Mon 24 Dec 00:14:45 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.8-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-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.8-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 00:14:49 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-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.8-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 938 and 0 Target number of residues in the AU: 938 Target solvent content: 0.6546 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 81.10 14859 reflections ( 99.83 % complete ) and 0 restraints for refining 8275 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3363 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3181 (Rfree = 0.000) for 8275 atoms. Found 45 (45 requested) and removed 44 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 2.93 Search for helices and strands: 0 residues in 0 chains, 8464 seeds are put forward NCS extension: 0 residues added, 8464 seeds are put forward Round 1: 445 peptides, 67 chains. Longest chain 14 peptides. Score 0.402 Round 2: 512 peptides, 59 chains. Longest chain 23 peptides. Score 0.512 Round 3: 533 peptides, 55 chains. Longest chain 27 peptides. Score 0.550 Round 4: 545 peptides, 51 chains. Longest chain 34 peptides. Score 0.578 Round 5: 532 peptides, 54 chains. Longest chain 36 peptides. Score 0.554 Taking the results from Round 4 Chains 58, Residues 494, Estimated correctness of the model 0.0 % 6 chains (77 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14566 restraints for refining 6768 atoms. 12376 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2541 (Rfree = 0.000) for 6768 atoms. Found 37 (37 requested) and removed 78 (18 requested) atoms. Cycle 2: After refmac, R = 0.2402 (Rfree = 0.000) for 6570 atoms. Found 36 (36 requested) and removed 50 (18 requested) atoms. Cycle 3: After refmac, R = 0.2318 (Rfree = 0.000) for 6486 atoms. Found 30 (36 requested) and removed 51 (18 requested) atoms. Cycle 4: After refmac, R = 0.2250 (Rfree = 0.000) for 6420 atoms. Found 28 (35 requested) and removed 43 (17 requested) atoms. Cycle 5: After refmac, R = 0.2209 (Rfree = 0.000) for 6377 atoms. Found 26 (35 requested) and removed 35 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 2.89 Search for helices and strands: 0 residues in 0 chains, 6631 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 6658 seeds are put forward Round 1: 519 peptides, 62 chains. Longest chain 26 peptides. Score 0.505 Round 2: 520 peptides, 61 chains. Longest chain 27 peptides. Score 0.511 Round 3: 556 peptides, 58 chains. Longest chain 33 peptides. Score 0.558 Round 4: 569 peptides, 54 chains. Longest chain 24 peptides. Score 0.587 Round 5: 566 peptides, 56 chains. Longest chain 37 peptides. Score 0.576 Taking the results from Round 4 Chains 60, Residues 515, Estimated correctness of the model 0.0 % 8 chains (81 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14382 restraints for refining 6772 atoms. 12135 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2543 (Rfree = 0.000) for 6772 atoms. Found 37 (37 requested) and removed 89 (18 requested) atoms. Cycle 7: After refmac, R = 0.2345 (Rfree = 0.000) for 6636 atoms. Found 36 (36 requested) and removed 59 (18 requested) atoms. Cycle 8: After refmac, R = 0.2245 (Rfree = 0.000) for 6562 atoms. Found 30 (36 requested) and removed 55 (18 requested) atoms. Cycle 9: After refmac, R = 0.2179 (Rfree = 0.000) for 6510 atoms. Found 25 (35 requested) and removed 38 (17 requested) atoms. Cycle 10: After refmac, R = 0.2120 (Rfree = 0.000) for 6472 atoms. Found 31 (35 requested) and removed 49 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 2.87 Search for helices and strands: 0 residues in 0 chains, 6710 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6725 seeds are put forward Round 1: 505 peptides, 66 chains. Longest chain 17 peptides. Score 0.472 Round 2: 535 peptides, 62 chains. Longest chain 33 peptides. Score 0.521 Round 3: 546 peptides, 61 chains. Longest chain 30 peptides. Score 0.536 Round 4: 534 peptides, 57 chains. Longest chain 27 peptides. Score 0.542 Round 5: 565 peptides, 65 chains. Longest chain 36 peptides. Score 0.536 Taking the results from Round 4 Chains 61, Residues 477, Estimated correctness of the model 0.0 % 10 chains (93 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14420 restraints for refining 6772 atoms. 