Mon 24 Dec 08:05:33 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 2oh1-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.6-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/2oh1-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.6-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 08:05:38 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/2oh1-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.6-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 517 and 0 Target number of residues in the AU: 517 Target solvent content: 0.6527 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: 2oh1-3.6-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: 2oh1-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 5728 target number of atoms Had to go as low as 0.80 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 3.600 Wilson plot Bfac: 79.82 9752 reflections ( 99.15 % complete ) and 0 restraints for refining 6381 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3238 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3054 (Rfree = 0.000) for 6381 atoms. Found 40 (40 requested) and removed 54 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 6508 seeds are put forward NCS extension: 0 residues added, 6508 seeds are put forward Round 1: 354 peptides, 62 chains. Longest chain 10 peptides. Score 0.400 Round 2: 423 peptides, 55 chains. Longest chain 24 peptides. Score 0.576 Round 3: 444 peptides, 53 chains. Longest chain 23 peptides. Score 0.621 Round 4: 453 peptides, 51 chains. Longest chain 44 peptides. Score 0.646 Round 5: 445 peptides, 48 chains. Longest chain 26 peptides. Score 0.654 Taking the results from Round 5 Chains 50, Residues 397, Estimated correctness of the model 34.5 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11409 restraints for refining 5191 atoms. 9824 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2417 (Rfree = 0.000) for 5191 atoms. Found 25 (33 requested) and removed 40 (16 requested) atoms. Cycle 2: After refmac, R = 0.2341 (Rfree = 0.000) for 5130 atoms. Found 23 (33 requested) and removed 36 (16 requested) atoms. Cycle 3: After refmac, R = 0.2211 (Rfree = 0.000) for 5094 atoms. Found 18 (32 requested) and removed 30 (16 requested) atoms. Cycle 4: After refmac, R = 0.2170 (Rfree = 0.000) for 5067 atoms. Found 11 (32 requested) and removed 31 (16 requested) atoms. Cycle 5: After refmac, R = 0.2200 (Rfree = 0.000) for 5038 atoms. Found 22 (32 requested) and removed 29 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 5215 seeds are put forward NCS extension: 13 residues added (7 deleted due to clashes), 5228 seeds are put forward Round 1: 413 peptides, 62 chains. Longest chain 13 peptides. Score 0.509 Round 2: 464 peptides, 53 chains. Longest chain 24 peptides. Score 0.648 Round 3: 447 peptides, 51 chains. Longest chain 26 peptides. Score 0.638 Round 4: 456 peptides, 45 chains. Longest chain 30 peptides. Score 0.686 Round 5: 437 peptides, 49 chains. Longest chain 25 peptides. Score 0.637 Taking the results from Round 4 Chains 46, Residues 411, Estimated correctness of the model 45.2 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11152 restraints for refining 5191 atoms. 9451 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2443 (Rfree = 0.000) for 5191 atoms. Found 22 (33 requested) and removed 39 (16 requested) atoms. Cycle 7: After refmac, R = 0.2275 (Rfree = 0.000) for 5143 atoms. Found 14 (33 requested) and removed 30 (16 requested) atoms. Cycle 8: After refmac, R = 0.2229 (Rfree = 0.000) for 5115 atoms. Found 25 (32 requested) and removed 39 (16 requested) atoms. Cycle 9: After refmac, R = 0.2113 (Rfree = 0.000) for 5092 atoms. Found 15 (32 requested) and removed 33 (16 requested) atoms. Cycle 10: After refmac, R = 0.2064 (Rfree = 0.000) for 5066 atoms. Found 23 (32 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 5228 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 5244 seeds are put forward Round 1: 409 peptides, 64 chains. Longest chain 20 peptides. Score 0.487 Round 2: 434 peptides, 57 chains. Longest chain 20 peptides. Score 0.580 Round 3: 453 peptides, 57 chains. Longest chain 30 peptides. Score 0.608 Round 4: 454 peptides, 54 chains. Longest chain 31 peptides. Score 0.629 Round 5: 434 peptides, 48 chains. Longest chain 32 peptides. Score 0.639 Taking the results from Round 5 Chains 48, Residues 386, Estimated correctness of the model 29.3 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11601 restraints for refining 5193 atoms. 