Sun 23 Dec 23:56:35 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.6-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 ============================================================ Sun 23 Dec 23:56:40 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.6-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 975 and 0 Target number of residues in the AU: 975 Target solvent content: 0.6410 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 72.53 17421 reflections ( 99.85 % complete ) and 0 restraints for refining 8252 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3348 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2900 (Rfree = 0.000) for 8252 atoms. Found 52 (52 requested) and removed 49 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 2.81 Search for helices and strands: 0 residues in 0 chains, 8433 seeds are put forward NCS extension: 0 residues added, 8433 seeds are put forward Round 1: 444 peptides, 65 chains. Longest chain 18 peptides. Score 0.411 Round 2: 542 peptides, 59 chains. Longest chain 28 peptides. Score 0.541 Round 3: 547 peptides, 58 chains. Longest chain 31 peptides. Score 0.550 Round 4: 551 peptides, 60 chains. Longest chain 32 peptides. Score 0.545 Round 5: 561 peptides, 54 chains. Longest chain 30 peptides. Score 0.580 Taking the results from Round 5 Chains 56, Residues 507, Estimated correctness of the model 6.7 % 5 chains (77 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14281 restraints for refining 6770 atoms. 12037 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2634 (Rfree = 0.000) for 6770 atoms. Found 43 (43 requested) and removed 60 (21 requested) atoms. Cycle 2: After refmac, R = 0.2450 (Rfree = 0.000) for 6602 atoms. Found 43 (43 requested) and removed 38 (21 requested) atoms. Cycle 3: After refmac, R = 0.2402 (Rfree = 0.000) for 6534 atoms. Found 36 (42 requested) and removed 49 (21 requested) atoms. Cycle 4: After refmac, R = 0.2368 (Rfree = 0.000) for 6477 atoms. Found 36 (41 requested) and removed 32 (20 requested) atoms. Cycle 5: After refmac, R = 0.2328 (Rfree = 0.000) for 6428 atoms. Found 37 (41 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 2.76 Search for helices and strands: 0 residues in 0 chains, 6696 seeds are put forward NCS extension: 34 residues added (8 deleted due to clashes), 6730 seeds are put forward Round 1: 526 peptides, 67 chains. Longest chain 32 peptides. Score 0.489 Round 2: 567 peptides, 60 chains. Longest chain 26 peptides. Score 0.559 Round 3: 554 peptides, 53 chains. Longest chain 26 peptides. Score 0.578 Round 4: 563 peptides, 56 chains. Longest chain 34 peptides. Score 0.573 Round 5: 554 peptides, 61 chains. Longest chain 24 peptides. Score 0.543 Taking the results from Round 3 Chains 59, Residues 501, Estimated correctness of the model 5.9 % 7 chains (88 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14057 restraints for refining 6744 atoms. 11816 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2538 (Rfree = 0.000) for 6744 atoms. Found 43 (43 requested) and removed 73 (21 requested) atoms. Cycle 7: After refmac, R = 0.2308 (Rfree = 0.000) for 6656 atoms. Found 18 (43 requested) and removed 45 (21 requested) atoms. Cycle 8: After refmac, R = 0.2203 (Rfree = 0.000) for 6597 atoms. Found 8 (42 requested) and removed 30 (21 requested) atoms. Cycle 9: After refmac, R = 0.2152 (Rfree = 0.000) for 6557 atoms. Found 19 (42 requested) and removed 32 (21 requested) atoms. Cycle 10: After refmac, R = 0.2073 (Rfree = 0.000) for 6536 atoms. Found 17 (41 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 2.81 Search for helices and strands: 0 residues in 0 chains, 6783 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 6810 seeds are put forward Round 1: 529 peptides, 66 chains. Longest chain 27 peptides. Score 0.496 Round 2: 552 peptides, 58 chains. Longest chain 31 peptides. Score 0.554 Round 3: 568 peptides, 63 chains. Longest chain 22 peptides. Score 0.547 Round 4: 575 peptides, 58 chains. Longest chain 25 peptides. Score 0.575 Round 5: 575 peptides, 55 chains. Longest chain 36 peptides. Score 0.588 Taking the results from Round 5 Chains 66, Residues 520, Estimated correctness of the model 9.9 % 8 chains (115 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 13669 restraints for refining 6785 atoms. 