Sun 23 Dec 23:57:54 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 1vme-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-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/1vme-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-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 ============================================================ Sun 23 Dec 23:57:59 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/1vme-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-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 642 and 0 Target number of residues in the AU: 642 Target solvent content: 0.6343 Checking the provided sequence file Detected sequence length: 410 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 820 Adjusted target solvent content: 0.53 Input MTZ file: 1vme-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: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6560 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: 48.998 3.200 Wilson plot Bfac: 68.69 15542 reflections ( 99.87 % complete ) and 0 restraints for refining 7311 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3039 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2792 (Rfree = 0.000) for 7311 atoms. Found 65 (65 requested) and removed 87 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 7448 seeds are put forward NCS extension: 0 residues added, 7448 seeds are put forward Round 1: 449 peptides, 76 chains. Longest chain 15 peptides. Score 0.432 Round 2: 534 peptides, 72 chains. Longest chain 20 peptides. Score 0.580 Round 3: 561 peptides, 62 chains. Longest chain 24 peptides. Score 0.666 Round 4: 583 peptides, 53 chains. Longest chain 31 peptides. Score 0.730 Round 5: 591 peptides, 58 chains. Longest chain 29 peptides. Score 0.715 Taking the results from Round 4 Chains 55, Residues 530, Estimated correctness of the model 71.3 % 7 chains (107 residues) have been docked in sequence Building loops using Loopy2018 55 chains (530 residues) following loop building 7 chains (107 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11599 restraints for refining 5987 atoms. 9100 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2612 (Rfree = 0.000) for 5987 atoms. Found 46 (53 requested) and removed 59 (26 requested) atoms. Cycle 2: After refmac, R = 0.2428 (Rfree = 0.000) for 5907 atoms. Found 18 (52 requested) and removed 34 (26 requested) atoms. Cycle 3: After refmac, R = 0.2323 (Rfree = 0.000) for 5853 atoms. Found 12 (50 requested) and removed 34 (26 requested) atoms. Cycle 4: After refmac, R = 0.2268 (Rfree = 0.000) for 5810 atoms. Found 15 (49 requested) and removed 30 (26 requested) atoms. Cycle 5: After refmac, R = 0.2266 (Rfree = 0.000) for 5776 atoms. Found 11 (48 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 5959 seeds are put forward NCS extension: 18 residues added (12 deleted due to clashes), 5977 seeds are put forward Round 1: 544 peptides, 67 chains. Longest chain 25 peptides. Score 0.621 Round 2: 601 peptides, 59 chains. Longest chain 38 peptides. Score 0.720 Round 3: 607 peptides, 52 chains. Longest chain 40 peptides. Score 0.755 Round 4: 605 peptides, 61 chains. Longest chain 28 peptides. Score 0.715 Round 5: 597 peptides, 58 chains. Longest chain 31 peptides. Score 0.721 Taking the results from Round 3 Chains 58, Residues 555, Estimated correctness of the model 76.0 % 11 chains (167 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 329 A and 338 A 56 chains (557 residues) following loop building 10 chains (175 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 10968 restraints for refining 5989 atoms. 