Mon 24 Dec 00:19:17 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 1vl5-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-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/1vl5-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-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 00:19:26 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/1vl5-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-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 835 and 0 Target number of residues in the AU: 835 Target solvent content: 0.6099 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-3.2-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: 4 Cell parameters: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8320 target number of atoms Had to go as low as 0.70 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: 49.849 3.200 Wilson plot Bfac: 56.78 19002 reflections ( 99.93 % complete ) and 0 restraints for refining 9183 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3007 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2413 (Rfree = 0.000) for 9183 atoms. Found 64 (82 requested) and removed 90 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 3.01 Search for helices and strands: 0 residues in 0 chains, 9335 seeds are put forward NCS extension: 0 residues added, 9335 seeds are put forward Round 1: 563 peptides, 86 chains. Longest chain 20 peptides. Score 0.489 Round 2: 639 peptides, 76 chains. Longest chain 23 peptides. Score 0.622 Round 3: 688 peptides, 75 chains. Longest chain 43 peptides. Score 0.672 Round 4: 730 peptides, 70 chains. Longest chain 30 peptides. Score 0.725 Round 5: 701 peptides, 66 chains. Longest chain 30 peptides. Score 0.717 Taking the results from Round 4 Chains 78, Residues 660, Estimated correctness of the model 70.3 % 14 chains (232 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 104 C and 114 C Built loop between residues 122 C and 127 C 75 chains (668 residues) following loop building 12 chains (245 residues) in sequence following loop building ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 13427 restraints for refining 7587 atoms. 9755 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2476 (Rfree = 0.000) for 7587 atoms. Found 62 (68 requested) and removed 70 (34 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2323 (Rfree = 0.000) for 7462 atoms. Found 34 (67 requested) and removed 47 (34 requested) atoms. Cycle 3: After refmac, R = 0.2254 (Rfree = 0.000) for 7388 atoms. Found 19 (63 requested) and removed 37 (33 requested) atoms. Cycle 4: After refmac, R = 0.2190 (Rfree = 0.000) for 7354 atoms. Found 25 (62 requested) and removed 35 (33 requested) atoms. Cycle 5: After refmac, R = 0.2161 (Rfree = 0.000) for 7323 atoms. Found 19 (60 requested) and removed 32 (32 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 3.02 Search for helices and strands: 0 residues in 0 chains, 7514 seeds are put forward NCS extension: 20 residues added (16 deleted due to clashes), 7534 seeds are put forward Round 1: 664 peptides, 75 chains. Longest chain 28 peptides. Score 0.651 Round 2: 708 peptides, 61 chains. Longest chain 39 peptides. Score 0.741 Round 3: 699 peptides, 59 chains. Longest chain 34 peptides. Score 0.741 Round 4: 691 peptides, 57 chains. Longest chain 46 peptides. Score 0.742 Round 5: 701 peptides, 63 chains. Longest chain 40 peptides. Score 0.728 Taking the results from Round 4 Chains 65, Residues 634, Estimated correctness of the model 73.6 % 16 chains (272 residues) have been docked in sequence Building loops using Loopy2018 65 chains (634 residues) following loop building 16 chains (272 residues) in sequence following loop building ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 13746 restraints for refining 7595 atoms. 