Mon 24 Dec 01:13:53 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 2afb-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-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/2afb-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-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 01:13:57 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/2afb-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-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 464 and 0 Target number of residues in the AU: 464 Target solvent content: 0.6576 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-4.0-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5616 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: 97.203 4.000 Wilson plot Bfac: 83.06 6408 reflections ( 99.24 % complete ) and 0 restraints for refining 6237 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3339 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3238 (Rfree = 0.000) for 6237 atoms. Found 29 (29 requested) and removed 42 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 6336 seeds are put forward NCS extension: 0 residues added, 6336 seeds are put forward Round 1: 213 peptides, 39 chains. Longest chain 9 peptides. Score 0.322 Round 2: 292 peptides, 51 chains. Longest chain 12 peptides. Score 0.385 Round 3: 313 peptides, 45 chains. Longest chain 15 peptides. Score 0.485 Round 4: 327 peptides, 49 chains. Longest chain 18 peptides. Score 0.478 Round 5: 318 peptides, 46 chains. Longest chain 17 peptides. Score 0.486 Taking the results from Round 5 Chains 48, Residues 272, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12004 restraints for refining 5072 atoms. 10900 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2514 (Rfree = 0.000) for 5072 atoms. Found 17 (24 requested) and removed 41 (12 requested) atoms. Cycle 2: After refmac, R = 0.2223 (Rfree = 0.000) for 4964 atoms. Found 12 (23 requested) and removed 33 (11 requested) atoms. Cycle 3: After refmac, R = 0.2098 (Rfree = 0.000) for 4907 atoms. Found 11 (23 requested) and removed 19 (11 requested) atoms. Cycle 4: After refmac, R = 0.2041 (Rfree = 0.000) for 4885 atoms. Found 5 (23 requested) and removed 20 (11 requested) atoms. Cycle 5: After refmac, R = 0.2033 (Rfree = 0.000) for 4866 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 5023 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5038 seeds are put forward Round 1: 282 peptides, 53 chains. Longest chain 10 peptides. Score 0.343 Round 2: 310 peptides, 50 chains. Longest chain 11 peptides. Score 0.434 Round 3: 312 peptides, 43 chains. Longest chain 17 peptides. Score 0.501 Round 4: 333 peptides, 46 chains. Longest chain 15 peptides. Score 0.515 Round 5: 345 peptides, 52 chains. Longest chain 16 peptides. Score 0.487 Taking the results from Round 4 Chains 50, Residues 287, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 11129 restraints for refining 4933 atoms. 9898 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2168 (Rfree = 0.000) for 4933 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 7: After refmac, R = 0.1996 (Rfree = 0.000) for 4880 atoms. Found 10 (23 requested) and removed 16 (11 requested) atoms. Cycle 8: After refmac, R = 0.1925 (Rfree = 0.000) for 4865 atoms. Found 2 (23 requested) and removed 16 (11 requested) atoms. Cycle 9: After refmac, R = 0.1912 (Rfree = 0.000) for 4846 atoms. Found 1 (23 requested) and removed 15 (11 requested) atoms. Cycle 10: After refmac, R = 0.1895 (Rfree = 0.000) for 4830 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 5002 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5019 seeds are put forward Round 1: 279 peptides, 50 chains. Longest chain 12 peptides. Score 0.366 Round 2: 307 peptides, 46 chains. Longest chain 18 peptides. Score 0.464 Round 3: 324 peptides, 44 chains. Longest chain 22 peptides. Score 0.515 Round 4: 316 peptides, 45 chains. Longest chain 17 peptides. Score 0.491 Round 5: 332 peptides, 44 chains. Longest chain 28 peptides. Score 0.530 Taking the results from Round 5 Chains 44, Residues 288, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 11797 restraints for refining 5072 atoms. 