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 1vlu-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-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/1vlu-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-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/1vlu-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-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 1001 and 0 Target number of residues in the AU: 1001 Target solvent content: 0.6314 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-3.4-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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.85 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 3.400 Wilson plot Bfac: 67.14 20628 reflections ( 99.87 % complete ) and 0 restraints for refining 8336 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Starting model: R = 0.3333 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3042 (Rfree = 0.000) for 8336 atoms. Found 62 (62 requested) and removed 81 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 2.65 Search for helices and strands: 0 residues in 0 chains, 8497 seeds are put forward NCS extension: 0 residues added, 8497 seeds are put forward Round 1: 469 peptides, 63 chains. Longest chain 27 peptides. Score 0.449 Round 2: 537 peptides, 69 chains. Longest chain 28 peptides. Score 0.491 Round 3: 575 peptides, 58 chains. Longest chain 30 peptides. Score 0.575 Round 4: 576 peptides, 61 chains. Longest chain 36 peptides. Score 0.563 Round 5: 569 peptides, 58 chains. Longest chain 38 peptides. Score 0.570 Taking the results from Round 3 Chains 67, Residues 517, Estimated correctness of the model 20.3 % 7 chains (96 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14323 restraints for refining 6799 atoms. 11994 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2574 (Rfree = 0.000) for 6799 atoms. Found 51 (51 requested) and removed 47 (25 requested) atoms. Cycle 2: After refmac, R = 0.2414 (Rfree = 0.000) for 6613 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. Cycle 3: After refmac, R = 0.2300 (Rfree = 0.000) for 6540 atoms. Found 40 (49 requested) and removed 30 (24 requested) atoms. Cycle 4: After refmac, R = 0.2265 (Rfree = 0.000) for 6500 atoms. Found 39 (49 requested) and removed 34 (24 requested) atoms. Cycle 5: After refmac, R = 0.2191 (Rfree = 0.000) for 6474 atoms. Found 23 (49 requested) and removed 29 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 2.65 Search for helices and strands: 0 residues in 0 chains, 6717 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 6746 seeds are put forward Round 1: 532 peptides, 64 chains. Longest chain 37 peptides. Score 0.509 Round 2: 556 peptides, 59 chains. Longest chain 38 peptides. Score 0.554 Round 3: 592 peptides, 56 chains. Longest chain 42 peptides. Score 0.598 Round 4: 596 peptides, 65 chains. Longest chain 38 peptides. Score 0.564 Round 5: 591 peptides, 63 chains. Longest chain 38 peptides. Score 0.568 Taking the results from Round 3 Chains 66, Residues 536, Estimated correctness of the model 28.0 % 9 chains (170 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 12646 restraints for refining 6625 atoms. 9907 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2613 (Rfree = 0.000) for 6625 atoms. Found 50 (50 requested) and removed 67 (25 requested) atoms. Cycle 7: After refmac, R = 0.2445 (Rfree = 0.000) for 6554 atoms. Found 29 (49 requested) and removed 40 (24 requested) atoms. Cycle 8: After refmac, R = 0.2381 (Rfree = 0.000) for 6510 atoms. Found 26 (49 requested) and removed 31 (24 requested) atoms. Cycle 9: After refmac, R = 0.2351 (Rfree = 0.000) for 6482 atoms. Found 25 (49 requested) and removed 33 (24 requested) atoms. Cycle 10: After refmac, R = 0.2300 (Rfree = 0.000) for 6457 atoms. Found 13 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 