10065 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2496 (Rfree = 0.000) for 7595 atoms. Found 54 (61 requested) and removed 70 (34 requested) atoms. Cycle 7: After refmac, R = 0.2263 (Rfree = 0.000) for 7550 atoms. Found 17 (60 requested) and removed 45 (34 requested) atoms. Cycle 8: After refmac, R = 0.2202 (Rfree = 0.000) for 7496 atoms. Found 19 (58 requested) and removed 35 (33 requested) atoms. Cycle 9: After refmac, R = 0.2124 (Rfree = 0.000) for 7472 atoms. Found 10 (56 requested) and removed 33 (33 requested) atoms. Cycle 10: After refmac, R = 0.2088 (Rfree = 0.000) for 7442 atoms. Found 9 (54 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 7622 seeds are put forward NCS extension: 15 residues added (29 deleted due to clashes), 7637 seeds are put forward Round 1: 659 peptides, 71 chains. Longest chain 31 peptides. Score 0.663 Round 2: 705 peptides, 64 chains. Longest chain 37 peptides. Score 0.728 Round 3: 705 peptides, 71 chains. Longest chain 26 peptides. Score 0.702 Round 4: 701 peptides, 60 chains. Longest chain 30 peptides. Score 0.739 Round 5: 675 peptides, 66 chains. Longest chain 35 peptides. Score 0.697 Taking the results from Round 4 Chains 71, Residues 641, Estimated correctness of the model 73.0 % 14 chains (238 residues) have been docked in sequence Building loops using Loopy2018 71 chains (641 residues) following loop building 14 chains (238 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 19002 reflections ( 99.93 % complete ) and 14058 restraints for refining 7596 atoms. 10529 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2470 (Rfree = 0.000) for 7596 atoms. Found 54 (54 requested) and removed 58 (34 requested) atoms. Cycle 12: After refmac, R = 0.2332 (Rfree = 0.000) for 7543 atoms. Found 30 (53 requested) and removed 35 (34 requested) atoms. Cycle 13: After refmac, R = 0.2278 (Rfree = 0.000) for 7519 atoms. Found 20 (51 requested) and removed 33 (33 requested) atoms. Cycle 14: After refmac, R = 0.2211 (Rfree = 0.000) for 7498 atoms. Found 16 (50 requested) and removed 33 (33 requested) atoms. Cycle 15: After refmac, R = 0.2172 (Rfree = 0.000) for 7475 atoms. Found 10 (48 requested) and removed 34 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 7641 seeds are put forward NCS extension: 19 residues added (17 deleted due to clashes), 7660 seeds are put forward Round 1: 625 peptides, 76 chains. Longest chain 24 peptides. Score 0.608 Round 2: 682 peptides, 72 chains. Longest chain 30 peptides. Score 0.679 Round 3: 663 peptides, 66 chains. Longest chain 33 peptides. Score 0.687 Round 4: 652 peptides, 73 chains. Longest chain 33 peptides. Score 0.648 Round 5: 639 peptides, 66 chains. Longest chain 34 peptides. Score 0.666 Taking the results from Round 3 Chains 72, Residues 597, Estimated correctness of the model 62.4 % 13 chains (195 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 14661 restraints for refining 7595 atoms. 11500 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2437 (Rfree = 0.000) for 7595 atoms. Found 48 (48 requested) and removed 48 (34 requested) atoms. Cycle 17: After refmac, R = 0.2284 (Rfree = 0.000) for 7565 atoms. Found 26 (48 requested) and removed 37 (34 requested) atoms. Cycle 18: After refmac, R = 0.2213 (Rfree = 0.000) for 7544 atoms. Found 13 (47 requested) and removed 34 (33 requested) atoms. Cycle 19: After refmac, R = 0.2165 (Rfree = 0.000) for 7509 atoms. Found 12 (47 requested) and removed 33 (33 requested) atoms. Cycle 20: After refmac, R = 0.2127 (Rfree = 0.000) for 7482 atoms. Found 8 (47 requested) and removed 34 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 7663 seeds are put forward NCS extension: 30 residues added (21 deleted due to clashes), 7693 seeds are put forward Round 1: 624 peptides, 82 chains. Longest chain 28 peptides. Score 0.579 Round 2: 638 peptides, 71 chains. Longest chain 34 peptides. Score 0.644 Round 3: 660 peptides, 71 chains. Longest chain 32 peptides. Score 0.664 Round 4: 659 peptides, 70 chains. Longest chain 28 peptides. Score 0.667 Round 5: 658 peptides, 76 chains. Longest chain 32 peptides. Score 0.641 Taking the results from Round 4 Chains 72, Residues 589, Estimated correctness of the model 57.9 % 10 chains (129 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 15436 restraints for refining 7594 atoms. 