Mon 24 Dec 00:13:02 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 1vkz-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-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/1vkz-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-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 00:13:06 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/1vkz-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-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 721 and 0 Target number of residues in the AU: 721 Target solvent content: 0.5393 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-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: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.55 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: 19.959 3.200 Wilson plot Bfac: 32.54 13478 reflections ( 96.64 % complete ) and 0 restraints for refining 7279 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.2890 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2477 (Rfree = 0.000) for 7279 atoms. Found 64 (65 requested) and removed 78 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.64 2.75 Search for helices and strands: 0 residues in 0 chains, 7401 seeds are put forward NCS extension: 0 residues added, 7401 seeds are put forward Round 1: 355 peptides, 71 chains. Longest chain 11 peptides. Score 0.319 Round 2: 466 peptides, 74 chains. Longest chain 20 peptides. Score 0.499 Round 3: 535 peptides, 67 chains. Longest chain 20 peptides. Score 0.643 Round 4: 522 peptides, 66 chains. Longest chain 27 peptides. Score 0.632 Round 5: 544 peptides, 61 chains. Longest chain 39 peptides. Score 0.686 Taking the results from Round 5 Chains 64, Residues 483, Estimated correctness of the model 62.2 % 12 chains (152 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11450 restraints for refining 6017 atoms. 9029 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2583 (Rfree = 0.000) for 6017 atoms. Found 54 (54 requested) and removed 72 (27 requested) atoms. Cycle 2: After refmac, R = 0.2448 (Rfree = 0.000) for 5883 atoms. Found 50 (53 requested) and removed 40 (26 requested) atoms. Cycle 3: After refmac, R = 0.2376 (Rfree = 0.000) for 5836 atoms. Found 39 (52 requested) and removed 31 (26 requested) atoms. Cycle 4: After refmac, R = 0.2277 (Rfree = 0.000) for 5800 atoms. Found 31 (52 requested) and removed 32 (26 requested) atoms. Cycle 5: After refmac, R = 0.2267 (Rfree = 0.000) for 5757 atoms. Found 42 (52 requested) and removed 34 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.72 2.83 Search for helices and strands: 0 residues in 0 chains, 5895 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 5922 seeds are put forward Round 1: 513 peptides, 75 chains. Longest chain 18 peptides. Score 0.565 Round 2: 547 peptides, 70 chains. Longest chain 25 peptides. Score 0.641 Round 3: 571 peptides, 65 chains. Longest chain 29 peptides. Score 0.696 Round 4: 573 peptides, 63 chains. Longest chain 31 peptides. Score 0.708 Round 5: 579 peptides, 65 chains. Longest chain 31 peptides. Score 0.705 Taking the results from Round 4 Chains 67, Residues 510, Estimated correctness of the model 66.9 % 15 chains (190 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 35 A and 46 A 65 chains (515 residues) following loop building 14 chains (200 residues) in sequence following loop building ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 10885 restraints for refining 6018 atoms. 