Mon 24 Dec 00:17:52 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 1vky-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.4-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/1vky-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.4-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 00:17:56 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/1vky-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.4-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 727 and 0 Target number of residues in the AU: 727 Target solvent content: 0.5922 Checking the provided sequence file Detected sequence length: 347 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 694 Adjusted target solvent content: 0.61 Input MTZ file: 1vky-3.4-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: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5552 target number of atoms Had to go as low as 0.75 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: 41.380 3.400 Wilson plot Bfac: 49.39 13613 reflections ( 99.72 % complete ) and 0 restraints for refining 6184 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3092 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2687 (Rfree = 0.000) for 6184 atoms. Found 46 (46 requested) and removed 66 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 2.65 Search for helices and strands: 0 residues in 0 chains, 6256 seeds are put forward NCS extension: 0 residues added, 6256 seeds are put forward Round 1: 349 peptides, 50 chains. Longest chain 22 peptides. Score 0.452 Round 2: 424 peptides, 49 chains. Longest chain 51 peptides. Score 0.569 Round 3: 409 peptides, 43 chains. Longest chain 30 peptides. Score 0.586 Round 4: 400 peptides, 42 chains. Longest chain 25 peptides. Score 0.580 Round 5: 410 peptides, 45 chains. Longest chain 25 peptides. Score 0.575 Taking the results from Round 3 Chains 47, Residues 366, Estimated correctness of the model 24.0 % 4 chains (80 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10062 restraints for refining 5046 atoms. 8335 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2453 (Rfree = 0.000) for 5046 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. Cycle 2: After refmac, R = 0.2300 (Rfree = 0.000) for 4960 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 3: After refmac, R = 0.2244 (Rfree = 0.000) for 4913 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 4: After refmac, R = 0.2129 (Rfree = 0.000) for 4894 atoms. Found 25 (37 requested) and removed 30 (18 requested) atoms. Cycle 5: After refmac, R = 0.2105 (Rfree = 0.000) for 4859 atoms. Found 35 (36 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 2.61 Search for helices and strands: 0 residues in 0 chains, 5004 seeds are put forward NCS extension: 34 residues added (8 deleted due to clashes), 5038 seeds are put forward Round 1: 397 peptides, 52 chains. Longest chain 27 peptides. Score 0.511 Round 2: 428 peptides, 45 chains. Longest chain 38 peptides. Score 0.598 Round 3: 434 peptides, 51 chains. Longest chain 27 peptides. Score 0.570 Round 4: 427 peptides, 47 chains. Longest chain 35 peptides. Score 0.585 Round 5: 415 peptides, 45 chains. Longest chain 24 peptides. Score 0.582 Taking the results from Round 2 Chains 45, Residues 383, Estimated correctness of the model 28.0 % 3 chains (68 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10109 restraints for refining 5028 atoms. 8308 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2427 (Rfree = 0.000) for 5028 atoms. Found 37 (37 requested) and removed 60 (18 requested) atoms. Cycle 7: After refmac, R = 0.2277 (Rfree = 0.000) for 4970 atoms. Found 29 (37 requested) and removed 38 (18 requested) atoms. Cycle 8: After refmac, R = 0.2176 (Rfree = 0.000) for 4945 atoms. Found 22 (37 requested) and removed 26 (18 requested) atoms. Cycle 9: After refmac, R = 0.2114 (Rfree = 0.000) for 4929 atoms. Found 15 (37 requested) and removed 28 (18 requested) atoms. Cycle 10: After refmac, R = 0.2052 (Rfree = 0.000) for 4904 atoms. Found 30 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.06 2.64 Search for helices and strands: 0 residues in 0 chains, 5036 seeds are put forward NCS extension: 23 residues added (13 deleted due to clashes), 5059 seeds are put forward Round 1: 397 peptides, 49 chains. Longest chain 29 peptides. Score 0.531 Round 2: 432 peptides, 43 chains. Longest chain 25 peptides. Score 0.615 Round 3: 438 peptides, 42 chains. Longest chain 51 peptides. Score 0.628 Round 4: 435 peptides, 38 chains. Longest chain 44 peptides. Score 0.648 Round 5: 418 peptides, 43 chains. Longest chain 38 peptides. Score 0.598 Taking the results from Round 4 Chains 39, Residues 397, Estimated correctness of the model 43.6 % 5 chains (135 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 9291 restraints for refining 5048 atoms. 