10638 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2167 (Rfree = 0.000) for 5072 atoms. Found 15 (24 requested) and removed 28 (12 requested) atoms. Cycle 12: After refmac, R = 0.2033 (Rfree = 0.000) for 5036 atoms. Found 4 (24 requested) and removed 17 (12 requested) atoms. Cycle 13: After refmac, R = 0.1988 (Rfree = 0.000) for 5014 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. Cycle 14: After refmac, R = 0.1961 (Rfree = 0.000) for 5006 atoms. Found 4 (23 requested) and removed 17 (11 requested) atoms. Cycle 15: After refmac, R = 0.1943 (Rfree = 0.000) for 4992 atoms. Found 0 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 5180 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 5211 seeds are put forward Round 1: 294 peptides, 55 chains. Longest chain 15 peptides. Score 0.351 Round 2: 302 peptides, 48 chains. Longest chain 17 peptides. Score 0.435 Round 3: 321 peptides, 46 chains. Longest chain 17 peptides. Score 0.492 Round 4: 306 peptides, 45 chains. Longest chain 14 peptides. Score 0.471 Round 5: 312 peptides, 48 chains. Longest chain 16 peptides. Score 0.456 Taking the results from Round 3 Chains 46, Residues 275, Estimated correctness of the model 0.0 % 5 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 11987 restraints for refining 5072 atoms. 10875 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1994 (Rfree = 0.000) for 5072 atoms. Found 17 (24 requested) and removed 20 (12 requested) atoms. Cycle 17: After refmac, R = 0.1888 (Rfree = 0.000) for 5045 atoms. Found 8 (24 requested) and removed 14 (12 requested) atoms. Cycle 18: After refmac, R = 0.1845 (Rfree = 0.000) for 5036 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.1838 (Rfree = 0.000) for 5025 atoms. Found 0 (23 requested) and removed 13 (11 requested) atoms. Cycle 20: After refmac, R = 0.1824 (Rfree = 0.000) for 5008 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 5195 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5215 seeds are put forward Round 1: 273 peptides, 50 chains. Longest chain 10 peptides. Score 0.352 Round 2: 294 peptides, 47 chains. Longest chain 12 peptides. Score 0.428 Round 3: 308 peptides, 47 chains. Longest chain 14 peptides. Score 0.457 Round 4: 307 peptides, 47 chains. Longest chain 16 peptides. Score 0.455 Round 5: 294 peptides, 43 chains. Longest chain 14 peptides. Score 0.465 Taking the results from Round 5 Chains 45, Residues 251, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12034 restraints for refining 5072 atoms. 10989 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2167 (Rfree = 0.000) for 5072 atoms. Found 20 (24 requested) and removed 21 (12 requested) atoms. Cycle 22: After refmac, R = 0.2045 (Rfree = 0.000) for 5053 atoms. Found 5 (24 requested) and removed 14 (12 requested) atoms. Cycle 23: After refmac, R = 0.2005 (Rfree = 0.000) for 5041 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.1975 (Rfree = 0.000) for 5030 atoms. Found 2 (23 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.1969 (Rfree = 0.000) for 5017 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 5182 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5201 seeds are put forward Round 1: 244 peptides, 44 chains. Longest chain 11 peptides. Score 0.344 Round 2: 282 peptides, 42 chains. Longest chain 14 peptides. Score 0.449 Round 3: 270 peptides, 38 chains. Longest chain 19 peptides. Score 0.461 Round 4: 276 peptides, 40 chains. Longest chain 15 peptides. Score 0.455 Round 5: 279 peptides, 40 chains. Longest chain 15 peptides. Score 0.461 Taking the results from Round 5 Chains 40, Residues 239, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12236 restraints for refining 5071 atoms. 11308 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2161 (Rfree = 0.000) for 5071 atoms. Found 20 (24 requested) and removed 16 (12 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2020 (Rfree = 0.000) for 5062 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.1989 (Rfree = 0.000) for 5048 atoms. Found 3 (24 requested) and removed 15 (12 requested) atoms. Cycle 29: After refmac, R = 0.1981 (Rfree = 0.000) for 5035 atoms. Found 5 (23 requested) and removed 19 (11 requested) atoms. Cycle 30: After refmac, R = 0.1925 (Rfree = 0.000) for 5020 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 5192 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5208 seeds are put forward Round 1: 278 peptides, 54 chains. Longest chain 10 peptides. Score 0.324 Round 2: 287 peptides, 47 chains. Longest chain 13 peptides. Score 0.412 Round 3: 292 peptides, 48 chains. Longest chain 15 peptides. Score 0.414 Round 4: 278 peptides, 46 chains. Longest chain 15 peptides. Score 0.402 Round 5: 297 peptides, 49 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 5 Chains 49, Residues 248, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12365 restraints for refining 5071 atoms. 