Mon 24 Dec 07:47:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oh1-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.2-parrot-noncs ############### 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 07:47:58 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/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.2-parrot-noncs/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 546 and 0 Target number of residues in the AU: 546 Target solvent content: 0.6332 Checking the provided sequence file Detected sequence length: 179 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 716 Adjusted target solvent content: 0.52 Input MTZ file: 2oh1-3.2-parrot-noncs.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: 19 Cell parameters: 65.646 99.855 122.905 90.000 90.000 90.000 Input sequence file: 2oh1-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 5728 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: 77.501 3.200 Wilson plot Bfac: 68.01 13772 reflections ( 99.14 % complete ) and 0 restraints for refining 6384 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3089 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2679 (Rfree = 0.000) for 6384 atoms. Found 47 (57 requested) and removed 62 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 6481 seeds are put forward NCS extension: 0 residues added, 6481 seeds are put forward Round 1: 367 peptides, 62 chains. Longest chain 14 peptides. Score 0.426 Round 2: 466 peptides, 66 chains. Longest chain 18 peptides. Score 0.567 Round 3: 506 peptides, 62 chains. Longest chain 22 peptides. Score 0.650 Round 4: 519 peptides, 51 chains. Longest chain 42 peptides. Score 0.725 Round 5: 530 peptides, 52 chains. Longest chain 31 peptides. Score 0.732 Taking the results from Round 5 Chains 57, Residues 478, Estimated correctness of the model 71.7 % 6 chains (87 residues) have been docked in sequence Building loops using Loopy2018 57 chains (478 residues) following loop building 6 chains (87 residues) in sequence following loop building ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10108 restraints for refining 5225 atoms. 7930 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2533 (Rfree = 0.000) for 5225 atoms. Found 46 (46 requested) and removed 41 (23 requested) atoms. Cycle 2: After refmac, R = 0.2349 (Rfree = 0.000) for 5158 atoms. Found 21 (45 requested) and removed 44 (23 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2280 (Rfree = 0.000) for 5097 atoms. Found 20 (44 requested) and removed 27 (23 requested) atoms. Cycle 4: After refmac, R = 0.2228 (Rfree = 0.000) for 5072 atoms. Found 22 (42 requested) and removed 25 (22 requested) atoms. Cycle 5: After refmac, R = 0.2412 (Rfree = 0.000) for 5047 atoms. Found 36 (41 requested) and removed 33 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.09 Search for helices and strands: 0 residues in 0 chains, 5225 seeds are put forward NCS extension: 8 residues added (11 deleted due to clashes), 5233 seeds are put forward Round 1: 510 peptides, 61 chains. Longest chain 19 peptides. Score 0.661 Round 2: 549 peptides, 51 chains. Longest chain 36 peptides. Score 0.756 Round 3: 521 peptides, 49 chains. Longest chain 37 peptides. Score 0.737 Round 4: 536 peptides, 50 chains. Longest chain 31 peptides. Score 0.748 Round 5: 533 peptides, 49 chains. Longest chain 41 peptides. Score 0.749 Taking the results from Round 2 Chains 53, Residues 498, Estimated correctness of the model 76.1 % 4 chains (75 residues) have been docked in sequence Building loops using Loopy2018 53 chains (498 residues) following loop building 4 chains (75 residues) in sequence following loop building ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10273 restraints for refining 5229 atoms. 