7155 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2508 (Rfree = 0.000) for 5048 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 12: After refmac, R = 0.2316 (Rfree = 0.000) for 4989 atoms. Found 38 (38 requested) and removed 29 (19 requested) atoms. Cycle 13: After refmac, R = 0.2242 (Rfree = 0.000) for 4963 atoms. Found 29 (37 requested) and removed 30 (18 requested) atoms. Cycle 14: After refmac, R = 0.2166 (Rfree = 0.000) for 4945 atoms. Found 27 (37 requested) and removed 28 (18 requested) atoms. Cycle 15: After refmac, R = 0.2103 (Rfree = 0.000) for 4936 atoms. Found 21 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 2.63 Search for helices and strands: 0 residues in 0 chains, 5051 seeds are put forward NCS extension: 33 residues added (18 deleted due to clashes), 5084 seeds are put forward Round 1: 407 peptides, 54 chains. Longest chain 17 peptides. Score 0.513 Round 2: 440 peptides, 42 chains. Longest chain 37 peptides. Score 0.631 Round 3: 434 peptides, 45 chains. Longest chain 52 peptides. Score 0.606 Round 4: 427 peptides, 45 chains. Longest chain 27 peptides. Score 0.597 Round 5: 441 peptides, 49 chains. Longest chain 39 peptides. Score 0.591 Taking the results from Round 2 Chains 42, Residues 398, Estimated correctness of the model 38.5 % 5 chains (98 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 9798 restraints for refining 5048 atoms. 7837 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2467 (Rfree = 0.000) for 5048 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 17: After refmac, R = 0.2274 (Rfree = 0.000) for 5018 atoms. Found 36 (38 requested) and removed 34 (19 requested) atoms. Cycle 18: After refmac, R = 0.2191 (Rfree = 0.000) for 5009 atoms. Found 26 (37 requested) and removed 27 (18 requested) atoms. Cycle 19: After refmac, R = 0.2189 (Rfree = 0.000) for 4992 atoms. Found 33 (37 requested) and removed 29 (18 requested) atoms. Cycle 20: After refmac, R = 0.2142 (Rfree = 0.000) for 4990 atoms. Found 23 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 2.63 Search for helices and strands: 0 residues in 0 chains, 5111 seeds are put forward NCS extension: 32 residues added (26 deleted due to clashes), 5143 seeds are put forward Round 1: 389 peptides, 45 chains. Longest chain 30 peptides. Score 0.546 Round 2: 441 peptides, 48 chains. Longest chain 32 peptides. Score 0.597 Round 3: 445 peptides, 49 chains. Longest chain 32 peptides. Score 0.596 Round 4: 451 peptides, 48 chains. Longest chain 35 peptides. Score 0.610 Round 5: 435 peptides, 44 chains. Longest chain 40 peptides. Score 0.613 Taking the results from Round 5 Chains 48, Residues 391, Estimated correctness of the model 32.9 % 8 chains (166 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 9162 restraints for refining 5047 atoms. 6938 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2535 (Rfree = 0.000) for 5047 atoms. Found 38 (38 requested) and removed 49 (19 requested) atoms. Cycle 22: After refmac, R = 0.2343 (Rfree = 0.000) for 4998 atoms. Found 34 (38 requested) and removed 24 (19 requested) atoms. Cycle 23: After refmac, R = 0.2284 (Rfree = 0.000) for 4980 atoms. Found 25 (37 requested) and removed 25 (18 requested) atoms. Cycle 24: After refmac, R = 0.2260 (Rfree = 0.000) for 4967 atoms. Found 23 (37 requested) and removed 23 (18 requested) atoms. Cycle 25: After refmac, R = 0.2251 (Rfree = 0.000) for 4955 atoms. Found 25 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 2.66 Search for helices and strands: 0 residues in 0 chains, 5085 seeds are put forward NCS extension: 33 residues added (34 deleted due to clashes), 5118 seeds are put forward Round 1: 401 peptides, 49 chains. Longest chain 36 peptides. Score 0.537 Round 2: 424 peptides, 47 chains. Longest chain 39 peptides. Score 0.581 Round 3: 427 peptides, 50 chains. Longest chain 21 peptides. Score 0.567 Round 4: 432 peptides, 46 chains. Longest chain 41 peptides. Score 0.597 Round 5: 434 peptides, 45 chains. Longest chain 44 peptides. Score 0.606 Taking the results from Round 5 Chains 52, Residues 389, Estimated correctness of the model 30.6 % 5 chains (90 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 9995 restraints for refining 5049 atoms. 8111 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2651 (Rfree = 0.000) for 5049 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 27: After refmac, R = 0.2473 (Rfree = 0.000) for 5026 atoms. Found 32 (38 requested) and removed 28 (19 requested) atoms. Cycle 28: After refmac, R = 0.2384 (Rfree = 0.000) for 5021 atoms. Found 14 (37 requested) and removed 28 (18 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2334 (Rfree = 0.000) for 4997 atoms. Found 17 (37 requested) and removed 20 (18 requested) atoms. Cycle 30: After refmac, R = 0.2330 (Rfree = 0.000) for 4986 atoms. Found 20 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.08 2.65 Search for helices and strands: 0 residues in 0 chains, 5116 seeds are put forward NCS extension: 22 residues added (12 deleted due to clashes), 5138 seeds are put forward Round 1: 407 peptides, 56 chains. Longest chain 18 peptides. Score 0.499 Round 2: 423 peptides, 52 chains. Longest chain 25 peptides. Score 0.548 Round 3: 414 peptides, 51 chains. Longest chain 25 peptides. Score 0.542 Round 4: 419 peptides, 49 chains. Longest chain 25 peptides. Score 0.562 Round 5: 435 peptides, 54 chains. Longest chain 20 peptides. Score 0.553 Taking the results from Round 4 Chains 51, Residues 370, Estimated correctness of the model 15.8 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10584 restraints for refining 5048 atoms. 