12595 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2353 (Rfree = 0.000) for 7594 atoms. Found 33 (48 requested) and removed 52 (34 requested) atoms. Cycle 22: After refmac, R = 0.2214 (Rfree = 0.000) for 7563 atoms. Found 19 (47 requested) and removed 36 (33 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2166 (Rfree = 0.000) for 7538 atoms. Found 11 (47 requested) and removed 33 (33 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2128 (Rfree = 0.000) for 7512 atoms. Found 10 (47 requested) and removed 33 (33 requested) atoms. Cycle 25: After refmac, R = 0.2119 (Rfree = 0.000) for 7482 atoms. Found 7 (47 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 7652 seeds are put forward NCS extension: 17 residues added (13 deleted due to clashes), 7669 seeds are put forward Round 1: 604 peptides, 81 chains. Longest chain 28 peptides. Score 0.562 Round 2: 644 peptides, 69 chains. Longest chain 33 peptides. Score 0.658 Round 3: 604 peptides, 65 chains. Longest chain 29 peptides. Score 0.638 Round 4: 621 peptides, 76 chains. Longest chain 27 peptides. Score 0.604 Round 5: 615 peptides, 69 chains. Longest chain 31 peptides. Score 0.630 Taking the results from Round 2 Chains 73, Residues 575, Estimated correctness of the model 55.7 % 7 chains (125 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 15309 restraints for refining 7596 atoms. 12488 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2376 (Rfree = 0.000) for 7596 atoms. Found 45 (48 requested) and removed 56 (34 requested) atoms. Cycle 27: After refmac, R = 0.2269 (Rfree = 0.000) for 7550 atoms. Found 15 (48 requested) and removed 35 (34 requested) atoms. Cycle 28: After refmac, R = 0.2156 (Rfree = 0.000) for 7518 atoms. Found 15 (47 requested) and removed 33 (33 requested) atoms. Cycle 29: After refmac, R = 0.2114 (Rfree = 0.000) for 7497 atoms. Found 10 (47 requested) and removed 33 (33 requested) atoms. Cycle 30: After refmac, R = 0.2117 (Rfree = 0.000) for 7466 atoms. Found 12 (47 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 7640 seeds are put forward NCS extension: 14 residues added (17 deleted due to clashes), 7654 seeds are put forward Round 1: 601 peptides, 84 chains. Longest chain 23 peptides. Score 0.544 Round 2: 626 peptides, 72 chains. Longest chain 31 peptides. Score 0.628 Round 3: 627 peptides, 75 chains. Longest chain 32 peptides. Score 0.615 Round 4: 620 peptides, 68 chains. Longest chain 27 peptides. Score 0.640 Round 5: 622 peptides, 68 chains. Longest chain 35 peptides. Score 0.642 Taking the results from Round 5 Chains 71, Residues 554, Estimated correctness of the model 51.9 % 6 chains (81 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 16232 restraints for refining 7596 atoms. 13767 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2267 (Rfree = 0.000) for 7596 atoms. Found 48 (48 requested) and removed 45 (34 requested) atoms. Cycle 32: After refmac, R = 0.2127 (Rfree = 0.000) for 7581 atoms. Found 18 (48 requested) and removed 39 (34 requested) atoms. Cycle 33: After refmac, R = 0.2074 (Rfree = 0.000) for 7542 atoms. Found 16 (47 requested) and removed 33 (33 requested) atoms. Cycle 34: After refmac, R = 0.2035 (Rfree = 0.000) for 7519 atoms. Found 6 (47 requested) and removed 33 (33 requested) atoms. Cycle 35: After refmac, R = 0.1998 (Rfree = 0.000) for 7491 atoms. Found 9 (47 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.05 Search for helices and strands: 0 residues in 0 chains, 7688 seeds are put forward NCS extension: 18 residues added (6 deleted due to clashes), 7706 seeds are put forward Round 1: 607 peptides, 85 chains. Longest chain 23 peptides. Score 0.546 Round 2: 660 peptides, 79 chains. Longest chain 25 peptides. Score 0.630 Round 3: 641 peptides, 80 chains. Longest chain 27 peptides. Score 0.606 Round 4: 669 peptides, 80 chains. Longest chain 38 peptides. Score 0.634 Round 5: 634 peptides, 68 chains. Longest chain 39 peptides. Score 0.653 Taking the results from Round 5 Chains 74, Residues 566, Estimated correctness of the model 54.6 % 9 chains (124 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 15621 restraints for refining 7595 atoms. 