8125 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2610 (Rfree = 0.000) for 6018 atoms. Found 54 (54 requested) and removed 61 (27 requested) atoms. Cycle 7: After refmac, R = 0.2409 (Rfree = 0.000) for 5948 atoms. Found 32 (52 requested) and removed 40 (26 requested) atoms. Cycle 8: After refmac, R = 0.2307 (Rfree = 0.000) for 5908 atoms. Found 33 (51 requested) and removed 34 (26 requested) atoms. Cycle 9: After refmac, R = 0.2209 (Rfree = 0.000) for 5892 atoms. Found 17 (50 requested) and removed 38 (26 requested) atoms. Cycle 10: After refmac, R = 0.2199 (Rfree = 0.000) for 5850 atoms. Found 33 (48 requested) and removed 32 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.65 2.76 Search for helices and strands: 0 residues in 0 chains, 6006 seeds are put forward NCS extension: 9 residues added (8 deleted due to clashes), 6015 seeds are put forward Round 1: 538 peptides, 67 chains. Longest chain 27 peptides. Score 0.647 Round 2: 591 peptides, 58 chains. Longest chain 29 peptides. Score 0.749 Round 3: 560 peptides, 63 chains. Longest chain 28 peptides. Score 0.694 Round 4: 588 peptides, 63 chains. Longest chain 27 peptides. Score 0.724 Round 5: 575 peptides, 63 chains. Longest chain 27 peptides. Score 0.710 Taking the results from Round 2 Chains 68, Residues 533, Estimated correctness of the model 74.9 % 16 chains (186 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 218 A and 228 A 65 chains (536 residues) following loop building 15 chains (195 residues) in sequence following loop building ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 10700 restraints for refining 6016 atoms. 7863 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2468 (Rfree = 0.000) for 6016 atoms. Found 49 (49 requested) and removed 68 (27 requested) atoms. Cycle 12: After refmac, R = 0.2237 (Rfree = 0.000) for 5954 atoms. Found 33 (47 requested) and removed 32 (26 requested) atoms. Cycle 13: After refmac, R = 0.2132 (Rfree = 0.000) for 5934 atoms. Found 20 (46 requested) and removed 30 (26 requested) atoms. Cycle 14: After refmac, R = 0.2064 (Rfree = 0.000) for 5913 atoms. Found 21 (45 requested) and removed 31 (26 requested) atoms. Cycle 15: After refmac, R = 0.1993 (Rfree = 0.000) for 5887 atoms. Found 22 (43 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.69 2.80 Search for helices and strands: 0 residues in 0 chains, 5986 seeds are put forward NCS extension: 17 residues added (10 deleted due to clashes), 6003 seeds are put forward Round 1: 506 peptides, 67 chains. Longest chain 26 peptides. Score 0.605 Round 2: 526 peptides, 56 chains. Longest chain 36 peptides. Score 0.692 Round 3: 542 peptides, 64 chains. Longest chain 26 peptides. Score 0.668 Round 4: 545 peptides, 60 chains. Longest chain 27 peptides. Score 0.693 Round 5: 531 peptides, 61 chains. Longest chain 26 peptides. Score 0.671 Taking the results from Round 4 Chains 63, Residues 485, Estimated correctness of the model 63.7 % 12 chains (133 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11618 restraints for refining 6016 atoms. 9233 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2356 (Rfree = 0.000) for 6016 atoms. Found 43 (43 requested) and removed 58 (27 requested) atoms. Cycle 17: After refmac, R = 0.2145 (Rfree = 0.000) for 5971 atoms. Found 21 (42 requested) and removed 31 (26 requested) atoms. Cycle 18: After refmac, R = 0.2077 (Rfree = 0.000) for 5945 atoms. Found 20 (42 requested) and removed 29 (26 requested) atoms. Cycle 19: After refmac, R = 0.2015 (Rfree = 0.000) for 5924 atoms. Found 17 (42 requested) and removed 29 (26 requested) atoms. Cycle 20: After refmac, R = 0.1989 (Rfree = 0.000) for 5906 atoms. Found 27 (42 requested) and removed 32 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.75 2.86 Search for helices and strands: 0 residues in 0 chains, 6024 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 6046 seeds are put forward Round 1: 517 peptides, 66 chains. Longest chain 22 peptides. Score 0.626 Round 2: 538 peptides, 61 chains. Longest chain 31 peptides. Score 0.680 Round 3: 553 peptides, 62 chains. Longest chain 27 peptides. Score 0.691 Round 4: 562 peptides, 64 chains. Longest chain 31 peptides. Score 0.691 Round 5: 547 peptides, 65 chains. Longest chain 26 peptides. Score 0.669 Taking the results from Round 4 Chains 66, Residues 498, Estimated correctness of the model 63.2 % 8 chains (106 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11944 restraints for refining 6018 atoms. 