11230 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2510 (Rfree = 0.000) for 6785 atoms. Found 43 (43 requested) and removed 54 (21 requested) atoms. Cycle 12: After refmac, R = 0.2272 (Rfree = 0.000) for 6712 atoms. Found 18 (43 requested) and removed 42 (21 requested) atoms. Cycle 13: After refmac, R = 0.2226 (Rfree = 0.000) for 6655 atoms. Found 28 (42 requested) and removed 37 (21 requested) atoms. Cycle 14: After refmac, R = 0.2145 (Rfree = 0.000) for 6628 atoms. Found 18 (42 requested) and removed 30 (21 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2119 (Rfree = 0.000) for 6586 atoms. Found 29 (42 requested) and removed 34 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 2.76 Search for helices and strands: 0 residues in 0 chains, 6815 seeds are put forward NCS extension: 28 residues added (6 deleted due to clashes), 6843 seeds are put forward Round 1: 547 peptides, 69 chains. Longest chain 23 peptides. Score 0.501 Round 2: 574 peptides, 64 chains. Longest chain 32 peptides. Score 0.549 Round 3: 562 peptides, 58 chains. Longest chain 44 peptides. Score 0.564 Round 4: 566 peptides, 58 chains. Longest chain 45 peptides. Score 0.567 Round 5: 551 peptides, 59 chains. Longest chain 29 peptides. Score 0.549 Taking the results from Round 4 Chains 60, Residues 508, Estimated correctness of the model 1.3 % 5 chains (103 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 13782 restraints for refining 6788 atoms. 11419 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2419 (Rfree = 0.000) for 6788 atoms. Found 43 (43 requested) and removed 61 (21 requested) atoms. Cycle 17: After refmac, R = 0.2179 (Rfree = 0.000) for 6713 atoms. Found 11 (43 requested) and removed 37 (21 requested) atoms. Cycle 18: After refmac, R = 0.2129 (Rfree = 0.000) for 6670 atoms. Found 25 (42 requested) and removed 41 (21 requested) atoms. Cycle 19: After refmac, R = 0.2086 (Rfree = 0.000) for 6642 atoms. Found 20 (42 requested) and removed 30 (21 requested) atoms. Cycle 20: After refmac, R = 0.2022 (Rfree = 0.000) for 6625 atoms. Found 14 (42 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 2.77 Search for helices and strands: 0 residues in 0 chains, 6864 seeds are put forward NCS extension: 35 residues added (14 deleted due to clashes), 6899 seeds are put forward Round 1: 536 peptides, 76 chains. Longest chain 24 peptides. Score 0.457 Round 2: 560 peptides, 67 chains. Longest chain 39 peptides. Score 0.522 Round 3: 565 peptides, 68 chains. Longest chain 27 peptides. Score 0.523 Round 4: 557 peptides, 63 chains. Longest chain 38 peptides. Score 0.537 Round 5: 534 peptides, 60 chains. Longest chain 38 peptides. Score 0.529 Taking the results from Round 4 Chains 68, Residues 494, Estimated correctness of the model 0.0 % 7 chains (81 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14284 restraints for refining 6786 atoms. 12112 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2305 (Rfree = 0.000) for 6786 atoms. Found 36 (43 requested) and removed 45 (21 requested) atoms. Cycle 22: After refmac, R = 0.2158 (Rfree = 0.000) for 6737 atoms. Found 32 (43 requested) and removed 35 (21 requested) atoms. Cycle 23: After refmac, R = 0.2094 (Rfree = 0.000) for 6714 atoms. Found 23 (43 requested) and removed 31 (21 requested) atoms. Cycle 24: After refmac, R = 0.2064 (Rfree = 0.000) for 6691 atoms. Found 18 (43 requested) and removed 31 (21 requested) atoms. Cycle 25: After refmac, R = 0.2012 (Rfree = 0.000) for 6667 atoms. Found 11 (42 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 2.80 Search for helices and strands: 0 residues in 0 chains, 6900 seeds are put forward NCS extension: 14 residues added (6 deleted due to clashes), 6914 seeds are put forward Round 1: 504 peptides, 70 chains. Longest chain 25 peptides. Score 0.452 Round 2: 537 peptides, 66 chains. Longest chain 24 peptides. Score 0.504 Round 3: 532 peptides, 60 chains. Longest chain 35 peptides. Score 0.527 Round 4: 551 peptides, 58 chains. Longest chain 37 peptides. Score 0.553 Round 5: 552 peptides, 62 chains. Longest chain 31 peptides. Score 0.537 Taking the results from Round 4 Chains 61, Residues 493, Estimated correctness of the model 0.0 % 5 chains (93 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14025 restraints for refining 6788 atoms. 11744 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2453 (Rfree = 0.000) for 6788 atoms. Found 43 (43 requested) and removed 44 (21 requested) atoms. Cycle 27: After refmac, R = 0.2298 (Rfree = 0.000) for 6702 atoms. Found 38 (43 requested) and removed 31 (21 requested) atoms. Cycle 28: After refmac, R = 0.2220 (Rfree = 0.000) for 6670 atoms. Found 30 (43 requested) and removed 30 (21 requested) atoms. Cycle 29: After refmac, R = 0.2116 (Rfree = 0.000) for 6644 atoms. Found 18 (42 requested) and removed 28 (21 requested) atoms. Cycle 30: After refmac, R = 0.2087 (Rfree = 0.000) for 6615 atoms. Found 10 (42 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 2.80 Search for helices and strands: 0 residues in 0 chains, 6825 seeds are put forward NCS extension: 10 residues added (6 deleted due to clashes), 6835 seeds are put forward Round 1: 487 peptides, 69 chains. Longest chain 18 peptides. Score 0.438 Round 2: 515 peptides, 68 chains. Longest chain 22 peptides. Score 0.473 Round 3: 516 peptides, 61 chains. Longest chain 23 peptides. Score 0.507 Round 4: 526 peptides, 65 chains. Longest chain 32 peptides. Score 0.498 Round 5: 518 peptides, 59 chains. Longest chain 25 peptides. Score 0.518 Taking the results from Round 5 Chains 62, Residues 459, Estimated correctness of the model 0.0 % 6 chains (64 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14751 restraints for refining 6786 atoms. 