2.65 Search for helices and strands: 0 residues in 0 chains, 6675 seeds are put forward NCS extension: 29 residues added (8 deleted due to clashes), 6704 seeds are put forward Round 1: 524 peptides, 63 chains. Longest chain 33 peptides. Score 0.505 Round 2: 576 peptides, 58 chains. Longest chain 36 peptides. Score 0.576 Round 3: 596 peptides, 63 chains. Longest chain 32 peptides. Score 0.573 Round 4: 563 peptides, 63 chains. Longest chain 29 peptides. Score 0.543 Round 5: 574 peptides, 62 chains. Longest chain 35 peptides. Score 0.557 Taking the results from Round 2 Chains 64, Residues 518, Estimated correctness of the model 20.7 % 10 chains (150 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13316 restraints for refining 6782 atoms. 10751 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2609 (Rfree = 0.000) for 6782 atoms. Found 51 (51 requested) and removed 61 (25 requested) atoms. Cycle 12: After refmac, R = 0.2489 (Rfree = 0.000) for 6715 atoms. Found 47 (51 requested) and removed 45 (25 requested) atoms. Cycle 13: After refmac, R = 0.2407 (Rfree = 0.000) for 6684 atoms. Found 39 (50 requested) and removed 40 (25 requested) atoms. Cycle 14: After refmac, R = 0.2320 (Rfree = 0.000) for 6652 atoms. Found 24 (50 requested) and removed 44 (25 requested) atoms. Cycle 15: After refmac, R = 0.2280 (Rfree = 0.000) for 6597 atoms. Found 29 (50 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 2.65 Search for helices and strands: 0 residues in 0 chains, 6838 seeds are put forward NCS extension: 39 residues added (19 deleted due to clashes), 6877 seeds are put forward Round 1: 544 peptides, 68 chains. Longest chain 23 peptides. Score 0.502 Round 2: 567 peptides, 61 chains. Longest chain 33 peptides. Score 0.555 Round 3: 582 peptides, 59 chains. Longest chain 36 peptides. Score 0.577 Round 4: 585 peptides, 61 chains. Longest chain 51 peptides. Score 0.571 Round 5: 593 peptides, 65 chains. Longest chain 38 peptides. Score 0.562 Taking the results from Round 3 Chains 67, Residues 523, Estimated correctness of the model 21.0 % 7 chains (123 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13634 restraints for refining 6809 atoms. 11155 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2534 (Rfree = 0.000) for 6809 atoms. Found 51 (51 requested) and removed 60 (25 requested) atoms. Cycle 17: After refmac, R = 0.2397 (Rfree = 0.000) for 6762 atoms. Found 24 (51 requested) and removed 45 (25 requested) atoms. Cycle 18: After refmac, R = 0.2355 (Rfree = 0.000) for 6715 atoms. Found 29 (50 requested) and removed 39 (25 requested) atoms. Cycle 19: After refmac, R = 0.2320 (Rfree = 0.000) for 6689 atoms. Found 19 (50 requested) and removed 34 (25 requested) atoms. Cycle 20: After refmac, R = 0.2272 (Rfree = 0.000) for 6664 atoms. Found 17 (50 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 2.66 Search for helices and strands: 0 residues in 0 chains, 6915 seeds are put forward NCS extension: 29 residues added (7 deleted due to clashes), 6944 seeds are put forward Round 1: 523 peptides, 66 chains. Longest chain 22 peptides. Score 0.490 Round 2: 565 peptides, 62 chains. Longest chain 23 peptides. Score 0.549 Round 3: 576 peptides, 57 chains. Longest chain 36 peptides. Score 0.580 Round 4: 580 peptides, 63 chains. Longest chain 33 peptides. Score 0.558 Round 5: 584 peptides, 63 chains. Longest chain 29 peptides. Score 0.562 Taking the results from Round 3 Chains 67, Residues 519, Estimated correctness of the model 22.0 % 11 chains (164 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13426 restraints for refining 6806 atoms. 