8933 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2629 (Rfree = 0.000) for 5048 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. Cycle 32: After refmac, R = 0.2450 (Rfree = 0.000) for 5035 atoms. Found 31 (38 requested) and removed 30 (19 requested) atoms. Cycle 33: After refmac, R = 0.2442 (Rfree = 0.000) for 5024 atoms. Found 22 (38 requested) and removed 30 (19 requested) atoms. Cycle 34: After refmac, R = 0.2413 (Rfree = 0.000) for 5006 atoms. Found 18 (37 requested) and removed 21 (18 requested) atoms. Cycle 35: After refmac, R = 0.2420 (Rfree = 0.000) for 4994 atoms. Found 19 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 2.66 Search for helices and strands: 0 residues in 0 chains, 5102 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5118 seeds are put forward Round 1: 359 peptides, 51 chains. Longest chain 20 peptides. Score 0.460 Round 2: 394 peptides, 49 chains. Longest chain 21 peptides. Score 0.527 Round 3: 405 peptides, 49 chains. Longest chain 22 peptides. Score 0.543 Round 4: 400 peptides, 45 chains. Longest chain 21 peptides. Score 0.561 Round 5: 402 peptides, 48 chains. Longest chain 28 peptides. Score 0.545 Taking the results from Round 4 Chains 45, Residues 355, Estimated correctness of the model 15.4 % 5 chains (72 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10473 restraints for refining 5049 atoms. 8788 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2579 (Rfree = 0.000) for 5049 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 37: After refmac, R = 0.2454 (Rfree = 0.000) for 5030 atoms. Found 28 (38 requested) and removed 28 (19 requested) atoms. Cycle 38: After refmac, R = 0.2404 (Rfree = 0.000) for 5019 atoms. Found 27 (37 requested) and removed 24 (18 requested) atoms. Cycle 39: After refmac, R = 0.2268 (Rfree = 0.000) for 5013 atoms. Found 23 (37 requested) and removed 20 (18 requested) atoms. Cycle 40: After refmac, R = 0.2300 (Rfree = 0.000) for 5007 atoms. Found 23 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 2.62 Search for helices and strands: 0 residues in 0 chains, 5136 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5154 seeds are put forward Round 1: 364 peptides, 54 chains. Longest chain 21 peptides. Score 0.447 Round 2: 405 peptides, 46 chains. Longest chain 26 peptides. Score 0.562 Round 3: 402 peptides, 47 chains. Longest chain 29 peptides. Score 0.551 Round 4: 390 peptides, 47 chains. Longest chain 26 peptides. Score 0.534 Round 5: 400 peptides, 46 chains. Longest chain 31 peptides. Score 0.555 Taking the results from Round 2 Chains 50, Residues 359, Estimated correctness of the model 15.8 % 5 chains (90 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10007 restraints for refining 5049 atoms. 8223 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2468 (Rfree = 0.000) for 5049 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Cycle 42: After refmac, R = 0.2343 (Rfree = 0.000) for 5045 atoms. Found 20 (38 requested) and removed 30 (19 requested) atoms. Cycle 43: After refmac, R = 0.2282 (Rfree = 0.000) for 5025 atoms. Found 24 (38 requested) and removed 22 (19 requested) atoms. Cycle 44: After refmac, R = 0.2276 (Rfree = 0.000) for 5015 atoms. Found 12 (37 requested) and removed 21 (18 requested) atoms. Cycle 45: After refmac, R = 0.2284 (Rfree = 0.000) for 4995 atoms. Found 26 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 2.66 Search for helices and strands: 0 residues in 0 chains, 5114 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 5150 seeds are put forward Round 1: 358 peptides, 52 chains. Longest chain 25 peptides. Score 0.452 Round 2: 392 peptides, 48 chains. Longest chain 25 peptides. Score 0.531 Round 3: 410 peptides, 49 chains. Longest chain 22 peptides. Score 0.550 Round 4: 405 peptides, 50 chains. Longest chain 36 peptides. Score 0.536 Round 5: 396 peptides, 48 chains. Longest chain 31 peptides. Score 0.536 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 361, Estimated correctness of the model 11.5 % 5 chains (73 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input Building loops using Loopy2018 50 chains (361 residues) following loop building 5 chains (73 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13613 reflections ( 99.72 % complete ) and 10310 restraints for refining 5048 atoms. 8586 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2580 (Rfree = 0.000) for 5048 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2547 (Rfree = 0.000) for 5011 atoms. Found 0 (37 requested) and removed 7 (18 requested) atoms. Cycle 48: After refmac, R = 0.2524 (Rfree = 0.000) for 4999 atoms. Found 0 (37 requested) and removed 8 (18 requested) atoms. Cycle 49: After refmac, R = 0.2485 (Rfree = 0.000) for 4987 atoms. TimeTaking 57.82