Sun 23 Dec 23:46:51 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-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 23:46:56 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-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 702 and 0 Target number of residues in the AU: 702 Target solvent content: 0.6063 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 55.00 11505 reflections ( 99.71 % complete ) and 0 restraints for refining 6125 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3077 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2761 (Rfree = 0.000) for 6125 atoms. Found 39 (39 requested) and removed 64 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 2.81 Search for helices and strands: 0 residues in 0 chains, 6192 seeds are put forward NCS extension: 0 residues added, 6192 seeds are put forward Round 1: 347 peptides, 51 chains. Longest chain 26 peptides. Score 0.441 Round 2: 396 peptides, 51 chains. Longest chain 21 peptides. Score 0.517 Round 3: 406 peptides, 43 chains. Longest chain 45 peptides. Score 0.582 Round 4: 418 peptides, 45 chains. Longest chain 24 peptides. Score 0.586 Round 5: 439 peptides, 47 chains. Longest chain 36 peptides. Score 0.600 Taking the results from Round 5 Chains 47, Residues 392, Estimated correctness of the model 14.7 % 4 chains (70 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10380 restraints for refining 5032 atoms. 8568 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2454 (Rfree = 0.000) for 5032 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 2: After refmac, R = 0.2445 (Rfree = 0.000) for 4955 atoms. Found 32 (32 requested) and removed 39 (16 requested) atoms. Cycle 3: After refmac, R = 0.2306 (Rfree = 0.000) for 4913 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 4: After refmac, R = 0.2259 (Rfree = 0.000) for 4895 atoms. Found 20 (31 requested) and removed 25 (15 requested) atoms. Cycle 5: After refmac, R = 0.2151 (Rfree = 0.000) for 4871 atoms. Found 13 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 2.78 Search for helices and strands: 0 residues in 0 chains, 4983 seeds are put forward NCS extension: 34 residues added (19 deleted due to clashes), 5017 seeds are put forward Round 1: 393 peptides, 45 chains. Longest chain 24 peptides. Score 0.552 Round 2: 439 peptides, 47 chains. Longest chain 33 peptides. Score 0.600 Round 3: 418 peptides, 43 chains. Longest chain 40 peptides. Score 0.598 Round 4: 419 peptides, 48 chains. Longest chain 25 peptides. Score 0.568 Round 5: 419 peptides, 47 chains. Longest chain 25 peptides. Score 0.575 Taking the results from Round 2 Chains 51, Residues 392, Estimated correctness of the model 14.7 % 8 chains (126 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 9553 restraints for refining 5033 atoms. 7515 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2415 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 54 (16 requested) atoms. Cycle 7: After refmac, R = 0.2279 (Rfree = 0.000) for 4971 atoms. Found 32 (32 requested) and removed 44 (16 requested) atoms. Cycle 8: After refmac, R = 0.2235 (Rfree = 0.000) for 4936 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. Cycle 9: After refmac, R = 0.2167 (Rfree = 0.000) for 4920 atoms. Found 29 (31 requested) and removed 28 (15 requested) atoms. Cycle 10: After refmac, R = 0.2119 (Rfree = 0.000) for 4910 atoms. Found 17 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 2.77 Search for helices and strands: 0 residues in 0 chains, 5056 seeds are put forward NCS extension: 19 residues added (12 deleted due to clashes), 5075 seeds are put forward Round 1: 397 peptides, 51 chains. Longest chain 25 peptides. Score 0.518 Round 2: 414 peptides, 44 chains. Longest chain 29 peptides. Score 0.586 Round 3: 416 peptides, 46 chains. Longest chain 42 peptides. Score 0.577 Round 4: 401 peptides, 41 chains. Longest chain 28 peptides. Score 0.588 Round 5: 412 peptides, 41 chains. Longest chain 26 peptides. Score 0.602 Taking the results from Round 5 Chains 47, Residues 371, Estimated correctness of the model 15.4 % 7 chains (94 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 9996 restraints for refining 5031 atoms. 