Sun 23 Dec 22:22:42 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gvh-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-4.0-parrot-hancs ############### 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 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-4.0-parrot-hancs/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: 0.6840 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-4.0-parrot-hancs.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: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 6912 target number of atoms Had to go as low as 0.90 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: 121.211 4.000 Wilson plot Bfac: 104.73 10161 reflections ( 99.57 % complete ) and 0 restraints for refining 7645 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3628 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3470 (Rfree = 0.000) for 7645 atoms. Found 36 (36 requested) and removed 103 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.96 3.41 Search for helices and strands: 0 residues in 0 chains, 7654 seeds are put forward NCS extension: 0 residues added, 7654 seeds are put forward Round 1: 299 peptides, 59 chains. Longest chain 9 peptides. Score 0.277 Round 2: 378 peptides, 58 chains. Longest chain 17 peptides. Score 0.401 Round 3: 419 peptides, 66 chains. Longest chain 17 peptides. Score 0.409 Round 4: 417 peptides, 65 chains. Longest chain 18 peptides. Score 0.412 Round 5: 405 peptides, 62 chains. Longest chain 18 peptides. Score 0.414 Taking the results from Round 5 Chains 62, Residues 343, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 15391 restraints for refining 6240 atoms. 14081 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2865 (Rfree = 0.000) for 6240 atoms. Found 20 (29 requested) and removed 49 (14 requested) atoms. Cycle 2: After refmac, R = 0.2549 (Rfree = 0.000) for 6087 atoms. Found 17 (29 requested) and removed 34 (14 requested) atoms. Cycle 3: After refmac, R = 0.2719 (Rfree = 0.000) for 6002 atoms. Found 17 (28 requested) and removed 63 (14 requested) atoms. Cycle 4: After refmac, R = 0.2819 (Rfree = 0.000) for 5915 atoms. Found 23 (28 requested) and removed 54 (14 requested) atoms. Cycle 5: After refmac, R = 0.2633 (Rfree = 0.000) for 5850 atoms. Found 11 (27 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.88 3.34 Search for helices and strands: 0 residues in 0 chains, 6013 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6030 seeds are put forward Round 1: 371 peptides, 69 chains. Longest chain 14 peptides. Score 0.322 Round 2: 394 peptides, 61 chains. Longest chain 21 peptides. Score 0.405 Round 3: 416 peptides, 61 chains. Longest chain 17 peptides. Score 0.434 Round 4: 419 peptides, 61 chains. Longest chain 15 peptides. Score 0.438 Round 5: 442 peptides, 69 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 4 Chains 63, Residues 358, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14282 restraints for refining 6230 atoms. 12800 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2610 (Rfree = 0.000) for 6230 atoms. Found 21 (29 requested) and removed 36 (14 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2404 (Rfree = 0.000) for 6170 atoms. Found 11 (29 requested) and removed 35 (14 requested) atoms. Cycle 8: After refmac, R = 0.2414 (Rfree = 0.000) for 6107 atoms. Found 13 (29 requested) and removed 35 (14 requested) atoms. Cycle 9: After refmac, R = 0.2373 (Rfree = 0.000) for 6063 atoms. Found 14 (28 requested) and removed 30 (14 requested) atoms. Cycle 10: After refmac, R = 0.2061 (Rfree = 0.000) for 6024 atoms. Found 5 (28 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.88 3.34 Search for helices and strands: 0 residues in 0 chains, 6158 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6171 seeds are put forward Round 1: 379 peptides, 71 chains. Longest chain 15 peptides. Score 0.321 Round 2: 424 peptides, 66 chains. Longest chain 16 peptides. Score 0.415 Round 3: 436 peptides, 66 chains. Longest chain 22 peptides. Score 0.431 Round 4: 446 peptides, 64 chains. Longest chain 30 peptides. Score 0.456 Round 5: 453 peptides, 63 chains. Longest chain 19 peptides. Score 0.470 Taking the results from Round 5 Chains 64, Residues 390, Estimated correctness of the model 0.0 % 5 chains (40 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14196 restraints for refining 6241 atoms. 