10039 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2440 (Rfree = 0.000) for 5193 atoms. Found 33 (33 requested) and removed 47 (16 requested) atoms. Cycle 12: After refmac, R = 0.2342 (Rfree = 0.000) for 5150 atoms. Found 33 (33 requested) and removed 35 (16 requested) atoms. Cycle 13: After refmac, R = 0.2305 (Rfree = 0.000) for 5131 atoms. Found 33 (33 requested) and removed 25 (16 requested) atoms. Cycle 14: After refmac, R = 0.2234 (Rfree = 0.000) for 5120 atoms. Found 26 (32 requested) and removed 32 (16 requested) atoms. Cycle 15: After refmac, R = 0.2154 (Rfree = 0.000) for 5100 atoms. Found 23 (32 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.40 Search for helices and strands: 0 residues in 0 chains, 5267 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 5282 seeds are put forward Round 1: 364 peptides, 53 chains. Longest chain 16 peptides. Score 0.493 Round 2: 396 peptides, 52 chains. Longest chain 22 peptides. Score 0.555 Round 3: 420 peptides, 55 chains. Longest chain 20 peptides. Score 0.572 Round 4: 405 peptides, 49 chains. Longest chain 24 peptides. Score 0.590 Round 5: 421 peptides, 54 chains. Longest chain 19 peptides. Score 0.580 Taking the results from Round 4 Chains 50, Residues 356, Estimated correctness of the model 10.7 % 4 chains (52 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9752 reflections ( 99.15 % complete ) and 10922 restraints for refining 5191 atoms. 9337 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2183 (Rfree = 0.000) for 5191 atoms. Found 23 (33 requested) and removed 34 (16 requested) atoms. Cycle 17: After refmac, R = 0.2058 (Rfree = 0.000) for 5155 atoms. Found 14 (33 requested) and removed 28 (16 requested) atoms. Cycle 18: After refmac, R = 0.2022 (Rfree = 0.000) for 5130 atoms. Found 5 (32 requested) and removed 41 (16 requested) atoms. Cycle 19: After refmac, R = 0.1973 (Rfree = 0.000) for 5082 atoms. Found 4 (32 requested) and removed 22 (16 requested) atoms. Cycle 20: After refmac, R = 0.1951 (Rfree = 0.000) for 5060 atoms. Found 9 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 5201 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 5212 seeds are put forward Round 1: 323 peptides, 56 chains. Longest chain 17 peptides. Score 0.390 Round 2: 382 peptides, 51 chains. Longest chain 20 peptides. Score 0.539 Round 3: 389 peptides, 50 chains. Longest chain 31 peptides. Score 0.558 Round 4: 403 peptides, 53 chains. Longest chain 30 peptides. Score 0.559 Round 5: 385 peptides, 57 chains. Longest chain 18 peptides. Score 0.499 Taking the results from Round 4 Chains 54, Residues 350, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11460 restraints for refining 5191 atoms. 10020 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2090 (Rfree = 0.000) for 5191 atoms. Found 8 (33 requested) and removed 26 (16 requested) atoms. Cycle 22: After refmac, R = 0.1998 (Rfree = 0.000) for 5153 atoms. Found 11 (33 requested) and removed 25 (16 requested) atoms. Cycle 23: After refmac, R = 0.1982 (Rfree = 0.000) for 5129 atoms. Found 7 (32 requested) and removed 19 (16 requested) atoms. Cycle 24: After refmac, R = 0.2021 (Rfree = 0.000) for 5108 atoms. Found 7 (32 requested) and removed 20 (16 requested) atoms. Cycle 25: After refmac, R = 0.2014 (Rfree = 0.000) for 5091 atoms. Found 5 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 5258 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 5282 seeds are put forward Round 1: 343 peptides, 58 chains. Longest chain 18 peptides. Score 0.413 Round 2: 373 peptides, 55 chains. Longest chain 18 peptides. Score 0.493 Round 3: 365 peptides, 49 chains. Longest chain 24 peptides. Score 0.526 Round 4: 346 peptides, 45 chains. Longest chain 20 peptides. Score 0.524 Round 5: 346 peptides, 48 chains. Longest chain 24 peptides. Score 0.501 Taking the results from Round 3 Chains 51, Residues 316, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11658 restraints for refining 5193 atoms. 10412 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2100 (Rfree = 0.000) for 5193 atoms. Found 12 (33 requested) and removed 24 (16 requested) atoms. Cycle 27: After refmac, R = 0.2019 (Rfree = 0.000) for 5158 atoms. Found 5 (33 requested) and removed 23 (16 requested) atoms. Cycle 28: After refmac, R = 0.1960 (Rfree = 0.000) for 5138 atoms. Found 6 (32 requested) and removed 22 (16 requested) atoms. Cycle 29: After refmac, R = 0.1940 (Rfree = 0.000) for 5120 atoms. Found 1 (32 requested) and removed 19 (16 requested) atoms. Cycle 30: After refmac, R = 0.1949 (Rfree = 0.000) for 5097 atoms. Found 9 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 5218 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 5251 seeds are put forward Round 1: 331 peptides, 57 chains. Longest chain 17 peptides. Score 0.397 Round 2: 375 peptides, 57 chains. Longest chain 20 peptides. Score 0.481 Round 3: 381 peptides, 51 chains. Longest chain 19 peptides. Score 0.538 Round 4: 362 peptides, 52 chains. Longest chain 20 peptides. Score 0.497 Round 5: 365 peptides, 50 chains. Longest chain 18 peptides. Score 0.518 Taking the results from Round 3 Chains 52, Residues 330, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11596 restraints for refining 5193 atoms. 