10807 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2665 (Rfree = 0.000) for 6806 atoms. Found 51 (51 requested) and removed 62 (25 requested) atoms. Cycle 22: After refmac, R = 0.2529 (Rfree = 0.000) for 6737 atoms. Found 41 (51 requested) and removed 44 (25 requested) atoms. Cycle 23: After refmac, R = 0.2460 (Rfree = 0.000) for 6698 atoms. Found 31 (50 requested) and removed 45 (25 requested) atoms. Cycle 24: After refmac, R = 0.2387 (Rfree = 0.000) for 6658 atoms. Found 26 (50 requested) and removed 39 (25 requested) atoms. Cycle 25: After refmac, R = 0.2331 (Rfree = 0.000) for 6628 atoms. Found 17 (50 requested) and removed 30 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 2.65 Search for helices and strands: 0 residues in 0 chains, 6865 seeds are put forward NCS extension: 23 residues added (6 deleted due to clashes), 6888 seeds are put forward Round 1: 542 peptides, 70 chains. Longest chain 30 peptides. Score 0.491 Round 2: 569 peptides, 58 chains. Longest chain 33 peptides. Score 0.570 Round 3: 583 peptides, 64 chains. Longest chain 35 peptides. Score 0.557 Round 4: 583 peptides, 62 chains. Longest chain 33 peptides. Score 0.565 Round 5: 550 peptides, 59 chains. Longest chain 34 peptides. Score 0.548 Taking the results from Round 2 Chains 62, Residues 511, Estimated correctness of the model 18.6 % 8 chains (133 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13547 restraints for refining 6809 atoms. 11065 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2548 (Rfree = 0.000) for 6809 atoms. Found 51 (51 requested) and removed 46 (25 requested) atoms. Cycle 27: After refmac, R = 0.2439 (Rfree = 0.000) for 6775 atoms. Found 22 (51 requested) and removed 39 (25 requested) atoms. Cycle 28: After refmac, R = 0.2404 (Rfree = 0.000) for 6737 atoms. Found 28 (51 requested) and removed 33 (25 requested) atoms. Cycle 29: After refmac, R = 0.2366 (Rfree = 0.000) for 6725 atoms. Found 17 (50 requested) and removed 32 (25 requested) atoms. Cycle 30: After refmac, R = 0.2375 (Rfree = 0.000) for 6695 atoms. Found 24 (50 requested) and removed 27 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 2.65 Search for helices and strands: 0 residues in 0 chains, 6940 seeds are put forward NCS extension: 16 residues added (12 deleted due to clashes), 6956 seeds are put forward Round 1: 525 peptides, 70 chains. Longest chain 34 peptides. Score 0.474 Round 2: 555 peptides, 67 chains. Longest chain 35 peptides. Score 0.517 Round 3: 571 peptides, 66 chains. Longest chain 28 peptides. Score 0.537 Round 4: 546 peptides, 62 chains. Longest chain 24 peptides. Score 0.531 Round 5: 565 peptides, 66 chains. Longest chain 34 peptides. Score 0.531 Taking the results from Round 3 Chains 70, Residues 505, Estimated correctness of the model 6.8 % 8 chains (117 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14043 restraints for refining 6808 atoms. 11663 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2652 (Rfree = 0.000) for 6808 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. Cycle 32: After refmac, R = 0.2510 (Rfree = 0.000) for 6773 atoms. Found 22 (51 requested) and removed 35 (25 requested) atoms. Cycle 33: After refmac, R = 0.2461 (Rfree = 0.000) for 6735 atoms. Found 20 (51 requested) and removed 30 (25 requested) atoms. Cycle 34: After refmac, R = 0.2441 (Rfree = 0.000) for 6711 atoms. Found 13 (50 requested) and removed 28 (25 requested) atoms. Cycle 35: After refmac, R = 0.2372 (Rfree = 0.000) for 6684 atoms. Found 12 (50 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 2.66 Search for helices and strands: 0 residues in 0 chains, 6911 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6930 seeds are put forward Round 1: 485 peptides, 77 chains. Longest chain 19 peptides. Score 0.396 Round 2: 528 peptides, 68 chains. Longest chain 28 peptides. Score 0.486 Round 3: 517 peptides, 66 chains. Longest chain 24 peptides. Score 0.484 Round 4: 560 peptides, 70 chains. Longest chain 24 peptides. Score 0.509 Round 5: 533 peptides, 68 chains. Longest chain 23 peptides. Score 0.491 Taking the results from Round 4 Chains 71, Residues 490, Estimated correctness of the model 0.0 % 7 chains (71 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14593 restraints for refining 6808 atoms. 