8082 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2513 (Rfree = 0.000) for 5989 atoms. Found 48 (48 requested) and removed 50 (26 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2603 (Rfree = 0.000) for 5957 atoms. Found 47 (47 requested) and removed 52 (26 requested) atoms. Cycle 8: After refmac, R = 0.2309 (Rfree = 0.000) for 5930 atoms. Found 30 (46 requested) and removed 42 (26 requested) atoms. Cycle 9: After refmac, R = 0.2274 (Rfree = 0.000) for 5906 atoms. Found 28 (45 requested) and removed 38 (26 requested) atoms. Cycle 10: After refmac, R = 0.2151 (Rfree = 0.000) for 5879 atoms. Found 15 (43 requested) and removed 34 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 6037 seeds are put forward NCS extension: 18 residues added (6 deleted due to clashes), 6055 seeds are put forward Round 1: 540 peptides, 62 chains. Longest chain 36 peptides. Score 0.643 Round 2: 578 peptides, 53 chains. Longest chain 37 peptides. Score 0.725 Round 3: 599 peptides, 56 chains. Longest chain 30 peptides. Score 0.731 Round 4: 606 peptides, 51 chains. Longest chain 37 peptides. Score 0.758 Round 5: 599 peptides, 54 chains. Longest chain 29 peptides. Score 0.740 Taking the results from Round 4 Chains 56, Residues 555, Estimated correctness of the model 76.5 % 9 chains (147 residues) have been docked in sequence Building loops using Loopy2018 56 chains (555 residues) following loop building 9 chains (147 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11135 restraints for refining 5988 atoms. 8377 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2414 (Rfree = 0.000) for 5988 atoms. Found 40 (42 requested) and removed 54 (26 requested) atoms. Cycle 12: After refmac, R = 0.2607 (Rfree = 0.000) for 5955 atoms. Found 41 (41 requested) and removed 45 (26 requested) atoms. Cycle 13: After refmac, R = 0.2485 (Rfree = 0.000) for 5938 atoms. Found 40 (40 requested) and removed 41 (26 requested) atoms. Cycle 14: After refmac, R = 0.2195 (Rfree = 0.000) for 5919 atoms. Found 21 (39 requested) and removed 35 (26 requested) atoms. Cycle 15: After refmac, R = 0.2097 (Rfree = 0.000) for 5886 atoms. Found 23 (37 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 6056 seeds are put forward NCS extension: 41 residues added (11 deleted due to clashes), 6097 seeds are put forward Round 1: 528 peptides, 59 chains. Longest chain 26 peptides. Score 0.645 Round 2: 573 peptides, 47 chains. Longest chain 45 peptides. Score 0.747 Round 3: 572 peptides, 56 chains. Longest chain 43 peptides. Score 0.706 Round 4: 578 peptides, 57 chains. Longest chain 30 peptides. Score 0.707 Round 5: 570 peptides, 55 chains. Longest chain 39 peptides. Score 0.709 Taking the results from Round 2 Chains 52, Residues 526, Estimated correctness of the model 74.5 % 8 chains (163 residues) have been docked in sequence Building loops using Loopy2018 52 chains (526 residues) following loop building 8 chains (163 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11167 restraints for refining 5987 atoms. 8493 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2243 (Rfree = 0.000) for 5987 atoms. Found 37 (37 requested) and removed 40 (26 requested) atoms. Cycle 17: After refmac, R = 0.2112 (Rfree = 0.000) for 5977 atoms. Found 18 (36 requested) and removed 36 (26 requested) atoms. Cycle 18: After refmac, R = 0.2078 (Rfree = 0.000) for 5948 atoms. Found 14 (35 requested) and removed 33 (26 requested) atoms. Cycle 19: After refmac, R = 0.2013 (Rfree = 0.000) for 5922 atoms. Found 23 (34 requested) and removed 29 (26 requested) atoms. Cycle 20: After refmac, R = 0.2110 (Rfree = 0.000) for 5910 atoms. Found 28 (33 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 6083 seeds are put forward NCS extension: 31 residues added (34 deleted due to clashes), 6114 seeds are put forward Round 1: 552 peptides, 68 chains. Longest chain 36 peptides. Score 0.625 Round 2: 577 peptides, 59 chains. Longest chain 46 peptides. Score 0.697 Round 3: 593 peptides, 59 chains. Longest chain 42 peptides. Score 0.713 Round 4: 574 peptides, 60 chains. Longest chain 37 peptides. Score 0.689 Round 5: 578 peptides, 61 chains. Longest chain 48 peptides. Score 0.689 Taking the results from Round 3 Chains 60, Residues 534, Estimated correctness of the model 67.9 % 6 chains (119 residues) have been docked in sequence Building loops using Loopy2018 60 chains (534 residues) following loop building 6 chains (119 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11518 restraints for refining 5989 atoms. 