12745 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2434 (Rfree = 0.000) for 6786 atoms. Found 40 (43 requested) and removed 36 (21 requested) atoms. Cycle 32: After refmac, R = 0.2270 (Rfree = 0.000) for 6765 atoms. Found 12 (43 requested) and removed 36 (21 requested) atoms. Cycle 33: After refmac, R = 0.2233 (Rfree = 0.000) for 6727 atoms. Found 14 (43 requested) and removed 40 (21 requested) atoms. Cycle 34: After refmac, R = 0.2188 (Rfree = 0.000) for 6690 atoms. Found 10 (42 requested) and removed 27 (21 requested) atoms. Cycle 35: After refmac, R = 0.2166 (Rfree = 0.000) for 6665 atoms. Found 11 (42 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 2.81 Search for helices and strands: 0 residues in 0 chains, 6879 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6898 seeds are put forward Round 1: 475 peptides, 68 chains. Longest chain 16 peptides. Score 0.430 Round 2: 518 peptides, 59 chains. Longest chain 37 peptides. Score 0.518 Round 3: 543 peptides, 60 chains. Longest chain 39 peptides. Score 0.537 Round 4: 533 peptides, 57 chains. Longest chain 40 peptides. Score 0.541 Round 5: 533 peptides, 57 chains. Longest chain 31 peptides. Score 0.541 Taking the results from Round 5 Chains 57, Residues 476, Estimated correctness of the model 0.0 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14865 restraints for refining 6788 atoms. 12869 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2587 (Rfree = 0.000) for 6788 atoms. Found 43 (43 requested) and removed 35 (21 requested) atoms. Cycle 37: After refmac, R = 0.2436 (Rfree = 0.000) for 6778 atoms. Found 23 (43 requested) and removed 36 (21 requested) atoms. Cycle 38: After refmac, R = 0.2385 (Rfree = 0.000) for 6752 atoms. Found 15 (43 requested) and removed 29 (21 requested) atoms. Cycle 39: After refmac, R = 0.2408 (Rfree = 0.000) for 6729 atoms. Found 17 (43 requested) and removed 32 (21 requested) atoms. Cycle 40: After refmac, R = 0.2356 (Rfree = 0.000) for 6705 atoms. Found 16 (43 requested) and removed 30 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 2.80 Search for helices and strands: 0 residues in 0 chains, 6927 seeds are put forward NCS extension: 44 residues added (3 deleted due to clashes), 6971 seeds are put forward Round 1: 442 peptides, 69 chains. Longest chain 14 peptides. Score 0.388 Round 2: 495 peptides, 61 chains. Longest chain 27 peptides. Score 0.486 Round 3: 498 peptides, 61 chains. Longest chain 25 peptides. Score 0.489 Round 4: 496 peptides, 56 chains. Longest chain 30 peptides. Score 0.510 Round 5: 493 peptides, 59 chains. Longest chain 22 peptides. Score 0.493 Taking the results from Round 4 Chains 59, Residues 440, Estimated correctness of the model 0.0 % 6 chains (61 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14786 restraints for refining 6787 atoms. 12872 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2614 (Rfree = 0.000) for 6787 atoms. Found 43 (43 requested) and removed 40 (21 requested) atoms. Cycle 42: After refmac, R = 0.2559 (Rfree = 0.000) for 6759 atoms. Found 27 (43 requested) and removed 38 (21 requested) atoms. Cycle 43: After refmac, R = 0.2469 (Rfree = 0.000) for 6733 atoms. Found 24 (43 requested) and removed 35 (21 requested) atoms. Cycle 44: After refmac, R = 0.2426 (Rfree = 0.000) for 6712 atoms. Found 16 (43 requested) and removed 31 (21 requested) atoms. Cycle 45: After refmac, R = 0.2362 (Rfree = 0.000) for 6687 atoms. Found 26 (42 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 2.84 Search for helices and strands: 0 residues in 0 chains, 6951 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 6979 seeds are put forward Round 1: 421 peptides, 70 chains. Longest chain 22 peptides. Score 0.358 Round 2: 468 peptides, 66 chains. Longest chain 22 peptides. Score 0.433 Round 3: 477 peptides, 63 chains. Longest chain 19 peptides. Score 0.457 Round 4: 456 peptides, 64 chains. Longest chain 19 peptides. Score 0.429 Round 5: 476 peptides, 60 chains. Longest chain 19 peptides. Score 0.471 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 416, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (416 residues) following loop building 4 chains (30 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17421 reflections ( 99.85 % complete ) and 15580 restraints for refining 6788 atoms. 13875 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2659 (Rfree = 0.000) for 6788 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.2616 (Rfree = 0.000) for 6739 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.2578 (Rfree = 0.000) for 6704 atoms. Found 0 (43 requested) and removed 12 (21 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2514 (Rfree = 0.000) for 6683 atoms. TimeTaking 91.33