Mon 24 Dec 00:32:09 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.2-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-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.2-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 00:32:14 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.2-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 1033 and 0 Target number of residues in the AU: 1033 Target solvent content: 0.6196 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-3.2-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-3.2-parrot-mrncs.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 3.200 Wilson plot Bfac: 61.18 24672 reflections ( 99.89 % complete ) and 0 restraints for refining 8369 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Starting model: R = 0.3418 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3201 (Rfree = 0.000) for 8369 atoms. Found 75 (75 requested) and removed 188 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 2.55 Search for helices and strands: 0 residues in 0 chains, 8418 seeds are put forward NCS extension: 0 residues added, 8418 seeds are put forward Round 1: 464 peptides, 70 chains. Longest chain 21 peptides. Score 0.408 Round 2: 565 peptides, 74 chains. Longest chain 21 peptides. Score 0.496 Round 3: 607 peptides, 69 chains. Longest chain 28 peptides. Score 0.557 Round 4: 628 peptides, 72 chains. Longest chain 27 peptides. Score 0.564 Round 5: 615 peptides, 71 chains. Longest chain 24 peptides. Score 0.556 Taking the results from Round 4 Chains 77, Residues 556, Estimated correctness of the model 31.0 % 8 chains (91 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13709 restraints for refining 6835 atoms. 11251 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2918 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 75 (30 requested) atoms. Cycle 2: After refmac, R = 0.2768 (Rfree = 0.000) for 6705 atoms. Found 61 (61 requested) and removed 46 (30 requested) atoms. Cycle 3: After refmac, R = 0.2662 (Rfree = 0.000) for 6674 atoms. Found 45 (60 requested) and removed 34 (30 requested) atoms. Cycle 4: After refmac, R = 0.2614 (Rfree = 0.000) for 6653 atoms. Found 32 (59 requested) and removed 36 (29 requested) atoms. Cycle 5: After refmac, R = 0.2561 (Rfree = 0.000) for 6626 atoms. Found 29 (59 requested) and removed 31 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 2.53 Search for helices and strands: 0 residues in 0 chains, 6860 seeds are put forward NCS extension: 32 residues added (4 deleted due to clashes), 6892 seeds are put forward Round 1: 553 peptides, 73 chains. Longest chain 23 peptides. Score 0.488 Round 2: 591 peptides, 67 chains. Longest chain 37 peptides. Score 0.551 Round 3: 587 peptides, 63 chains. Longest chain 25 peptides. Score 0.565 Round 4: 601 peptides, 61 chains. Longest chain 29 peptides. Score 0.585 Round 5: 594 peptides, 56 chains. Longest chain 31 peptides. Score 0.600 Taking the results from Round 5 Chains 61, Residues 538, Estimated correctness of the model 41.1 % 9 chains (151 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13456 restraints for refining 6836 atoms. 10799 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2836 (Rfree = 0.000) for 6836 atoms. Found 61 (61 requested) and removed 60 (30 requested) atoms. Cycle 7: After refmac, R = 0.2637 (Rfree = 0.000) for 6766 atoms. Found 53 (61 requested) and removed 40 (30 requested) atoms. Cycle 8: After refmac, R = 0.2531 (Rfree = 0.000) for 6736 atoms. Found 30 (60 requested) and removed 44 (30 requested) atoms. Cycle 9: After refmac, R = 0.2457 (Rfree = 0.000) for 6697 atoms. Found 24 (60 requested) and removed 34 (30 requested) atoms. Cycle 10: After refmac, R = 0.2381 (Rfree = 0.000) for 6663 atoms. Found 25 (59 requested) and removed 33 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.53 