45:24 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 1vlu-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-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/1vlu-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-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 00:45:29 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/1vlu-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-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 909 and 0 Target number of residues in the AU: 909 Target solvent content: 0.6653 Checking the provided sequence file Detected sequence length: 468 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 936 Adjusted target solvent content: 0.66 Input MTZ file: 1vlu-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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.90 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: 44.569 4.000 Wilson plot Bfac: 88.66 12767 reflections ( 99.80 % complete ) and 0 restraints for refining 8323 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3407 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3337 (Rfree = 0.000) for 8323 atoms. Found 39 (39 requested) and removed 56 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 3.06 Search for helices and strands: 0 residues in 0 chains, 8513 seeds are put forward NCS extension: 0 residues added, 8513 seeds are put forward Round 1: 426 peptides, 64 chains. Longest chain 14 peptides. Score 0.396 Round 2: 484 peptides, 57 chains. Longest chain 21 peptides. Score 0.493 Round 3: 495 peptides, 50 chains. Longest chain 19 peptides. Score 0.537 Round 4: 488 peptides, 50 chains. Longest chain 24 peptides. Score 0.530 Round 5: 487 peptides, 51 chains. Longest chain 36 peptides. Score 0.525 Taking the results from Round 3 Chains 51, Residues 445, Estimated correctness of the model 0.0 % 4 chains (54 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 15396 restraints for refining 6753 atoms. 13483 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2633 (Rfree = 0.000) for 6753 atoms. Found 32 (32 requested) and removed 84 (16 requested) atoms. Cycle 2: After refmac, R = 0.2467 (Rfree = 0.000) for 6515 atoms. Found 31 (31 requested) and removed 63 (15 requested) atoms. Cycle 3: After refmac, R = 0.2396 (Rfree = 0.000) for 6404 atoms. Found 30 (30 requested) and removed 57 (15 requested) atoms. Cycle 4: After refmac, R = 0.2324 (Rfree = 0.000) for 6297 atoms. Found 30 (30 requested) and removed 47 (15 requested) atoms. Cycle 5: After refmac, R = 0.2204 (Rfree = 0.000) for 6242 atoms. Found 29 (29 requested) and removed 37 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.01 Search for helices and strands: 0 residues in 0 chains, 6541 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6555 seeds are put forward Round 1: 477 peptides, 65 chains. Longest chain 18 peptides. Score 0.447 Round 2: 494 peptides, 58 chains. Longest chain 26 peptides. Score 0.499 Round 3: 491 peptides, 57 chains. Longest chain 21 peptides. Score 0.501 Round 4: 494 peptides, 50 chains. Longest chain 22 peptides. Score 0.536 Round 5: 530 peptides, 56 chains. Longest chain 27 peptides. Score 0.543 Taking the results from Round 5 Chains 62, Residues 474, Estimated correctness of the model 0.0 % 7 chains (95 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14237 restraints for refining 6758 atoms. 12071 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2403 (Rfree = 0.000) for 6758 atoms. Found 32 (32 requested) and removed 102 (16 requested) atoms. Cycle 7: After refmac, R = 0.2186 (Rfree = 0.000) for 6576 atoms. Found 31 (31 requested) and removed 69 (15 requested) atoms. Cycle 8: After refmac, R = 0.2113 (Rfree = 0.000) for 6491 atoms. Found 30 (31 requested) and removed 59 (15 requested) atoms. Cycle 9: After refmac, R = 0.2049 (Rfree = 0.000) for 6432 atoms. Found 28 (30 requested) and removed 54 (15 requested) atoms. Cycle 10: After refmac, R = 0.2010 (Rfree = 0.000) for 6384 atoms. Found 18 (30 requested) and removed 58 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 2.99 Search for helices and strands: 0 residues in 0 chains, 6640 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6664 seeds are put forward Round 1: 474 peptides, 58 chains. Longest chain 28 peptides. Score 0.478 Round 2: 502 peptides, 57 chains. Longest chain 18 peptides. Score 0.511 Round 3: 498 peptides, 56 chains. Longest chain 19 peptides. Score 0.512 Round 4: 493 peptides, 59 chains. Longest chain 29 peptides. Score 0.493 Round 5: 519 peptides, 56 chains. Longest chain 26 peptides. Score 0.533 Taking the results from Round 5 Chains 56, Residues 463, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14871 restraints for refining 6762 atoms. 