9600 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2318 (Rfree = 0.000) for 6018 atoms. Found 43 (43 requested) and removed 43 (27 requested) atoms. Cycle 22: After refmac, R = 0.2175 (Rfree = 0.000) for 6000 atoms. Found 30 (43 requested) and removed 33 (27 requested) atoms. Cycle 23: After refmac, R = 0.2116 (Rfree = 0.000) for 5986 atoms. Found 13 (42 requested) and removed 30 (26 requested) atoms. Cycle 24: After refmac, R = 0.2070 (Rfree = 0.000) for 5957 atoms. Found 19 (42 requested) and removed 28 (26 requested) atoms. Cycle 25: After refmac, R = 0.2048 (Rfree = 0.000) for 5940 atoms. Found 16 (42 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.72 2.83 Search for helices and strands: 0 residues in 0 chains, 6099 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6118 seeds are put forward Round 1: 492 peptides, 66 chains. Longest chain 21 peptides. Score 0.592 Round 2: 533 peptides, 64 chains. Longest chain 29 peptides. Score 0.657 Round 3: 531 peptides, 59 chains. Longest chain 29 peptides. Score 0.682 Round 4: 534 peptides, 63 chains. Longest chain 29 peptides. Score 0.664 Round 5: 533 peptides, 62 chains. Longest chain 26 peptides. Score 0.668 Taking the results from Round 3 Chains 64, Residues 472, Estimated correctness of the model 61.3 % 12 chains (138 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11526 restraints for refining 6018 atoms. 9108 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2368 (Rfree = 0.000) for 6018 atoms. Found 43 (43 requested) and removed 61 (27 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2279 (Rfree = 0.000) for 5979 atoms. Found 23 (42 requested) and removed 34 (26 requested) atoms. Cycle 28: After refmac, R = 0.2241 (Rfree = 0.000) for 5952 atoms. Found 27 (42 requested) and removed 31 (26 requested) atoms. Cycle 29: After refmac, R = 0.2194 (Rfree = 0.000) for 5930 atoms. Found 30 (42 requested) and removed 29 (26 requested) atoms. Cycle 30: After refmac, R = 0.2123 (Rfree = 0.000) for 5917 atoms. Found 30 (42 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.70 2.81 Search for helices and strands: 0 residues in 0 chains, 6052 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 6080 seeds are put forward Round 1: 500 peptides, 68 chains. Longest chain 22 peptides. Score 0.590 Round 2: 528 peptides, 61 chains. Longest chain 25 peptides. Score 0.668 Round 3: 539 peptides, 61 chains. Longest chain 26 peptides. Score 0.681 Round 4: 527 peptides, 59 chains. Longest chain 31 peptides. Score 0.678 Round 5: 515 peptides, 64 chains. Longest chain 25 peptides. Score 0.635 Taking the results from Round 3 Chains 67, Residues 478, Estimated correctness of the model 61.0 % 9 chains (94 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12002 restraints for refining 6017 atoms. 9769 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2432 (Rfree = 0.000) for 6017 atoms. Found 43 (43 requested) and removed 50 (27 requested) atoms. Cycle 32: After refmac, R = 0.2315 (Rfree = 0.000) for 5984 atoms. Found 35 (42 requested) and removed 37 (26 requested) atoms. Cycle 33: After refmac, R = 0.2233 (Rfree = 0.000) for 5962 atoms. Found 30 (42 requested) and removed 29 (26 requested) atoms. Cycle 34: After refmac, R = 0.2173 (Rfree = 0.000) for 5951 atoms. Found 23 (42 requested) and removed 31 (26 requested) atoms. Cycle 35: After refmac, R = 0.2138 (Rfree = 0.000) for 5929 atoms. Found 32 (42 requested) and removed 31 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.71 2.82 Search for helices and strands: 0 residues in 0 chains, 6051 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6064 seeds are put forward Round 1: 474 peptides, 67 chains. Longest chain 19 peptides. Score 0.559 Round 2: 510 peptides, 63 chains. Longest chain 26 peptides. Score 0.634 Round 3: 506 peptides, 63 chains. Longest chain 27 peptides. Score 0.629 Round 4: 512 peptides, 64 chains. Longest chain 22 peptides. Score 0.631 Round 5: 521 peptides, 67 chains. Longest chain 22 peptides. Score 0.625 Taking the results from Round 2 Chains 66, Residues 447, Estimated correctness of the model 49.9 % 11 chains (72 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12382 restraints for refining 6017 atoms. 