Search for helices and strands: 0 residues in 0 chains, 6873 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 6901 seeds are put forward Round 1: 549 peptides, 60 chains. Longest chain 30 peptides. Score 0.543 Round 2: 584 peptides, 51 chains. Longest chain 30 peptides. Score 0.612 Round 3: 600 peptides, 59 chains. Longest chain 31 peptides. Score 0.593 Round 4: 600 peptides, 61 chains. Longest chain 29 peptides. Score 0.584 Round 5: 591 peptides, 56 chains. Longest chain 35 peptides. Score 0.597 Taking the results from Round 2 Chains 53, Residues 533, Estimated correctness of the model 44.3 % 8 chains (90 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13698 restraints for refining 6759 atoms. 11288 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2558 (Rfree = 0.000) for 6759 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Cycle 12: After refmac, R = 0.2419 (Rfree = 0.000) for 6731 atoms. Found 55 (60 requested) and removed 39 (30 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2369 (Rfree = 0.000) for 6725 atoms. Found 31 (60 requested) and removed 36 (30 requested) atoms. Cycle 14: After refmac, R = 0.2337 (Rfree = 0.000) for 6700 atoms. Found 30 (60 requested) and removed 33 (30 requested) atoms. Cycle 15: After refmac, R = 0.2277 (Rfree = 0.000) for 6684 atoms. Found 25 (60 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.51 Search for helices and strands: 0 residues in 0 chains, 6930 seeds are put forward NCS extension: 31 residues added (6 deleted due to clashes), 6961 seeds are put forward Round 1: 572 peptides, 69 chains. Longest chain 32 peptides. Score 0.525 Round 2: 603 peptides, 59 chains. Longest chain 47 peptides. Score 0.595 Round 3: 628 peptides, 57 chains. Longest chain 33 peptides. Score 0.624 Round 4: 609 peptides, 62 chains. Longest chain 31 peptides. Score 0.588 Round 5: 619 peptides, 56 chains. Longest chain 54 peptides. Score 0.620 Taking the results from Round 3 Chains 67, Residues 571, Estimated correctness of the model 47.4 % 14 chains (187 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 12656 restraints for refining 6835 atoms. 9755 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2645 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 61 (30 requested) atoms. Cycle 17: After refmac, R = 0.2445 (Rfree = 0.000) for 6804 atoms. Found 41 (61 requested) and removed 36 (30 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2395 (Rfree = 0.000) for 6780 atoms. Found 27 (61 requested) and removed 35 (30 requested) atoms. Cycle 19: After refmac, R = 0.2353 (Rfree = 0.000) for 6758 atoms. Found 31 (60 requested) and removed 31 (30 requested) atoms. Cycle 20: After refmac, R = 0.2296 (Rfree = 0.000) for 6745 atoms. Found 24 (60 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 2.53 Search for helices and strands: 0 residues in 0 chains, 6957 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 6971 seeds are put forward Round 1: 572 peptides, 73 chains. Longest chain 21 peptides. Score 0.507 Round 2: 608 peptides, 63 chains. Longest chain 28 peptides. Score 0.583 Round 3: 582 peptides, 61 chains. Longest chain 32 peptides. Score 0.569 Round 4: 596 peptides, 63 chains. Longest chain 25 peptides. Score 0.573 Round 5: 585 peptides, 63 chains. Longest chain 28 peptides. Score 0.563 Taking the results from Round 2 Chains 69, Residues 545, Estimated correctness of the model 36.4 % 11 chains (166 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13253 restraints for refining 6835 atoms. 