12973 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2504 (Rfree = 0.000) for 6762 atoms. Found 32 (32 requested) and removed 86 (16 requested) atoms. Cycle 12: After refmac, R = 0.2290 (Rfree = 0.000) for 6618 atoms. Found 31 (31 requested) and removed 58 (15 requested) atoms. Cycle 13: After refmac, R = 0.2229 (Rfree = 0.000) for 6524 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 14: After refmac, R = 0.2121 (Rfree = 0.000) for 6459 atoms. Found 30 (30 requested) and removed 41 (15 requested) atoms. Cycle 15: After refmac, R = 0.2043 (Rfree = 0.000) for 6410 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.00 Search for helices and strands: 0 residues in 0 chains, 6702 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 6734 seeds are put forward Round 1: 488 peptides, 72 chains. Longest chain 17 peptides. Score 0.425 Round 2: 516 peptides, 60 chains. Longest chain 29 peptides. Score 0.511 Round 3: 503 peptides, 52 chains. Longest chain 29 peptides. Score 0.536 Round 4: 514 peptides, 54 chains. Longest chain 29 peptides. Score 0.537 Round 5: 510 peptides, 56 chains. Longest chain 29 peptides. Score 0.524 Taking the results from Round 4 Chains 59, Residues 460, Estimated correctness of the model 0.0 % 6 chains (55 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14577 restraints for refining 6760 atoms. 12581 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2447 (Rfree = 0.000) for 6760 atoms. Found 32 (32 requested) and removed 75 (16 requested) atoms. Cycle 17: After refmac, R = 0.2371 (Rfree = 0.000) for 6655 atoms. Found 31 (31 requested) and removed 50 (15 requested) atoms. Cycle 18: After refmac, R = 0.2296 (Rfree = 0.000) for 6590 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 19: After refmac, R = 0.2239 (Rfree = 0.000) for 6549 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2246 (Rfree = 0.000) for 6524 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.79 3.04 Search for helices and strands: 0 residues in 0 chains, 6757 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 6777 seeds are put forward Round 1: 465 peptides, 74 chains. Longest chain 15 peptides. Score 0.389 Round 2: 492 peptides, 61 chains. Longest chain 20 peptides. Score 0.482 Round 3: 500 peptides, 60 chains. Longest chain 24 peptides. Score 0.495 Round 4: 496 peptides, 52 chains. Longest chain 22 peptides. Score 0.529 Round 5: 494 peptides, 52 chains. Longest chain 22 peptides. Score 0.527 Taking the results from Round 4 Chains 53, Residues 444, Estimated correctness of the model 0.0 % 4 chains (60 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14924 restraints for refining 6759 atoms. 12976 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2387 (Rfree = 0.000) for 6759 atoms. Found 32 (32 requested) and removed 59 (16 requested) atoms. Cycle 22: After refmac, R = 0.2310 (Rfree = 0.000) for 6660 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 23: After refmac, R = 0.2241 (Rfree = 0.000) for 6617 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. Cycle 24: After refmac, R = 0.2204 (Rfree = 0.000) for 6569 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 25: After refmac, R = 0.2217 (Rfree = 0.000) for 6525 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.04 Search for helices and strands: 0 residues in 0 chains, 6759 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 6789 seeds are put forward Round 1: 453 peptides, 65 chains. Longest chain 22 peptides. Score 0.421 Round 2: 489 peptides, 61 chains. Longest chain 18 peptides. Score 0.479 Round 3: 496 peptides, 59 chains. Longest chain 20 peptides. Score 0.496 Round 4: 511 peptides, 61 chains. Longest chain 21 peptides. Score 0.502 Round 5: 494 peptides, 61 chains. Longest chain 23 peptides. Score 0.485 Taking the results from Round 4 Chains 63, Residues 450, Estimated correctness of the model 0.0 % 5 chains (53 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14975 restraints for refining 6761 atoms. 13070 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2658 (Rfree = 0.000) for 6761 atoms. Found 32 (32 requested) and removed 85 (16 requested) atoms. Cycle 27: After refmac, R = 0.2491 (Rfree = 0.000) for 6626 atoms. Found 31 (31 requested) and removed 52 (15 requested) atoms. Cycle 28: After refmac, R = 0.2299 (Rfree = 0.000) for 6556 atoms. Found 31 (31 requested) and removed 41 (15 requested) atoms. Cycle 29: After refmac, R = 0.2204 (Rfree = 0.000) for 6491 atoms. Found 31 (31 requested) and removed 44 (15 requested) atoms. Cycle 30: After refmac, R = 0.2203 (Rfree = 0.000) for 6450 atoms. Found 30 (30 requested) and removed 34 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 3.05 Search for helices and strands: 0 residues in 0 chains, 6656 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6675 seeds are put forward Round 1: 415 peptides, 67 chains. Longest chain 12 peptides. Score 0.367 Round 2: 474 peptides, 62 chains. Longest chain 32 peptides. Score 0.459 Round 3: 493 peptides, 67 chains. Longest chain 20 peptides. Score 0.455 Round 4: 497 peptides, 61 chains. Longest chain 29 peptides. Score 0.488 Round 5: 492 peptides, 65 chains. Longest chain 26 peptides. Score 0.463 Taking the results from Round 4 Chains 62, Residues 436, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 15105 restraints for refining 6744 atoms. 