12581 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2620 (Rfree = 0.000) for 6241 atoms. Found 17 (29 requested) and removed 39 (14 requested) atoms. Cycle 12: After refmac, R = 0.2403 (Rfree = 0.000) for 6158 atoms. Found 18 (29 requested) and removed 40 (14 requested) atoms. Cycle 13: After refmac, R = 0.2302 (Rfree = 0.000) for 6102 atoms. Found 15 (29 requested) and removed 28 (14 requested) atoms. Cycle 14: After refmac, R = 0.2226 (Rfree = 0.000) for 6064 atoms. Found 10 (28 requested) and removed 29 (14 requested) atoms. Cycle 15: After refmac, R = 0.2208 (Rfree = 0.000) for 6014 atoms. Found 16 (28 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.90 3.36 Search for helices and strands: 0 residues in 0 chains, 6150 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6169 seeds are put forward Round 1: 356 peptides, 64 chains. Longest chain 13 peptides. Score 0.331 Round 2: 421 peptides, 70 chains. Longest chain 17 peptides. Score 0.387 Round 3: 433 peptides, 66 chains. Longest chain 20 peptides. Score 0.427 Round 4: 449 peptides, 66 chains. Longest chain 18 peptides. Score 0.448 Round 5: 447 peptides, 66 chains. Longest chain 16 peptides. Score 0.446 Taking the results from Round 4 Chains 70, Residues 383, Estimated correctness of the model 0.0 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14168 restraints for refining 6242 atoms. 12550 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2360 (Rfree = 0.000) for 6242 atoms. Found 18 (29 requested) and removed 30 (14 requested) atoms. Cycle 17: After refmac, R = 0.2279 (Rfree = 0.000) for 6189 atoms. Found 6 (29 requested) and removed 23 (14 requested) atoms. Cycle 18: After refmac, R = 0.2241 (Rfree = 0.000) for 6145 atoms. Found 10 (29 requested) and removed 30 (14 requested) atoms. Cycle 19: After refmac, R = 0.2331 (Rfree = 0.000) for 6101 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 20: After refmac, R = 0.2126 (Rfree = 0.000) for 6082 atoms. Found 11 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.87 3.33 Search for helices and strands: 0 residues in 0 chains, 6221 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6245 seeds are put forward Round 1: 382 peptides, 73 chains. Longest chain 14 peptides. Score 0.312 Round 2: 429 peptides, 66 chains. Longest chain 18 peptides. Score 0.422 Round 3: 393 peptides, 66 chains. Longest chain 14 peptides. Score 0.373 Round 4: 396 peptides, 64 chains. Longest chain 21 peptides. Score 0.389 Round 5: 409 peptides, 63 chains. Longest chain 21 peptides. Score 0.413 Taking the results from Round 2 Chains 66, Residues 363, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14206 restraints for refining 6242 atoms. 12722 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2240 (Rfree = 0.000) for 6242 atoms. Found 13 (29 requested) and removed 42 (14 requested) atoms. Cycle 22: After refmac, R = 0.2107 (Rfree = 0.000) for 6184 atoms. Found 24 (29 requested) and removed 29 (14 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1999 (Rfree = 0.000) for 6165 atoms. Found 9 (29 requested) and removed 28 (14 requested) atoms. Cycle 24: After refmac, R = 0.2081 (Rfree = 0.000) for 6129 atoms. Found 24 (29 requested) and removed 37 (14 requested) atoms. Cycle 25: After refmac, R = 0.1775 (Rfree = 0.000) for 6105 atoms. Found 2 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.93 3.39 Search for helices and strands: 0 residues in 0 chains, 6207 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 6231 seeds are put forward Round 1: 351 peptides, 68 chains. Longest chain 15 peptides. Score 0.298 Round 2: 394 peptides, 66 chains. Longest chain 15 peptides. Score 0.374 Round 3: 390 peptides, 66 chains. Longest chain 15 peptides. Score 0.368 Round 4: 390 peptides, 62 chains. Longest chain 16 peptides. Score 0.393 Round 5: 407 peptides, 63 chains. Longest chain 18 peptides. Score 0.410 Taking the results from Round 5 Chains 64, Residues 344, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14740 restraints for refining 6242 atoms. 13395 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2295 (Rfree = 0.000) for 6242 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 27: After refmac, R = 0.2187 (Rfree = 0.000) for 6210 atoms. Found 22 (29 requested) and removed 31 (14 requested) atoms. Cycle 28: After refmac, R = 0.2075 (Rfree = 0.000) for 6187 atoms. Found 10 (29 requested) and removed 17 (14 requested) atoms. Cycle 29: After refmac, R = 0.2148 (Rfree = 0.000) for 6172 atoms. Found 14 (29 requested) and removed 28 (14 requested) atoms. Cycle 30: After refmac, R = 0.2119 (Rfree = 0.000) for 6149 atoms. Found 24 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.98 3.43 Search for helices and strands: 0 residues in 0 chains, 6295 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 6316 seeds are put forward Round 1: 366 peptides, 72 chains. Longest chain 11 peptides. Score 0.295 Round 2: 363 peptides, 60 chains. Longest chain 15 peptides. Score 0.368 Round 3: 366 peptides, 56 chains. Longest chain 16 peptides. Score 0.397 Round 4: 368 peptides, 61 chains. Longest chain 14 peptides. Score 0.368 Round 5: 390 peptides, 61 chains. Longest chain 14 peptides. Score 0.399 Taking the results from Round 5 Chains 62, Residues 329, Estimated correctness of the model 0.0 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14439 restraints for refining 6242 atoms. 