10532 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2574 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 60 (30 requested) atoms. Cycle 22: After refmac, R = 0.2432 (Rfree = 0.000) for 6816 atoms. Found 34 (61 requested) and removed 38 (30 requested) atoms. Cycle 23: After refmac, R = 0.2363 (Rfree = 0.000) for 6796 atoms. Found 36 (61 requested) and removed 33 (30 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2356 (Rfree = 0.000) for 6790 atoms. Found 19 (61 requested) and removed 31 (30 requested) atoms. Cycle 25: After refmac, R = 0.2302 (Rfree = 0.000) for 6769 atoms. Found 15 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 2.52 Search for helices and strands: 0 residues in 0 chains, 6990 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 7005 seeds are put forward Round 1: 559 peptides, 64 chains. Longest chain 23 peptides. Score 0.535 Round 2: 579 peptides, 63 chains. Longest chain 31 peptides. Score 0.557 Round 3: 581 peptides, 59 chains. Longest chain 45 peptides. Score 0.576 Round 4: 579 peptides, 56 chains. Longest chain 31 peptides. Score 0.587 Round 5: 569 peptides, 61 chains. Longest chain 30 peptides. Score 0.557 Taking the results from Round 4 Chains 61, Residues 523, Estimated correctness of the model 37.5 % 13 chains (193 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 12908 restraints for refining 6833 atoms. 10156 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2612 (Rfree = 0.000) for 6833 atoms. Found 61 (61 requested) and removed 49 (30 requested) atoms. Cycle 27: After refmac, R = 0.2425 (Rfree = 0.000) for 6817 atoms. Found 30 (61 requested) and removed 34 (30 requested) atoms. Cycle 28: After refmac, R = 0.2363 (Rfree = 0.000) for 6799 atoms. Found 18 (61 requested) and removed 31 (30 requested) atoms. Cycle 29: After refmac, R = 0.2314 (Rfree = 0.000) for 6771 atoms. Found 17 (60 requested) and removed 31 (30 requested) atoms. Cycle 30: After refmac, R = 0.2270 (Rfree = 0.000) for 6749 atoms. Found 12 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 2.53 Search for helices and strands: 0 residues in 0 chains, 6952 seeds are put forward NCS extension: 16 residues added (14 deleted due to clashes), 6968 seeds are put forward Round 1: 549 peptides, 65 chains. Longest chain 37 peptides. Score 0.521 Round 2: 571 peptides, 57 chains. Longest chain 38 peptides. Score 0.576 Round 3: 558 peptides, 57 chains. Longest chain 39 peptides. Score 0.564 Round 4: 569 peptides, 57 chains. Longest chain 35 peptides. Score 0.574 Round 5: 597 peptides, 64 chains. Longest chain 39 peptides. Score 0.569 Taking the results from Round 2 Chains 61, Residues 514, Estimated correctness of the model 34.4 % 9 chains (124 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13832 restraints for refining 6835 atoms. 11420 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2500 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 46 (30 requested) atoms. Cycle 32: After refmac, R = 0.2395 (Rfree = 0.000) for 6836 atoms. Found 37 (61 requested) and removed 35 (30 requested) atoms. Cycle 33: After refmac, R = 0.2315 (Rfree = 0.000) for 6825 atoms. Found 23 (61 requested) and removed 32 (30 requested) atoms. Cycle 34: After refmac, R = 0.2273 (Rfree = 0.000) for 6808 atoms. Found 25 (61 requested) and removed 30 (30 requested) atoms. Cycle 35: After refmac, R = 0.2246 (Rfree = 0.000) for 6789 atoms. Found 17 (61 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 2.54 Search for helices and strands: 0 residues in 0 chains, 6975 seeds are put forward NCS extension: 12 residues added (9 deleted due to clashes), 6987 seeds are put forward Round 1: 550 peptides, 64 chains. Longest chain 33 peptides. Score 0.526 Round 2: 572 peptides, 62 chains. Longest chain 34 peptides. Score 0.555 Round 3: 572 peptides, 63 chains. Longest chain 37 peptides. Score 0.551 Round 4: 589 peptides, 61 chains. Longest chain 51 peptides. Score 0.575 Round 5: 588 peptides, 60 chains. Longest chain 27 peptides. Score 0.578 Taking the results from Round 5 Chains 64, Residues 528, Estimated correctness of the model 35.0 % 11 chains (158 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13378 restraints for refining 6836 atoms. 