12255 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2428 (Rfree = 0.000) for 6772 atoms. Found 34 (37 requested) and removed 83 (18 requested) atoms. Cycle 12: After refmac, R = 0.2286 (Rfree = 0.000) for 6647 atoms. Found 29 (36 requested) and removed 40 (18 requested) atoms. Cycle 13: After refmac, R = 0.2264 (Rfree = 0.000) for 6605 atoms. Found 35 (36 requested) and removed 52 (18 requested) atoms. Cycle 14: After refmac, R = 0.2231 (Rfree = 0.000) for 6574 atoms. Found 26 (36 requested) and removed 37 (18 requested) atoms. Cycle 15: After refmac, R = 0.2153 (Rfree = 0.000) for 6546 atoms. Found 20 (36 requested) and removed 35 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 2.92 Search for helices and strands: 0 residues in 0 chains, 6781 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 6811 seeds are put forward Round 1: 491 peptides, 64 chains. Longest chain 25 peptides. Score 0.467 Round 2: 526 peptides, 55 chains. Longest chain 30 peptides. Score 0.544 Round 3: 549 peptides, 57 chains. Longest chain 43 peptides. Score 0.556 Round 4: 528 peptides, 55 chains. Longest chain 31 peptides. Score 0.545 Round 5: 532 peptides, 53 chains. Longest chain 32 peptides. Score 0.558 Taking the results from Round 5 Chains 55, Residues 479, Estimated correctness of the model 0.0 % 5 chains (67 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14810 restraints for refining 6773 atoms. 12725 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2525 (Rfree = 0.000) for 6773 atoms. Found 37 (37 requested) and removed 60 (18 requested) atoms. Cycle 17: After refmac, R = 0.2369 (Rfree = 0.000) for 6673 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. Cycle 18: After refmac, R = 0.2296 (Rfree = 0.000) for 6615 atoms. Found 32 (36 requested) and removed 33 (18 requested) atoms. Cycle 19: After refmac, R = 0.2227 (Rfree = 0.000) for 6566 atoms. Found 35 (36 requested) and removed 26 (18 requested) atoms. Cycle 20: After refmac, R = 0.2205 (Rfree = 0.000) for 6539 atoms. Found 32 (36 requested) and removed 38 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 2.91 Search for helices and strands: 0 residues in 0 chains, 6778 seeds are put forward NCS extension: 48 residues added (5 deleted due to clashes), 6826 seeds are put forward Round 1: 496 peptides, 67 chains. Longest chain 18 peptides. Score 0.458 Round 2: 532 peptides, 56 chains. Longest chain 21 peptides. Score 0.545 Round 3: 548 peptides, 63 chains. Longest chain 24 peptides. Score 0.529 Round 4: 517 peptides, 53 chains. Longest chain 24 peptides. Score 0.544 Round 5: 552 peptides, 59 chains. Longest chain 23 peptides. Score 0.550 Taking the results from Round 5 Chains 63, Residues 493, Estimated correctness of the model 0.0 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14809 restraints for refining 6773 atoms. 12781 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2516 (Rfree = 0.000) for 6773 atoms. Found 37 (37 requested) and removed 47 (18 requested) atoms. Cycle 22: After refmac, R = 0.2306 (Rfree = 0.000) for 6696 atoms. Found 26 (37 requested) and removed 35 (18 requested) atoms. Cycle 23: After refmac, R = 0.2255 (Rfree = 0.000) for 6659 atoms. Found 26 (36 requested) and removed 28 (18 requested) atoms. Cycle 24: After refmac, R = 0.2228 (Rfree = 0.000) for 6631 atoms. Found 33 (36 requested) and removed 30 (18 requested) atoms. Cycle 25: After refmac, R = 0.2181 (Rfree = 0.000) for 6613 atoms. Found 24 (36 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 2.91 Search for helices and strands: 0 residues in 0 chains, 6874 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6892 seeds are put forward Round 1: 482 peptides, 68 chains. Longest chain 22 peptides. Score 0.438 Round 2: 525 peptides, 62 chains. Longest chain 21 peptides. Score 0.511 Round 3: 516 peptides, 62 chains. Longest chain 22 peptides. Score 0.502 Round 4: 528 peptides, 62 chains. Longest chain 23 peptides. Score 0.514 Round 5: 533 peptides, 61 chains. Longest chain 25 peptides. Score 0.523 Taking the results from Round 5 Chains 65, Residues 472, Estimated correctness of the model 0.0 % 5 chains (50 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14766 restraints for refining 6773 atoms. 12781 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2412 (Rfree = 0.000) for 6773 atoms. Found 36 (37 requested) and removed 46 (18 requested) atoms. Cycle 27: After refmac, R = 0.2188 (Rfree = 0.000) for 6704 atoms. Found 23 (37 requested) and removed 36 (18 requested) atoms. Cycle 28: After refmac, R = 0.2159 (Rfree = 0.000) for 6663 atoms. Found 23 (36 requested) and removed 31 (18 requested) atoms. Cycle 29: After refmac, R = 0.2194 (Rfree = 0.000) for 6634 atoms. Found 36 (36 requested) and removed 36 (18 requested) atoms. Cycle 30: After refmac, R = 0.2157 (Rfree = 0.000) for 6616 atoms. Found 36 (36 requested) and removed 35 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 2.89 Search for helices and strands: 0 residues in 0 chains, 6884 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 6911 seeds are put forward Round 1: 510 peptides, 71 chains. Longest chain 21 peptides. Score 0.453 Round 2: 543 peptides, 61 chains. Longest chain 28 peptides. Score 0.533 Round 3: 550 peptides, 62 chains. Longest chain 34 peptides. Score 0.535 Round 4: 544 peptides, 60 chains. Longest chain 28 peptides. Score 0.538 Round 5: 519 peptides, 55 chains. Longest chain 30 peptides. Score 0.537 Taking the results from Round 4 Chains 66, Residues 484, Estimated correctness of the model 0.0 % 7 chains (79 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14443 restraints for refining 6772 atoms. 