8960 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2256 (Rfree = 0.000) for 5989 atoms. Found 32 (32 requested) and removed 44 (26 requested) atoms. Cycle 22: After refmac, R = 0.2134 (Rfree = 0.000) for 5961 atoms. Found 10 (31 requested) and removed 27 (26 requested) atoms. Cycle 23: After refmac, R = 0.2199 (Rfree = 0.000) for 5935 atoms. Found 30 (30 requested) and removed 28 (26 requested) atoms. Cycle 24: After refmac, R = 0.2004 (Rfree = 0.000) for 5925 atoms. Found 12 (29 requested) and removed 28 (26 requested) atoms. Cycle 25: After refmac, R = 0.1973 (Rfree = 0.000) for 5904 atoms. Found 13 (28 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 6063 seeds are put forward NCS extension: 24 residues added (16 deleted due to clashes), 6087 seeds are put forward Round 1: 523 peptides, 67 chains. Longest chain 31 peptides. Score 0.595 Round 2: 576 peptides, 62 chains. Longest chain 44 peptides. Score 0.682 Round 3: 601 peptides, 59 chains. Longest chain 25 peptides. Score 0.720 Round 4: 585 peptides, 54 chains. Longest chain 46 peptides. Score 0.727 Round 5: 583 peptides, 63 chains. Longest chain 36 peptides. Score 0.684 Taking the results from Round 4 Chains 59, Residues 531, Estimated correctness of the model 70.7 % 8 chains (134 residues) have been docked in sequence Building loops using Loopy2018 59 chains (531 residues) following loop building 8 chains (134 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11502 restraints for refining 5989 atoms. 8927 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2221 (Rfree = 0.000) for 5989 atoms. Found 26 (26 requested) and removed 43 (26 requested) atoms. Cycle 27: After refmac, R = 0.2155 (Rfree = 0.000) for 5959 atoms. Found 26 (26 requested) and removed 30 (26 requested) atoms. Cycle 28: After refmac, R = 0.1970 (Rfree = 0.000) for 5945 atoms. Found 22 (26 requested) and removed 32 (26 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1947 (Rfree = 0.000) for 5928 atoms. Found 17 (26 requested) and removed 29 (26 requested) atoms. Cycle 30: After refmac, R = 0.2069 (Rfree = 0.000) for 5912 atoms. Found 26 (26 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 6086 seeds are put forward NCS extension: 40 residues added (18 deleted due to clashes), 6126 seeds are put forward Round 1: 518 peptides, 65 chains. Longest chain 43 peptides. Score 0.600 Round 2: 573 peptides, 59 chains. Longest chain 44 peptides. Score 0.693 Round 3: 570 peptides, 65 chains. Longest chain 44 peptides. Score 0.661 Round 4: 541 peptides, 55 chains. Longest chain 24 peptides. Score 0.679 Round 5: 559 peptides, 61 chains. Longest chain 46 peptides. Score 0.669 Taking the results from Round 2 Chains 64, Residues 514, Estimated correctness of the model 63.7 % 8 chains (118 residues) have been docked in sequence ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11491 restraints for refining 5989 atoms. 9044 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2144 (Rfree = 0.000) for 5989 atoms. Found 26 (26 requested) and removed 40 (26 requested) atoms. Cycle 32: After refmac, R = 0.2023 (Rfree = 0.000) for 5960 atoms. Found 9 (26 requested) and removed 26 (26 requested) atoms. Cycle 33: After refmac, R = 0.1995 (Rfree = 0.000) for 5932 atoms. Found 15 (26 requested) and removed 26 (26 requested) atoms. Cycle 34: After refmac, R = 0.1952 (Rfree = 0.000) for 5917 atoms. Found 18 (26 requested) and removed 26 (26 requested) atoms. Cycle 35: After refmac, R = 0.1937 (Rfree = 0.000) for 5902 atoms. Found 14 (26 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 6063 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 6082 seeds are put forward Round 1: 473 peptides, 