11396 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2088 (Rfree = 0.000) for 5071 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 32: After refmac, R = 0.1960 (Rfree = 0.000) for 5050 atoms. Found 12 (24 requested) and removed 16 (12 requested) atoms. Cycle 33: After refmac, R = 0.1941 (Rfree = 0.000) for 5039 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1924 (Rfree = 0.000) for 5025 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1945 (Rfree = 0.000) for 5013 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 5189 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5203 seeds are put forward Round 1: 248 peptides, 51 chains. Longest chain 11 peptides. Score 0.282 Round 2: 269 peptides, 49 chains. Longest chain 11 peptides. Score 0.353 Round 3: 284 peptides, 50 chains. Longest chain 11 peptides. Score 0.377 Round 4: 271 peptides, 46 chains. Longest chain 15 peptides. Score 0.387 Round 5: 291 peptides, 49 chains. Longest chain 16 peptides. Score 0.402 Taking the results from Round 5 Chains 49, Residues 242, Estimated correctness of the model 0.0 % 5 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12305 restraints for refining 5071 atoms. 11352 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2199 (Rfree = 0.000) for 5071 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 37: After refmac, R = 0.1941 (Rfree = 0.000) for 5038 atoms. Found 16 (24 requested) and removed 15 (12 requested) atoms. Cycle 38: After refmac, R = 0.1823 (Rfree = 0.000) for 5024 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 39: After refmac, R = 0.1802 (Rfree = 0.000) for 5010 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.1730 (Rfree = 0.000) for 4998 atoms. Found 1 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 5174 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 5203 seeds are put forward Round 1: 235 peptides, 53 chains. Longest chain 8 peptides. Score 0.228 Round 2: 263 peptides, 52 chains. Longest chain 11 peptides. Score 0.308 Round 3: 264 peptides, 48 chains. Longest chain 13 peptides. Score 0.351 Round 4: 262 peptides, 49 chains. Longest chain 11 peptides. Score 0.336 Round 5: 265 peptides, 46 chains. Longest chain 13 peptides. Score 0.373 Taking the results from Round 5 Chains 46, Residues 219, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12438 restraints for refining 5053 atoms. 11596 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1982 (Rfree = 0.000) for 5053 atoms. Found 16 (24 requested) and removed 32 (12 requested) atoms. Cycle 42: After refmac, R = 0.1770 (Rfree = 0.000) for 5014 atoms. Found 0 (23 requested) and removed 21 (11 requested) atoms. Cycle 43: After refmac, R = 0.1729 (Rfree = 0.000) for 4990 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.1723 (Rfree = 0.000) for 4980 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1731 (Rfree = 0.000) for 4971 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 5130 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5142 seeds are put forward Round 1: 204 peptides, 46 chains. Longest chain 9 peptides. Score 0.222 Round 2: 220 peptides, 41 chains. Longest chain 10 peptides. Score 0.318 Round 3: 231 peptides, 43 chains. Longest chain 11 peptides. Score 0.323 Round 4: 225 peptides, 40 chains. Longest chain 10 peptides. Score 0.340 Round 5: 227 peptides, 38 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 189, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2afb-4_warpNtrace.pdb as input Building loops using Loopy2018 38 chains (189 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6408 reflections ( 99.24 % complete ) and 12702 restraints for refining 5072 atoms. 11971 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2026 (Rfree = 0.000) for 5072 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1959 (Rfree = 0.000) for 5055 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1953 (Rfree = 0.000) for 5040 atoms. Found 0 (23 requested) and removed 4 (11 requested) atoms. Cycle 49: After refmac, R = 0.1957 (Rfree = 0.000) for 5035 atoms. Found 0 (23 requested) and removed 1 (11 requested) atoms. Writing output files ... TimeTaking 64.7