8168 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2515 (Rfree = 0.000) for 5031 atoms. Found 32 (32 requested) and removed 37 (16 requested) atoms. Cycle 12: After refmac, R = 0.2321 (Rfree = 0.000) for 4989 atoms. Found 21 (32 requested) and removed 46 (16 requested) atoms. Cycle 13: After refmac, R = 0.2204 (Rfree = 0.000) for 4945 atoms. Found 21 (31 requested) and removed 36 (15 requested) atoms. Cycle 14: After refmac, R = 0.2104 (Rfree = 0.000) for 4917 atoms. Found 11 (31 requested) and removed 29 (15 requested) atoms. Cycle 15: After refmac, R = 0.2091 (Rfree = 0.000) for 4882 atoms. Found 15 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 2.76 Search for helices and strands: 0 residues in 0 chains, 5007 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 5021 seeds are put forward Round 1: 392 peptides, 53 chains. Longest chain 26 peptides. Score 0.497 Round 2: 427 peptides, 48 chains. Longest chain 33 peptides. Score 0.579 Round 3: 430 peptides, 43 chains. Longest chain 39 peptides. Score 0.613 Round 4: 437 peptides, 48 chains. Longest chain 50 peptides. Score 0.592 Round 5: 440 peptides, 48 chains. Longest chain 29 peptides. Score 0.596 Taking the results from Round 3 Chains 47, Residues 387, Estimated correctness of the model 19.7 % 6 chains (110 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 9681 restraints for refining 5031 atoms. 7712 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2620 (Rfree = 0.000) for 5031 atoms. Found 32 (32 requested) and removed 48 (16 requested) atoms. Cycle 17: After refmac, R = 0.2504 (Rfree = 0.000) for 4980 atoms. Found 26 (32 requested) and removed 30 (16 requested) atoms. Cycle 18: After refmac, R = 0.2349 (Rfree = 0.000) for 4950 atoms. Found 15 (31 requested) and removed 36 (15 requested) atoms. Cycle 19: After refmac, R = 0.2267 (Rfree = 0.000) for 4919 atoms. Found 18 (31 requested) and removed 38 (15 requested) atoms. Cycle 20: After refmac, R = 0.2237 (Rfree = 0.000) for 4885 atoms. Found 20 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 2.77 Search for helices and strands: 0 residues in 0 chains, 5031 seeds are put forward NCS extension: 49 residues added (2 deleted due to clashes), 5080 seeds are put forward Round 1: 370 peptides, 56 chains. Longest chain 17 peptides. Score 0.442 Round 2: 395 peptides, 48 chains. Longest chain 20 peptides. Score 0.535 Round 3: 427 peptides, 51 chains. Longest chain 28 peptides. Score 0.560 Round 4: 423 peptides, 54 chains. Longest chain 20 peptides. Score 0.536 Round 5: 440 peptides, 53 chains. Longest chain 29 peptides. Score 0.566 Taking the results from Round 5 Chains 56, Residues 387, Estimated correctness of the model 0.9 % 10 chains (93 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 9961 restraints for refining 5033 atoms. 8109 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2654 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 43 (16 requested) atoms. Cycle 22: After refmac, R = 0.2528 (Rfree = 0.000) for 4994 atoms. Found 30 (32 requested) and removed 43 (16 requested) atoms. Cycle 23: After refmac, R = 0.2528 (Rfree = 0.000) for 4965 atoms. Found 21 (31 requested) and removed 38 (15 requested) atoms. Cycle 24: After refmac, R = 0.2440 (Rfree = 0.000) for 4940 atoms. Found 20 (31 requested) and removed 26 (15 requested) atoms. Cycle 25: After refmac, R = 0.2392 (Rfree = 0.000) for 4924 atoms. Found 10 (31 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 2.78 Search for helices and strands: 0 residues in 0 chains, 5029 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 5067 seeds are put forward Round 1: 377 peptides, 63 chains. Longest chain 20 peptides. Score 0.403 Round 2: 419 peptides, 55 chains. Longest chain 18 peptides. Score 0.524 Round 3: 399 peptides, 49 chains. Longest chain 25 peptides. Score 0.534 Round 4: 403 peptides, 50 chains. Longest chain 23 peptides. Score 0.533 Round 5: 401 peptides, 54 chains. Longest chain 24 peptides. Score 0.504 Taking the results from Round 3 Chains 53, Residues 350, Estimated correctness of the model 0.0 % 5 chains (66 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10585 restraints for refining 5033 atoms. 8986 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2622 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 31 (16 requested) atoms. Cycle 27: After refmac, R = 0.2448 (Rfree = 0.000) for 5007 atoms. Found 23 (32 requested) and removed 34 (16 requested) atoms. Cycle 28: After refmac, R = 0.2393 (Rfree = 0.000) for 4989 atoms. Found 18 (32 requested) and removed 34 (16 requested) atoms. Cycle 29: After refmac, R = 0.2349 (Rfree = 0.000) for 4968 atoms. Found 17 (31 requested) and removed 26 (15 requested) atoms. Cycle 30: After refmac, R = 0.2257 (Rfree = 0.000) for 4958 atoms. Found 18 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 2.76 Search for helices and strands: 0 residues in 0 chains, 5077 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 5101 seeds are put forward Round 1: 363 peptides, 55 chains. Longest chain 22 peptides. Score 0.438 Round 2: 359 peptides, 49 chains. Longest chain 35 peptides. Score 0.474 Round 3: 371 peptides, 49 chains. Longest chain 22 peptides. Score 0.493 Round 4: 375 peptides, 46 chains. Longest chain 20 peptides. Score 0.519 Round 5: 384 peptides, 48 chains. Longest chain 40 peptides. Score 0.519 Taking the results from Round 5 Chains 49, Residues 336, Estimated correctness of the model 0.0 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10964 restraints for refining 5030 atoms. 