Mon 24 Dec 08:02:31 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 1vme-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vme-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vme-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-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/1vme-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-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 08:02:36 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/1vme-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-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 593 and 0 Target number of residues in the AU: 593 Target solvent content: 0.6622 Checking the provided sequence file Detected sequence length: 410 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 820 Adjusted target solvent content: 0.53 Input MTZ file: 1vme-3.8-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: 4 Cell parameters: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 6560 target number of atoms Had to go as low as 0.70 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: 48.998 3.800 Wilson plot Bfac: 86.28 9324 reflections ( 99.79 % complete ) and 0 restraints for refining 7285 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3320 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3081 (Rfree = 0.000) for 7285 atoms. Found 40 (40 requested) and removed 64 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 7413 seeds are put forward NCS extension: 0 residues added, 7413 seeds are put forward Round 1: 336 peptides, 62 chains. Longest chain 10 peptides. Score 0.341 Round 2: 420 peptides, 68 chains. Longest chain 15 peptides. Score 0.441 Round 3: 443 peptides, 64 chains. Longest chain 18 peptides. Score 0.503 Round 4: 473 peptides, 64 chains. Longest chain 25 peptides. Score 0.546 Round 5: 464 peptides, 62 chains. Longest chain 16 peptides. Score 0.546 Taking the results from Round 5 Chains 63, Residues 402, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13490 restraints for refining 5932 atoms. 11874 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2596 (Rfree = 0.000) for 5932 atoms. Found 17 (32 requested) and removed 42 (16 requested) atoms. Cycle 2: After refmac, R = 0.2487 (Rfree = 0.000) for 5826 atoms. Found 10 (32 requested) and removed 39 (16 requested) atoms. Cycle 3: After refmac, R = 0.2419 (Rfree = 0.000) for 5757 atoms. Found 15 (31 requested) and removed 31 (15 requested) atoms. Cycle 4: After refmac, R = 0.2360 (Rfree = 0.000) for 5712 atoms. Found 22 (31 requested) and removed 30 (15 requested) atoms. Cycle 5: After refmac, R = 0.2078 (Rfree = 0.000) for 5681 atoms. Found 3 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 5893 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5911 seeds are put forward Round 1: 407 peptides, 72 chains. Longest chain 16 peptides. Score 0.391 Round 2: 468 peptides, 68 chains. Longest chain 17 peptides. Score 0.514 Round 3: 460 peptides, 62 chains. Longest chain 18 peptides. Score 0.541 Round 4: 467 peptides, 59 chains. Longest chain 27 peptides. Score 0.569 Round 5: 470 peptides, 63 chains. Longest chain 16 peptides. Score 0.548 Taking the results from Round 4 Chains 61, Residues 408, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13275 restraints for refining 5931 atoms. 11618 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2361 (Rfree = 0.000) for 5931 atoms. Found 28 (32 requested) and removed 34 (16 requested) atoms. Cycle 7: After refmac, R = 0.2306 (Rfree = 0.000) for 5860 atoms. Found 21 (32 requested) and removed 40 (16 requested) atoms. Cycle 8: After refmac, R = 0.2251 (Rfree = 0.000) for 5812 atoms. Found 18 (32 requested) and removed 30 (16 requested) atoms. Cycle 9: After refmac, R = 0.2178 (Rfree = 0.000) for 5782 atoms. Found 26 (31 requested) and removed 34 (15 requested) atoms. Cycle 10: After refmac, R = 0.1974 (Rfree = 0.000) for 5757 atoms. Found 9 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 5941 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 5968 seeds are put forward Round 1: 382 peptides, 65 chains. Longest chain 14 peptides. Score 0.399 Round 2: 426 peptides, 63 chains. Longest chain 20 peptides. Score 0.484 Round 3: 440 peptides, 63 chains. Longest chain 16 peptides. Score 0.505 Round 4: 453 peptides, 60 chains. Longest chain 23 peptides. Score 0.544 Round 5: 444 peptides, 57 chains. Longest chain 24 peptides. Score 0.550 Taking the results from Round 5 Chains 58, Residues 387, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13555 restraints for refining 5933 atoms. 