10758 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2591 (Rfree = 0.000) for 6836 atoms. Found 61 (61 requested) and removed 54 (30 requested) atoms. Cycle 37: After refmac, R = 0.2411 (Rfree = 0.000) for 6818 atoms. Found 23 (61 requested) and removed 32 (30 requested) atoms. Cycle 38: After refmac, R = 0.2353 (Rfree = 0.000) for 6787 atoms. Found 19 (61 requested) and removed 31 (30 requested) atoms. Cycle 39: After refmac, R = 0.2299 (Rfree = 0.000) for 6759 atoms. Found 19 (60 requested) and removed 30 (30 requested) atoms. Cycle 40: After refmac, R = 0.2275 (Rfree = 0.000) for 6736 atoms. Found 18 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 2.53 Search for helices and strands: 0 residues in 0 chains, 6951 seeds are put forward NCS extension: 29 residues added (7 deleted due to clashes), 6980 seeds are put forward Round 1: 526 peptides, 69 chains. Longest chain 26 peptides. Score 0.479 Round 2: 573 peptides, 61 chains. Longest chain 48 peptides. Score 0.561 Round 3: 588 peptides, 65 chains. Longest chain 35 peptides. Score 0.557 Round 4: 576 peptides, 54 chains. Longest chain 37 peptides. Score 0.593 Round 5: 574 peptides, 60 chains. Longest chain 46 peptides. Score 0.566 Taking the results from Round 4 Chains 62, Residues 522, Estimated correctness of the model 39.2 % 13 chains (185 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13120 restraints for refining 6834 atoms. 10432 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2567 (Rfree = 0.000) for 6834 atoms. Found 61 (61 requested) and removed 69 (30 requested) atoms. Cycle 42: After refmac, R = 0.2406 (Rfree = 0.000) for 6785 atoms. Found 43 (61 requested) and removed 41 (30 requested) atoms. Cycle 43: After refmac, R = 0.2248 (Rfree = 0.000) for 6774 atoms. Found 23 (60 requested) and removed 33 (30 requested) atoms. Cycle 44: After refmac, R = 0.2212 (Rfree = 0.000) for 6748 atoms. Found 13 (60 requested) and removed 31 (30 requested) atoms. Cycle 45: After refmac, R = 0.2188 (Rfree = 0.000) for 6725 atoms. Found 7 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 2.52 Search for helices and strands: 0 residues in 0 chains, 6942 seeds are put forward NCS extension: 26 residues added (8 deleted due to clashes), 6968 seeds are put forward Round 1: 492 peptides, 63 chains. Longest chain 24 peptides. Score 0.473 Round 2: 550 peptides, 58 chains. Longest chain 51 peptides. Score 0.553 Round 3: 578 peptides, 63 chains. Longest chain 33 peptides. Score 0.557 Round 4: 574 peptides, 57 chains. Longest chain 41 peptides. Score 0.578 Round 5: 571 peptides, 62 chains. Longest chain 46 peptides. Score 0.554 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 517, Estimated correctness of the model 35.0 % 10 chains (165 residues) have been docked in sequence Sequence coverage is 31 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 125 A and 128 A Built loop between residues 133 B and 144 B 59 chains (523 residues) following loop building 8 chains (177 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 24672 reflections ( 99.89 % complete ) and 13023 restraints for refining 6834 atoms. 10413 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2560 (Rfree = 0.000) for 6834 atoms. Found 0 (61 requested) and removed 18 (30 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2487 (Rfree = 0.000) for 6787 atoms. Found 0 (61 requested) and removed 2 (30 requested) atoms. Cycle 48: After refmac, R = 0.2425 (Rfree = 0.000) for 6777 atoms. Found 0 (60 requested) and removed 8 (30 requested) atoms. Cycle 49: After refmac, R = 0.2389 (Rfree = 0.000) for 6762 atoms. Found 0 (60 requested) and removed 4 (30 requested) atoms. Writing output files ... TimeTaking 95.85