8029 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2466 (Rfree = 0.000) for 5229 atoms. Found 23 (41 requested) and removed 44 (23 requested) atoms. Cycle 7: After refmac, R = 0.2298 (Rfree = 0.000) for 5188 atoms. Found 9 (40 requested) and removed 32 (23 requested) atoms. Cycle 8: After refmac, R = 0.2429 (Rfree = 0.000) for 5155 atoms. Found 19 (40 requested) and removed 30 (23 requested) atoms. Cycle 9: After refmac, R = 0.2199 (Rfree = 0.000) for 5135 atoms. Found 8 (39 requested) and removed 26 (23 requested) atoms. Cycle 10: After refmac, R = 0.2169 (Rfree = 0.000) for 5106 atoms. Found 9 (37 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.10 Search for helices and strands: 0 residues in 0 chains, 5236 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 5250 seeds are put forward Round 1: 506 peptides, 55 chains. Longest chain 35 peptides. Score 0.690 Round 2: 523 peptides, 46 chains. Longest chain 37 peptides. Score 0.754 Round 3: 515 peptides, 53 chains. Longest chain 26 peptides. Score 0.711 Round 4: 526 peptides, 49 chains. Longest chain 32 peptides. Score 0.743 Round 5: 502 peptides, 53 chains. Longest chain 32 peptides. Score 0.696 Taking the results from Round 2 Chains 53, Residues 477, Estimated correctness of the model 75.8 % 6 chains (88 residues) have been docked in sequence Building loops using Loopy2018 53 chains (477 residues) following loop building 6 chains (88 residues) in sequence following loop building ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10221 restraints for refining 5229 atoms. 8003 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2339 (Rfree = 0.000) for 5229 atoms. Found 12 (37 requested) and removed 36 (23 requested) atoms. Cycle 12: After refmac, R = 0.2213 (Rfree = 0.000) for 5195 atoms. Found 8 (36 requested) and removed 30 (23 requested) atoms. Cycle 13: After refmac, R = 0.2147 (Rfree = 0.000) for 5156 atoms. Found 22 (35 requested) and removed 31 (23 requested) atoms. Cycle 14: After refmac, R = 0.2079 (Rfree = 0.000) for 5135 atoms. Found 5 (34 requested) and removed 34 (23 requested) atoms. Cycle 15: After refmac, R = 0.2045 (Rfree = 0.000) for 5098 atoms. Found 10 (32 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 3.11 Search for helices and strands: 0 residues in 0 chains, 5242 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5255 seeds are put forward Round 1: 470 peptides, 58 chains. Longest chain 20 peptides. Score 0.626 Round 2: 496 peptides, 49 chains. Longest chain 34 peptides. Score 0.711 Round 3: 522 peptides, 51 chains. Longest chain 43 peptides. Score 0.729 Round 4: 499 peptides, 49 chains. Longest chain 33 peptides. Score 0.714 Round 5: 509 peptides, 52 chains. Longest chain 35 peptides. Score 0.709 Taking the results from Round 3 Chains 54, Residues 471, Estimated correctness of the model 71.1 % 4 chains (56 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 97 A 54 chains (471 residues) following loop building 3 chains (64 residues) in sequence following loop building ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10454 restraints for refining 5228 atoms. 8406 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2395 (Rfree = 0.000) for 5228 atoms. Found 28 (32 requested) and removed 54 (23 requested) atoms. Cycle 17: After refmac, R = 0.2390 (Rfree = 0.000) for 5193 atoms. Found 31 (31 requested) and removed 36 (23 requested) atoms. Cycle 18: After refmac, R = 0.2160 (Rfree = 0.000) for 5178 atoms. Found 13 (30 requested) and removed 39 (23 requested) atoms. Cycle 19: After refmac, R = 0.2465 (Rfree = 0.000) for 5148 atoms. Found 29 (29 requested) and removed 42 (23 requested) atoms. Cycle 20: After refmac, R = 0.2038 (Rfree = 0.000) for 5127 atoms. Found 15 (29 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 5268 seeds are put forward NCS extension: 73 residues added (20 deleted due to clashes), 5341 seeds are put forward Round 1: 465 peptides, 57 chains. Longest chain 27 peptides. Score 0.625 Round 2: 518 peptides, 51 chains. Longest chain 34 peptides. Score 0.724 Round 3: 497 peptides, 51 chains. Longest chain 27 peptides. Score 0.701 Round 4: 484 peptides, 55 chains. Longest chain 32 peptides. Score 0.663 Round 5: 500 peptides, 55 chains. Longest chain 23 peptides. Score 0.683 Taking the results from Round 2 Chains 57, Residues 467, Estimated correctness of the model 70.1 % 7 chains (85 residues) have been docked in sequence Building loops using Loopy2018 57 chains (467 residues) following loop building 7 chains (85 residues) in sequence following loop building ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10229 restraints for refining 5229 atoms. 