10281 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2123 (Rfree = 0.000) for 5193 atoms. Found 7 (33 requested) and removed 29 (16 requested) atoms. Cycle 32: After refmac, R = 0.2069 (Rfree = 0.000) for 5160 atoms. Found 4 (33 requested) and removed 19 (16 requested) atoms. Cycle 33: After refmac, R = 0.2026 (Rfree = 0.000) for 5136 atoms. Found 7 (33 requested) and removed 20 (16 requested) atoms. Cycle 34: After refmac, R = 0.2020 (Rfree = 0.000) for 5121 atoms. Found 7 (32 requested) and removed 18 (16 requested) atoms. Cycle 35: After refmac, R = 0.1942 (Rfree = 0.000) for 5105 atoms. Found 1 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 5222 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 5247 seeds are put forward Round 1: 300 peptides, 50 chains. Longest chain 17 peptides. Score 0.396 Round 2: 341 peptides, 50 chains. Longest chain 15 peptides. Score 0.475 Round 3: 350 peptides, 53 chains. Longest chain 16 peptides. Score 0.468 Round 4: 340 peptides, 52 chains. Longest chain 21 peptides. Score 0.457 Round 5: 334 peptides, 48 chains. Longest chain 16 peptides. Score 0.479 Taking the results from Round 5 Chains 48, Residues 286, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11926 restraints for refining 5193 atoms. 10830 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2191 (Rfree = 0.000) for 5193 atoms. Found 10 (33 requested) and removed 28 (16 requested) atoms. Cycle 37: After refmac, R = 0.2089 (Rfree = 0.000) for 5164 atoms. Found 7 (33 requested) and removed 18 (16 requested) atoms. Cycle 38: After refmac, R = 0.2092 (Rfree = 0.000) for 5145 atoms. Found 10 (33 requested) and removed 19 (16 requested) atoms. Cycle 39: After refmac, R = 0.1991 (Rfree = 0.000) for 5133 atoms. Found 3 (32 requested) and removed 19 (16 requested) atoms. Cycle 40: After refmac, R = 0.2034 (Rfree = 0.000) for 5116 atoms. Found 6 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 5263 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5282 seeds are put forward Round 1: 283 peptides, 55 chains. Longest chain 13 peptides. Score 0.315 Round 2: 315 peptides, 51 chains. Longest chain 18 peptides. Score 0.417 Round 3: 320 peptides, 55 chains. Longest chain 13 peptides. Score 0.393 Round 4: 352 peptides, 54 chains. Longest chain 17 peptides. Score 0.463 Round 5: 337 peptides, 51 chains. Longest chain 15 peptides. Score 0.460 Taking the results from Round 4 Chains 57, Residues 298, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11624 restraints for refining 5193 atoms. 10417 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2183 (Rfree = 0.000) for 5193 atoms. Found 10 (33 requested) and removed 25 (16 requested) atoms. Cycle 42: After refmac, R = 0.2145 (Rfree = 0.000) for 5169 atoms. Found 7 (33 requested) and removed 25 (16 requested) atoms. Cycle 43: After refmac, R = 0.2064 (Rfree = 0.000) for 5143 atoms. Found 7 (33 requested) and removed 19 (16 requested) atoms. Cycle 44: After refmac, R = 0.2088 (Rfree = 0.000) for 5125 atoms. Found 5 (32 requested) and removed 22 (16 requested) atoms. Cycle 45: After refmac, R = 0.2037 (Rfree = 0.000) for 5105 atoms. Found 3 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 5229 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5245 seeds are put forward Round 1: 264 peptides, 49 chains. Longest chain 14 peptides. Score 0.329 Round 2: 306 peptides, 48 chains. Longest chain 16 peptides. Score 0.426 Round 3: 299 peptides, 45 chains. Longest chain 17 peptides. Score 0.438 Round 4: 290 peptides, 41 chains. Longest chain 19 peptides. Score 0.455 Round 5: 297 peptides, 40 chains. Longest chain 18 peptides. Score 0.477 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 257, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2oh1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9752 reflections ( 99.15 % complete ) and 11941 restraints for refining 5193 atoms. 10953 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2107 (Rfree = 0.000) for 5193 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2080 (Rfree = 0.000) for 5171 atoms. Found 0 (33 requested) and removed 14 (16 requested) atoms. Cycle 48: After refmac, R = 0.2076 (Rfree = 0.000) for 5154 atoms. Found 0 (33 requested) and removed 9 (16 requested) atoms. Cycle 49: After refmac, R = 0.2090 (Rfree = 0.000) for 5142 atoms. TimeTaking 54.97