12327 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2403 (Rfree = 0.000) for 6772 atoms. Found 33 (37 requested) and removed 53 (18 requested) atoms. Cycle 32: After refmac, R = 0.2256 (Rfree = 0.000) for 6686 atoms. Found 32 (37 requested) and removed 38 (18 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2206 (Rfree = 0.000) for 6639 atoms. Found 30 (36 requested) and removed 34 (18 requested) atoms. Cycle 34: After refmac, R = 0.2179 (Rfree = 0.000) for 6602 atoms. Found 35 (36 requested) and removed 25 (18 requested) atoms. Cycle 35: After refmac, R = 0.2119 (Rfree = 0.000) for 6593 atoms. Found 18 (36 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 2.91 Search for helices and strands: 0 residues in 0 chains, 6825 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6844 seeds are put forward Round 1: 452 peptides, 74 chains. Longest chain 14 peptides. Score 0.374 Round 2: 487 peptides, 63 chains. Longest chain 20 peptides. Score 0.468 Round 3: 510 peptides, 65 chains. Longest chain 23 peptides. Score 0.482 Round 4: 524 peptides, 65 chains. Longest chain 27 peptides. Score 0.496 Round 5: 513 peptides, 66 chains. Longest chain 27 peptides. Score 0.480 Taking the results from Round 4 Chains 72, Residues 459, Estimated correctness of the model 0.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14997 restraints for refining 6772 atoms. 13110 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2464 (Rfree = 0.000) for 6772 atoms. Found 37 (37 requested) and removed 42 (18 requested) atoms. Cycle 37: After refmac, R = 0.2415 (Rfree = 0.000) for 6699 atoms. Found 37 (37 requested) and removed 44 (18 requested) atoms. Cycle 38: After refmac, R = 0.2334 (Rfree = 0.000) for 6660 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. Cycle 39: After refmac, R = 0.2275 (Rfree = 0.000) for 6634 atoms. Found 25 (36 requested) and removed 35 (18 requested) atoms. Cycle 40: After refmac, R = 0.2219 (Rfree = 0.000) for 6611 atoms. Found 34 (36 requested) and removed 37 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 2.89 Search for helices and strands: 0 residues in 0 chains, 6821 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6838 seeds are put forward Round 1: 419 peptides, 68 chains. Longest chain 14 peptides. Score 0.366 Round 2: 502 peptides, 69 chains. Longest chain 20 peptides. Score 0.454 Round 3: 489 peptides, 69 chains. Longest chain 23 peptides. Score 0.441 Round 4: 482 peptides, 64 chains. Longest chain 23 peptides. Score 0.458 Round 5: 475 peptides, 63 chains. Longest chain 19 peptides. Score 0.455 Taking the results from Round 4 Chains 69, Residues 418, Estimated correctness of the model 0.0 % 5 chains (61 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14915 restraints for refining 6773 atoms. 13105 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2363 (Rfree = 0.000) for 6773 atoms. Found 37 (37 requested) and removed 52 (18 requested) atoms. Cycle 42: After refmac, R = 0.2320 (Rfree = 0.000) for 6699 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 43: After refmac, R = 0.2185 (Rfree = 0.000) for 6679 atoms. Found 36 (36 requested) and removed 26 (18 requested) atoms. Cycle 44: After refmac, R = 0.2190 (Rfree = 0.000) for 6661 atoms. Found 31 (36 requested) and removed 29 (18 requested) atoms. Cycle 45: After refmac, R = 0.2153 (Rfree = 0.000) for 6646 atoms. Found 27 (36 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 2.94 Search for helices and strands: 0 residues in 0 chains, 6879 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6900 seeds are put forward Round 1: 410 peptides, 70 chains. Longest chain 12 peptides. Score 0.345 Round 2: 443 peptides, 64 chains. Longest chain 29 peptides. Score 0.415 Round 3: 481 peptides, 60 chains. Longest chain 29 peptides. Score 0.476 Round 4: 477 peptides, 65 chains. Longest chain 18 peptides. Score 0.447 Round 5: 481 peptides, 62 chains. Longest chain 20 peptides. Score 0.466 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 421, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (421 residues) following loop building 4 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14859 reflections ( 99.83 % complete ) and 15295 restraints for refining 6773 atoms. 13580 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2383 (Rfree = 0.000) for 6773 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2298 (Rfree = 0.000) for 6704 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2274 (Rfree = 0.000) for 6667 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2250 (Rfree = 0.000) for 6634 atoms. TimeTaking 76.22