12979 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2297 (Rfree = 0.000) for 7595 atoms. Found 35 (48 requested) and removed 56 (34 requested) atoms. Cycle 37: After refmac, R = 0.2140 (Rfree = 0.000) for 7554 atoms. Found 11 (47 requested) and removed 36 (33 requested) atoms. Cycle 38: After refmac, R = 0.2073 (Rfree = 0.000) for 7520 atoms. Found 10 (47 requested) and removed 33 (33 requested) atoms. Cycle 39: After refmac, R = 0.2036 (Rfree = 0.000) for 7488 atoms. Found 13 (47 requested) and removed 33 (33 requested) atoms. Cycle 40: After refmac, R = 0.1977 (Rfree = 0.000) for 7465 atoms. Found 6 (47 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 7630 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 7645 seeds are put forward Round 1: 552 peptides, 74 chains. Longest chain 25 peptides. Score 0.539 Round 2: 564 peptides, 70 chains. Longest chain 29 peptides. Score 0.573 Round 3: 578 peptides, 72 chains. Longest chain 40 peptides. Score 0.578 Round 4: 561 peptides, 72 chains. Longest chain 25 peptides. Score 0.559 Round 5: 563 peptides, 73 chains. Longest chain 22 peptides. Score 0.557 Taking the results from Round 3 Chains 74, Residues 506, Estimated correctness of the model 35.0 % 5 chains (73 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 16588 restraints for refining 7596 atoms. 14360 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2209 (Rfree = 0.000) for 7596 atoms. Found 36 (48 requested) and removed 44 (34 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2087 (Rfree = 0.000) for 7575 atoms. Found 8 (48 requested) and removed 36 (34 requested) atoms. Cycle 43: After refmac, R = 0.2045 (Rfree = 0.000) for 7540 atoms. Found 6 (47 requested) and removed 34 (33 requested) atoms. Cycle 44: After refmac, R = 0.2029 (Rfree = 0.000) for 7507 atoms. Found 7 (47 requested) and removed 33 (33 requested) atoms. Cycle 45: After refmac, R = 0.2034 (Rfree = 0.000) for 7479 atoms. Found 7 (47 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.06 Search for helices and strands: 0 residues in 0 chains, 7683 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 7699 seeds are put forward Round 1: 495 peptides, 81 chains. Longest chain 26 peptides. Score 0.429 Round 2: 555 peptides, 77 chains. Longest chain 30 peptides. Score 0.527 Round 3: 545 peptides, 77 chains. Longest chain 16 peptides. Score 0.515 Round 4: 569 peptides, 76 chains. Longest chain 24 peptides. Score 0.548 Round 5: 572 peptides, 72 chains. Longest chain 27 peptides. Score 0.572 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 75, Residues 500, Estimated correctness of the model 33.3 % 5 chains (66 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 1vl5-3_warpNtrace.pdb as input Building loops using Loopy2018 75 chains (500 residues) following loop building 5 chains (66 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19002 reflections ( 99.93 % complete ) and 16600 restraints for refining 7595 atoms. 14403 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2181 (Rfree = 0.000) for 7595 atoms. Found 0 (48 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.2159 (Rfree = 0.000) for 7534 atoms. Found 0 (47 requested) and removed 19 (33 requested) atoms. Cycle 48: After refmac, R = 0.2157 (Rfree = 0.000) for 7507 atoms. Found 0 (47 requested) and removed 18 (33 requested) atoms. Cycle 49: After refmac, R = 0.2134 (Rfree = 0.000) for 7482 atoms. TimeTaking 97.13