8095 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2229 (Rfree = 0.000) for 5229 atoms. Found 27 (28 requested) and removed 34 (23 requested) atoms. Cycle 22: After refmac, R = 0.2071 (Rfree = 0.000) for 5212 atoms. Found 12 (27 requested) and removed 36 (23 requested) atoms. Cycle 23: After refmac, R = 0.2046 (Rfree = 0.000) for 5182 atoms. Found 9 (26 requested) and removed 28 (23 requested) atoms. Cycle 24: After refmac, R = 0.1980 (Rfree = 0.000) for 5154 atoms. Found 3 (25 requested) and removed 23 (23 requested) atoms. Cycle 25: After refmac, R = 0.1939 (Rfree = 0.000) for 5132 atoms. Found 4 (24 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 5273 seeds are put forward NCS extension: 19 residues added (7 deleted due to clashes), 5292 seeds are put forward Round 1: 454 peptides, 57 chains. Longest chain 22 peptides. Score 0.609 Round 2: 494 peptides, 54 chains. Longest chain 28 peptides. Score 0.681 Round 3: 512 peptides, 52 chains. Longest chain 27 peptides. Score 0.713 Round 4: 496 peptides, 49 chains. Longest chain 31 peptides. Score 0.711 Round 5: 493 peptides, 51 chains. Longest chain 28 peptides. Score 0.696 Taking the results from Round 3 Chains 56, Residues 460, Estimated correctness of the model 67.9 % 9 chains (130 residues) have been docked in sequence Building loops using Loopy2018 56 chains (460 residues) following loop building 9 chains (130 residues) in sequence following loop building ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 9622 restraints for refining 5228 atoms. 7308 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2343 (Rfree = 0.000) for 5228 atoms. Found 20 (23 requested) and removed 39 (23 requested) atoms. Cycle 27: After refmac, R = 0.2370 (Rfree = 0.000) for 5198 atoms. Found 23 (23 requested) and removed 32 (23 requested) atoms. Cycle 28: After refmac, R = 0.2057 (Rfree = 0.000) for 5177 atoms. Found 15 (23 requested) and removed 30 (23 requested) atoms. Cycle 29: After refmac, R = 0.2284 (Rfree = 0.000) for 5157 atoms. Found 23 (23 requested) and removed 29 (23 requested) atoms. Cycle 30: After refmac, R = 0.2159 (Rfree = 0.000) for 5143 atoms. Found 23 (23 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 5297 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 5317 seeds are put forward Round 1: 439 peptides, 57 chains. Longest chain 23 peptides. Score 0.587 Round 2: 477 peptides, 49 chains. Longest chain 25 peptides. Score 0.688 Round 3: 475 peptides, 50 chains. Longest chain 30 peptides. Score 0.680 Round 4: 468 peptides, 49 chains. Longest chain 24 peptides. Score 0.677 Round 5: 468 peptides, 57 chains. Longest chain 41 peptides. Score 0.629 Taking the results from Round 2 Chains 54, Residues 428, Estimated correctness of the model 62.6 % 6 chains (75 residues) have been docked in sequence ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10372 restraints for refining 5228 atoms. 8366 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2214 (Rfree = 0.000) for 5228 atoms. Found 23 (23 requested) and removed 35 (23 requested) atoms. Cycle 32: After refmac, R = 0.2079 (Rfree = 0.000) for 5207 atoms. Found 8 (23 requested) and removed 25 (23 requested) atoms. Cycle 33: After refmac, R = 0.2219 (Rfree = 0.000) for 5183 atoms. Found 12 (23 requested) and removed 26 (23 requested) atoms. Cycle 34: After refmac, R = 0.2064 (Rfree = 0.000) for 5166 atoms. Found 10 (23 requested) and removed 24 (23 requested) atoms. Cycle 35: After refmac, R = 0.2481 (Rfree = 0.000) for 5150 atoms. Found 19 (23 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.13 Search for helices and strands: 0 residues in 0 chains, 5278 seeds are put forward NCS extension: 11 residues added (8 deleted due to clashes), 5289 seeds are put forward Round 1: 416 peptides, 56 chains. Longest chain 21 peptides. Score 0.558 Round 2: 456 peptides, 50 chains. Longest chain 23 peptides. Score 0.656 Round 3: 470 peptides, 51 chains. Longest chain 27 peptides. Score 0.668 Round 4: 466 peptides, 45 chains. Longest chain 27 peptides. Score 0.698 Round 5: 460 peptides, 52 chains. Longest chain 28 peptides. Score 0.649 Taking the results from Round 4 Chains 49, Residues 421, Estimated correctness of the model 64.8 % 5 chains (80 residues) have been docked in sequence ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10389 restraints for refining 5229 atoms. 