61 chains. Longest chain 36 peptides. Score 0.565 Round 2: 535 peptides, 60 chains. Longest chain 43 peptides. Score 0.647 Round 3: 521 peptides, 54 chains. Longest chain 43 peptides. Score 0.663 Round 4: 531 peptides, 59 chains. Longest chain 43 peptides. Score 0.648 Round 5: 521 peptides, 54 chains. Longest chain 28 peptides. Score 0.663 Taking the results from Round 5 Chains 60, Residues 467, Estimated correctness of the model 56.9 % 7 chains (94 residues) have been docked in sequence ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 12047 restraints for refining 5988 atoms. 9849 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2213 (Rfree = 0.000) for 5988 atoms. Found 26 (26 requested) and removed 43 (26 requested) atoms. Cycle 37: After refmac, R = 0.2106 (Rfree = 0.000) for 5961 atoms. Found 16 (26 requested) and removed 30 (26 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2012 (Rfree = 0.000) for 5940 atoms. Found 15 (26 requested) and removed 28 (26 requested) atoms. Cycle 39: After refmac, R = 0.1997 (Rfree = 0.000) for 5923 atoms. Found 12 (26 requested) and removed 28 (26 requested) atoms. Cycle 40: After refmac, R = 0.1964 (Rfree = 0.000) for 5900 atoms. Found 17 (26 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 6057 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 6078 seeds are put forward Round 1: 474 peptides, 61 chains. Longest chain 21 peptides. Score 0.566 Round 2: 506 peptides, 55 chains. Longest chain 25 peptides. Score 0.641 Round 3: 511 peptides, 53 chains. Longest chain 26 peptides. Score 0.657 Round 4: 500 peptides, 53 chains. Longest chain 29 peptides. Score 0.644 Round 5: 492 peptides, 54 chains. Longest chain 42 peptides. Score 0.630 Taking the results from Round 3 Chains 56, Residues 458, Estimated correctness of the model 55.5 % 6 chains (79 residues) have been docked in sequence ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 12172 restraints for refining 5989 atoms. 10077 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2108 (Rfree = 0.000) for 5989 atoms. Found 26 (26 requested) and removed 39 (26 requested) atoms. Cycle 42: After refmac, R = 0.1994 (Rfree = 0.000) for 5965 atoms. Found 11 (26 requested) and removed 28 (26 requested) atoms. Cycle 43: After refmac, R = 0.2015 (Rfree = 0.000) for 5941 atoms. Found 14 (26 requested) and removed 27 (26 requested) atoms. Cycle 44: After refmac, R = 0.1973 (Rfree = 0.000) for 5925 atoms. Found 14 (26 requested) and removed 26 (26 requested) atoms. Cycle 45: After refmac, R = 0.1896 (Rfree = 0.000) for 5909 atoms. Found 6 (26 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 6049 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6070 seeds are put forward Round 1: 445 peptides, 63 chains. Longest chain 35 peptides. Score 0.513 Round 2: 497 peptides, 56 chains. Longest chain 42 peptides. Score 0.625 Round 3: 510 peptides, 57 chains. Longest chain 42 peptides. Score 0.634 Round 4: 493 peptides, 56 chains. Longest chain 35 peptides. Score 0.620 Round 5: 498 peptides, 54 chains. Longest chain 42 peptides. Score 0.637 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 444, Estimated correctness of the model 50.7 % 7 chains (98 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (444 residues) following loop building 7 chains (98 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15542 reflections ( 99.87 % complete ) and 11979 restraints for refining 5989 atoms. 9885 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2193 (Rfree = 0.000) for 5989 atoms. Found 0 (26 requested) and removed 21 (26 requested) atoms. Cycle 47: After refmac, R = 0.2104 (Rfree = 0.000) for 5960 atoms. Found 0 (26 requested) and removed 12 (26 requested) atoms. Cycle 48: After refmac, R = 0.2059 (Rfree = 0.000) for 5940 atoms. Found 0 (26 requested) and removed 9 (26 requested) atoms. Cycle 49: After refmac, R = 0.2280 (Rfree = 0.000) for 5930 atoms. TimeTaking 67