10404 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2217 (Rfree = 0.000) for 6017 atoms. Found 43 (43 requested) and removed 39 (27 requested) atoms. Cycle 37: After refmac, R = 0.2145 (Rfree = 0.000) for 5998 atoms. Found 21 (43 requested) and removed 35 (27 requested) atoms. Cycle 38: After refmac, R = 0.2109 (Rfree = 0.000) for 5970 atoms. Found 30 (42 requested) and removed 32 (26 requested) atoms. Cycle 39: After refmac, R = 0.2091 (Rfree = 0.000) for 5959 atoms. Found 28 (42 requested) and removed 31 (26 requested) atoms. Cycle 40: After refmac, R = 0.2033 (Rfree = 0.000) for 5951 atoms. Found 19 (42 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.72 2.83 Search for helices and strands: 0 residues in 0 chains, 6054 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6074 seeds are put forward Round 1: 445 peptides, 68 chains. Longest chain 16 peptides. Score 0.507 Round 2: 470 peptides, 62 chains. Longest chain 22 peptides. Score 0.586 Round 3: 499 peptides, 63 chains. Longest chain 19 peptides. Score 0.620 Round 4: 506 peptides, 68 chains. Longest chain 16 peptides. Score 0.599 Round 5: 486 peptides, 61 chains. Longest chain 22 peptides. Score 0.614 Taking the results from Round 3 Chains 64, Residues 436, Estimated correctness of the model 46.3 % 8 chains (65 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12495 restraints for refining 6018 atoms. 10571 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2284 (Rfree = 0.000) for 6018 atoms. Found 43 (43 requested) and removed 49 (27 requested) atoms. Cycle 42: After refmac, R = 0.2190 (Rfree = 0.000) for 5995 atoms. Found 29 (42 requested) and removed 27 (26 requested) atoms. Cycle 43: After refmac, R = 0.2120 (Rfree = 0.000) for 5993 atoms. Found 36 (42 requested) and removed 31 (26 requested) atoms. Cycle 44: After refmac, R = 0.2045 (Rfree = 0.000) for 5988 atoms. Found 36 (42 requested) and removed 28 (26 requested) atoms. Cycle 45: After refmac, R = 0.1983 (Rfree = 0.000) for 5988 atoms. Found 19 (42 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.75 2.86 Search for helices and strands: 0 residues in 0 chains, 6102 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 6119 seeds are put forward Round 1: 413 peptides, 65 chains. Longest chain 14 peptides. Score 0.475 Round 2: 455 peptides, 61 chains. Longest chain 22 peptides. Score 0.570 Round 3: 456 peptides, 63 chains. Longest chain 18 peptides. Score 0.559 Round 4: 438 peptides, 55 chains. Longest chain 29 peptides. Score 0.585 Round 5: 440 peptides, 59 chains. Longest chain 28 peptides. Score 0.561 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 383, Estimated correctness of the model 37.0 % 11 chains (90 residues) have been docked in sequence Sequence coverage is 23 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 58 chains (383 residues) following loop building 11 chains (90 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13478 reflections ( 96.64 % complete ) and 12566 restraints for refining 6017 atoms. 10781 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2148 (Rfree = 0.000) for 6017 atoms. Found 0 (43 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2157 (Rfree = 0.000) for 5969 atoms. Found 0 (42 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2111 (Rfree = 0.000) for 5935 atoms. Found 0 (42 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.2085 (Rfree = 0.000) for 5900 atoms. TimeTaking 59.18