13346 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2648 (Rfree = 0.000) for 6744 atoms. Found 32 (32 requested) and removed 77 (16 requested) atoms. Cycle 32: After refmac, R = 0.2433 (Rfree = 0.000) for 6633 atoms. Found 31 (31 requested) and removed 46 (15 requested) atoms. Cycle 33: After refmac, R = 0.2383 (Rfree = 0.000) for 6580 atoms. Found 31 (31 requested) and removed 38 (15 requested) atoms. Cycle 34: After refmac, R = 0.2437 (Rfree = 0.000) for 6526 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 35: After refmac, R = 0.2084 (Rfree = 0.000) for 6487 atoms. Found 20 (30 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.04 Search for helices and strands: 0 residues in 0 chains, 6728 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 6742 seeds are put forward Round 1: 428 peptides, 70 chains. Longest chain 16 peptides. Score 0.366 Round 2: 482 peptides, 65 chains. Longest chain 16 peptides. Score 0.453 Round 3: 470 peptides, 62 chains. Longest chain 23 peptides. Score 0.455 Round 4: 480 peptides, 61 chains. Longest chain 25 peptides. Score 0.470 Round 5: 482 peptides, 65 chains. Longest chain 18 peptides. Score 0.453 Taking the results from Round 4 Chains 61, Residues 419, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14901 restraints for refining 6679 atoms. 13222 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2550 (Rfree = 0.000) for 6679 atoms. Found 31 (31 requested) and removed 68 (15 requested) atoms. Cycle 37: After refmac, R = 0.2428 (Rfree = 0.000) for 6583 atoms. Found 31 (31 requested) and removed 56 (15 requested) atoms. Cycle 38: After refmac, R = 0.2336 (Rfree = 0.000) for 6523 atoms. Found 31 (31 requested) and removed 50 (15 requested) atoms. Cycle 39: After refmac, R = 0.2278 (Rfree = 0.000) for 6478 atoms. Found 30 (30 requested) and removed 42 (15 requested) atoms. Cycle 40: After refmac, R = 0.2247 (Rfree = 0.000) for 6446 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.06 Search for helices and strands: 0 residues in 0 chains, 6734 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 6763 seeds are put forward Round 1: 406 peptides, 69 chains. Longest chain 15 peptides. Score 0.345 Round 2: 476 peptides, 70 chains. Longest chain 17 peptides. Score 0.421 Round 3: 459 peptides, 60 chains. Longest chain 18 peptides. Score 0.453 Round 4: 482 peptides, 62 chains. Longest chain 21 peptides. Score 0.467 Round 5: 459 peptides, 59 chains. Longest chain 22 peptides. Score 0.458 Taking the results from Round 4 Chains 65, Residues 420, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14820 restraints for refining 6761 atoms. 13082 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2398 (Rfree = 0.000) for 6761 atoms. Found 32 (32 requested) and removed 53 (16 requested) atoms. Cycle 42: After refmac, R = 0.2310 (Rfree = 0.000) for 6697 atoms. Found 32 (32 requested) and removed 47 (16 requested) atoms. Cycle 43: After refmac, R = 0.2328 (Rfree = 0.000) for 6643 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 44: After refmac, R = 0.2256 (Rfree = 0.000) for 6583 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 45: After refmac, R = 0.1879 (Rfree = 0.000) for 6537 atoms. Found 18 (31 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.02 Search for helices and strands: 0 residues in 0 chains, 6786 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6808 seeds are put forward Round 1: 399 peptides, 69 chains. Longest chain 16 peptides. Score 0.337 Round 2: 426 peptides, 58 chains. Longest chain 21 peptides. Score 0.427 Round 3: 436 peptides, 57 chains. Longest chain 28 peptides. Score 0.443 Round 4: 449 peptides, 58 chains. Longest chain 21 peptides. Score 0.452 Round 5: 460 peptides, 60 chains. Longest chain 18 peptides. Score 0.454 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 400, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vlu-4_warpNtrace.pdb as input Building loops using Loopy2018 60 chains (400 residues) following loop building 4 chains (26 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12767 reflections ( 99.80 % complete ) and 15344 restraints for refining 6762 atoms. 13730 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2438 (Rfree = 0.000) for 6762 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2319 (Rfree = 0.000) for 6694 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2295 (Rfree = 0.000) for 6651 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2290 (Rfree = 0.000) for 6602 atoms. TimeTaking 75.93