13039 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2481 (Rfree = 0.000) for 6242 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 32: After refmac, R = 0.2275 (Rfree = 0.000) for 6205 atoms. Found 13 (29 requested) and removed 20 (14 requested) atoms. Cycle 33: After refmac, R = 0.2241 (Rfree = 0.000) for 6179 atoms. Found 12 (29 requested) and removed 27 (14 requested) atoms. Cycle 34: After refmac, R = 0.1980 (Rfree = 0.000) for 6152 atoms. Found 7 (29 requested) and removed 18 (14 requested) atoms. Cycle 35: After refmac, R = 0.1994 (Rfree = 0.000) for 6130 atoms. Found 9 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.89 3.35 Search for helices and strands: 0 residues in 0 chains, 6259 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 6274 seeds are put forward Round 1: 334 peptides, 67 chains. Longest chain 11 peptides. Score 0.278 Round 2: 340 peptides, 62 chains. Longest chain 10 peptides. Score 0.321 Round 3: 346 peptides, 59 chains. Longest chain 10 peptides. Score 0.349 Round 4: 377 peptides, 62 chains. Longest chain 12 peptides. Score 0.375 Round 5: 372 peptides, 60 chains. Longest chain 15 peptides. Score 0.380 Taking the results from Round 5 Chains 60, Residues 312, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10161 reflections ( 99.57 % complete ) and 14869 restraints for refining 6241 atoms. 13641 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2530 (Rfree = 0.000) for 6241 atoms. Found 24 (29 requested) and removed 28 (14 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2331 (Rfree = 0.000) for 6197 atoms. Found 17 (29 requested) and removed 24 (14 requested) atoms. Cycle 38: After refmac, R = 0.2260 (Rfree = 0.000) for 6171 atoms. Found 14 (29 requested) and removed 24 (14 requested) atoms. Cycle 39: After refmac, R = 0.2184 (Rfree = 0.000) for 6147 atoms. Found 11 (29 requested) and removed 19 (14 requested) atoms. Cycle 40: After refmac, R = 0.2137 (Rfree = 0.000) for 6132 atoms. Found 17 (29 requested) and removed 32 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.30 Search for helices and strands: 0 residues in 0 chains, 6244 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6263 seeds are put forward Round 1: 313 peptides, 64 chains. Longest chain 8 peptides. Score 0.265 Round 2: 336 peptides, 61 chains. Longest chain 12 peptides. Score 0.321 Round 3: 351 peptides, 61 chains. Longest chain 12 peptides. Score 0.344 Round 4: 373 peptides, 61 chains. Longest chain 17 peptides. Score 0.376 Round 5: 347 peptides, 58 chains. Longest chain 19 peptides. Score 0.357 Taking the results from Round 4 Chains 62, Residues 312, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14589 restraints for refining 6240 atoms. 13328 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2383 (Rfree = 0.000) for 6240 atoms. Found 23 (29 requested) and removed 19 (14 requested) atoms. Cycle 42: After refmac, R = 0.2283 (Rfree = 0.000) for 6199 atoms. Found 20 (29 requested) and removed 26 (14 requested) atoms. Cycle 43: After refmac, R = 0.1981 (Rfree = 0.000) for 6168 atoms. Found 11 (29 requested) and removed 22 (14 requested) atoms. Cycle 44: After refmac, R = 0.1879 (Rfree = 0.000) for 6142 atoms. Found 6 (29 requested) and removed 21 (14 requested) atoms. Cycle 45: After refmac, R = 0.1866 (Rfree = 0.000) for 6117 atoms. Found 3 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.31 Search for helices and strands: 0 residues in 0 chains, 6242 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6258 seeds are put forward Round 1: 293 peptides, 61 chains. Longest chain 12 peptides. Score 0.253 Round 2: 315 peptides, 55 chains. Longest chain 10 peptides. Score 0.329 Round 3: 332 peptides, 56 chains. Longest chain 14 peptides. Score 0.348 Round 4: 314 peptides, 48 chains. Longest chain 21 peptides. Score 0.375 Round 5: 331 peptides, 50 chains. Longest chain 31 peptides. Score 0.386 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 281, 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 2gvh-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10161 reflections ( 99.57 % complete ) and 15225 restraints for refining 6242 atoms. 14151 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2087 (Rfree = 0.000) for 6242 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2315 (Rfree = 0.000) for 6192 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2215 (Rfree = 0.000) for 6165 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2086 (Rfree = 0.000) for 6140 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... TimeTaking 152.32