9516 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2553 (Rfree = 0.000) for 5030 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 32: After refmac, R = 0.2358 (Rfree = 0.000) for 5001 atoms. Found 30 (32 requested) and removed 35 (16 requested) atoms. Cycle 33: After refmac, R = 0.2264 (Rfree = 0.000) for 4986 atoms. Found 27 (32 requested) and removed 38 (16 requested) atoms. Cycle 34: After refmac, R = 0.2161 (Rfree = 0.000) for 4963 atoms. Found 17 (31 requested) and removed 33 (15 requested) atoms. Cycle 35: After refmac, R = 0.2148 (Rfree = 0.000) for 4938 atoms. Found 24 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 2.72 Search for helices and strands: 0 residues in 0 chains, 5060 seeds are put forward NCS extension: 37 residues added (4 deleted due to clashes), 5097 seeds are put forward Round 1: 322 peptides, 53 chains. Longest chain 24 peptides. Score 0.384 Round 2: 366 peptides, 48 chains. Longest chain 26 peptides. Score 0.492 Round 3: 369 peptides, 47 chains. Longest chain 23 peptides. Score 0.504 Round 4: 397 peptides, 47 chains. Longest chain 26 peptides. Score 0.544 Round 5: 385 peptides, 47 chains. Longest chain 24 peptides. Score 0.527 Taking the results from Round 4 Chains 49, Residues 350, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10982 restraints for refining 5033 atoms. 9548 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2383 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 37: After refmac, R = 0.2313 (Rfree = 0.000) for 5015 atoms. Found 24 (32 requested) and removed 36 (16 requested) atoms. Cycle 38: After refmac, R = 0.2150 (Rfree = 0.000) for 4987 atoms. Found 23 (32 requested) and removed 32 (16 requested) atoms. Cycle 39: After refmac, R = 0.2126 (Rfree = 0.000) for 4972 atoms. Found 16 (31 requested) and removed 28 (15 requested) atoms. Cycle 40: After refmac, R = 0.2069 (Rfree = 0.000) for 4954 atoms. Found 18 (31 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 2.71 Search for helices and strands: 0 residues in 0 chains, 5067 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 5094 seeds are put forward Round 1: 326 peptides, 52 chains. Longest chain 17 peptides. Score 0.398 Round 2: 357 peptides, 47 chains. Longest chain 18 peptides. Score 0.486 Round 3: 372 peptides, 49 chains. Longest chain 37 peptides. Score 0.494 Round 4: 371 peptides, 45 chains. Longest chain 26 peptides. Score 0.520 Round 5: 356 peptides, 46 chains. Longest chain 23 peptides. Score 0.491 Taking the results from Round 4 Chains 45, Residues 326, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 11151 restraints for refining 5032 atoms. 9765 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2374 (Rfree = 0.000) for 5032 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 42: After refmac, R = 0.2239 (Rfree = 0.000) for 5019 atoms. Found 25 (32 requested) and removed 35 (16 requested) atoms. Cycle 43: After refmac, R = 0.2180 (Rfree = 0.000) for 5004 atoms. Found 24 (32 requested) and removed 27 (16 requested) atoms. Cycle 44: After refmac, R = 0.2127 (Rfree = 0.000) for 4994 atoms. Found 22 (32 requested) and removed 24 (16 requested) atoms. Cycle 45: After refmac, R = 0.2089 (Rfree = 0.000) for 4986 atoms. Found 22 (32 requested) and removed 30 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 2.77 Search for helices and strands: 0 residues in 0 chains, 5108 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5122 seeds are put forward Round 1: 316 peptides, 57 chains. Longest chain 19 peptides. Score 0.342 Round 2: 348 peptides, 51 chains. Longest chain 28 peptides. Score 0.443 Round 3: 364 peptides, 48 chains. Longest chain 20 peptides. Score 0.489 Round 4: 374 peptides, 51 chains. Longest chain 27 peptides. Score 0.484 Round 5: 344 peptides, 50 chains. Longest chain 21 peptides. Score 0.443 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 316, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input Building loops using Loopy2018 49 chains (316 residues) following loop building 5 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11505 reflections ( 99.71 % complete ) and 11146 restraints for refining 5033 atoms. 9838 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2392 (Rfree = 0.000) for 5033 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2279 (Rfree = 0.000) for 5004 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2172 (Rfree = 0.000) for 4984 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2123 (Rfree = 0.000) for 4964 atoms. TimeTaking 67.97