8417 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2274 (Rfree = 0.000) for 5229 atoms. Found 20 (23 requested) and removed 34 (23 requested) atoms. Cycle 37: After refmac, R = 0.2068 (Rfree = 0.000) for 5202 atoms. Found 11 (23 requested) and removed 26 (23 requested) atoms. Cycle 38: After refmac, R = 0.2233 (Rfree = 0.000) for 5180 atoms. Found 23 (23 requested) and removed 26 (23 requested) atoms. Cycle 39: After refmac, R = 0.2003 (Rfree = 0.000) for 5171 atoms. Found 10 (23 requested) and removed 23 (23 requested) atoms. Cycle 40: After refmac, R = 0.2221 (Rfree = 0.000) for 5152 atoms. Found 23 (23 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.09 Search for helices and strands: 0 residues in 0 chains, 5273 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 5283 seeds are put forward Round 1: 416 peptides, 54 chains. Longest chain 22 peptides. Score 0.572 Round 2: 441 peptides, 47 chains. Longest chain 27 peptides. Score 0.655 Round 3: 434 peptides, 52 chains. Longest chain 23 peptides. Score 0.613 Round 4: 427 peptides, 48 chains. Longest chain 29 peptides. Score 0.629 Round 5: 433 peptides, 45 chains. Longest chain 28 peptides. Score 0.656 Taking the results from Round 5 Chains 45, Residues 388, Estimated correctness of the model 55.3 % 2 chains (46 residues) have been docked in sequence ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10770 restraints for refining 5229 atoms. 9051 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2216 (Rfree = 0.000) for 5229 atoms. Found 23 (23 requested) and removed 31 (23 requested) atoms. Cycle 42: After refmac, R = 0.2094 (Rfree = 0.000) for 5211 atoms. Found 21 (23 requested) and removed 29 (23 requested) atoms. Cycle 43: After refmac, R = 0.2234 (Rfree = 0.000) for 5198 atoms. Found 23 (23 requested) and removed 30 (23 requested) atoms. Cycle 44: After refmac, R = 0.1978 (Rfree = 0.000) for 5189 atoms. Found 15 (23 requested) and removed 24 (23 requested) atoms. Cycle 45: After refmac, R = 0.1929 (Rfree = 0.000) for 5175 atoms. Found 12 (23 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.10 Search for helices and strands: 0 residues in 0 chains, 5305 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 5330 seeds are put forward Round 1: 362 peptides, 52 chains. Longest chain 22 peptides. Score 0.497 Round 2: 410 peptides, 48 chains. Longest chain 22 peptides. Score 0.605 Round 3: 414 peptides, 44 chains. Longest chain 23 peptides. Score 0.637 Round 4: 401 peptides, 44 chains. Longest chain 23 peptides. Score 0.619 Round 5: 398 peptides, 48 chains. Longest chain 23 peptides. Score 0.587 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 370, Estimated correctness of the model 50.7 % 3 chains (53 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2oh1-3_warpNtrace.pdb as input Building loops using Loopy2018 44 chains (370 residues) following loop building 3 chains (53 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13772 reflections ( 99.14 % complete ) and 10643 restraints for refining 5227 atoms. 8974 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2111 (Rfree = 0.000) for 5227 atoms. Found 0 (23 requested) and removed 17 (23 requested) atoms. Cycle 47: After refmac, R = 0.2116 (Rfree = 0.000) for 5204 atoms. Found 0 (23 requested) and removed 10 (23 requested) atoms. Cycle 48: After refmac, R = 0.1911 (Rfree = 0.000) for 5190 atoms. Found 0 (23 requested) and removed 16 (23 requested) atoms. Cycle 49: After refmac, R = 0.1908 (Rfree = 0.000) for 5172 atoms. Found 0 (23 requested) and removed 8 (23 requested) atoms. Writing output files ... TimeTaking 58.07