12442 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2599 (Rfree = 0.000) for 6808 atoms. Found 36 (51 requested) and removed 49 (25 requested) atoms. Cycle 37: After refmac, R = 0.2426 (Rfree = 0.000) for 6764 atoms. Found 25 (51 requested) and removed 31 (25 requested) atoms. Cycle 38: After refmac, R = 0.2366 (Rfree = 0.000) for 6740 atoms. Found 23 (51 requested) and removed 30 (25 requested) atoms. Cycle 39: After refmac, R = 0.2310 (Rfree = 0.000) for 6723 atoms. Found 19 (50 requested) and removed 29 (25 requested) atoms. Cycle 40: After refmac, R = 0.2282 (Rfree = 0.000) for 6703 atoms. Found 15 (50 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 2.66 Search for helices and strands: 0 residues in 0 chains, 6950 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6969 seeds are put forward Round 1: 477 peptides, 73 chains. Longest chain 19 peptides. Score 0.407 Round 2: 506 peptides, 68 chains. Longest chain 26 peptides. Score 0.463 Round 3: 523 peptides, 63 chains. Longest chain 32 peptides. Score 0.504 Round 4: 500 peptides, 62 chains. Longest chain 31 peptides. Score 0.486 Round 5: 502 peptides, 63 chains. Longest chain 19 peptides. Score 0.483 Taking the results from Round 3 Chains 71, Residues 460, Estimated correctness of the model 0.0 % 8 chains (83 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14704 restraints for refining 6809 atoms. 12643 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2540 (Rfree = 0.000) for 6809 atoms. Found 51 (51 requested) and removed 35 (25 requested) atoms. Cycle 42: After refmac, R = 0.2412 (Rfree = 0.000) for 6792 atoms. Found 22 (51 requested) and removed 33 (25 requested) atoms. Cycle 43: After refmac, R = 0.2405 (Rfree = 0.000) for 6764 atoms. Found 23 (51 requested) and removed 28 (25 requested) atoms. Cycle 44: After refmac, R = 0.2354 (Rfree = 0.000) for 6746 atoms. Found 14 (51 requested) and removed 28 (25 requested) atoms. Cycle 45: After refmac, R = 0.2325 (Rfree = 0.000) for 6722 atoms. Found 11 (50 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 2.66 Search for helices and strands: 0 residues in 0 chains, 6948 seeds are put forward NCS extension: 15 residues added (9 deleted due to clashes), 6963 seeds are put forward Round 1: 461 peptides, 69 chains. Longest chain 18 peptides. Score 0.410 Round 2: 501 peptides, 62 chains. Longest chain 30 peptides. Score 0.487 Round 3: 508 peptides, 61 chains. Longest chain 25 peptides. Score 0.499 Round 4: 507 peptides, 59 chains. Longest chain 35 peptides. Score 0.507 Round 5: 513 peptides, 60 chains. Longest chain 37 peptides. Score 0.508 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 453, Estimated correctness of the model 0.0 % 3 chains (72 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 62 chains (453 residues) following loop building 3 chains (72 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20628 reflections ( 99.87 % complete ) and 14601 restraints for refining 6807 atoms. 12573 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2604 (Rfree = 0.000) for 6807 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 47: After refmac, R = 0.2521 (Rfree = 0.000) for 6753 atoms. Found 0 (51 requested) and removed 13 (25 requested) atoms. Cycle 48: After refmac, R = 0.2454 (Rfree = 0.000) for 6730 atoms. Found 0 (50 requested) and removed 10 (25 requested) atoms. Cycle 49: After refmac, R = 0.2397 (Rfree = 0.000) for 6707 atoms. Found 0 (50 requested) and removed 6 (25 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:00:54 GMT 2018 Job finished. TimeTaking 98.22 Used memory is bytes: 21080960