12037 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2297 (Rfree = 0.000) for 5933 atoms. Found 16 (32 requested) and removed 43 (16 requested) atoms. Cycle 12: After refmac, R = 0.2239 (Rfree = 0.000) for 5873 atoms. Found 27 (32 requested) and removed 29 (16 requested) atoms. Cycle 13: After refmac, R = 0.2198 (Rfree = 0.000) for 5845 atoms. Found 25 (32 requested) and removed 29 (16 requested) atoms. Cycle 14: After refmac, R = 0.2158 (Rfree = 0.000) for 5825 atoms. Found 27 (32 requested) and removed 33 (16 requested) atoms. Cycle 15: After refmac, R = 0.2117 (Rfree = 0.000) for 5810 atoms. Found 23 (32 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.48 Search for helices and strands: 0 residues in 0 chains, 6003 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 6038 seeds are put forward Round 1: 361 peptides, 71 chains. Longest chain 10 peptides. Score 0.317 Round 2: 423 peptides, 69 chains. Longest chain 13 peptides. Score 0.438 Round 3: 433 peptides, 66 chains. Longest chain 13 peptides. Score 0.475 Round 4: 440 peptides, 65 chains. Longest chain 16 peptides. Score 0.492 Round 5: 444 peptides, 61 chains. Longest chain 15 peptides. Score 0.524 Taking the results from Round 5 Chains 61, Residues 383, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13443 restraints for refining 5931 atoms. 11918 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2319 (Rfree = 0.000) for 5931 atoms. Found 27 (32 requested) and removed 33 (16 requested) atoms. Cycle 17: After refmac, R = 0.2279 (Rfree = 0.000) for 5887 atoms. Found 28 (32 requested) and removed 32 (16 requested) atoms. Cycle 18: After refmac, R = 0.2228 (Rfree = 0.000) for 5865 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 19: After refmac, R = 0.2090 (Rfree = 0.000) for 5844 atoms. Found 27 (32 requested) and removed 23 (16 requested) atoms. Cycle 20: After refmac, R = 0.1812 (Rfree = 0.000) for 5831 atoms. Found 7 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 6005 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 6017 seeds are put forward Round 1: 349 peptides, 68 chains. Longest chain 10 peptides. Score 0.318 Round 2: 389 peptides, 57 chains. Longest chain 12 peptides. Score 0.468 Round 3: 401 peptides, 59 chains. Longest chain 14 peptides. Score 0.473 Round 4: 377 peptides, 55 chains. Longest chain 21 peptides. Score 0.463 Round 5: 368 peptides, 56 chains. Longest chain 21 peptides. Score 0.442 Taking the results from Round 3 Chains 59, Residues 342, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13904 restraints for refining 5930 atoms. 12583 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2234 (Rfree = 0.000) for 5930 atoms. Found 24 (32 requested) and removed 27 (16 requested) atoms. Cycle 22: After refmac, R = 0.2248 (Rfree = 0.000) for 5914 atoms. Found 30 (32 requested) and removed 29 (16 requested) atoms. Cycle 23: After refmac, R = 0.2144 (Rfree = 0.000) for 5898 atoms. Found 29 (32 requested) and removed 36 (16 requested) atoms. Cycle 24: After refmac, R = 0.2134 (Rfree = 0.000) for 5879 atoms. Found 27 (32 requested) and removed 25 (16 requested) atoms. Cycle 25: After refmac, R = 0.1760 (Rfree = 0.000) for 5867 atoms. Found 5 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 6037 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 6048 seeds are put forward Round 1: 333 peptides, 64 chains. Longest chain 10 peptides. Score 0.320 Round 2: 376 peptides, 59 chains. Longest chain 15 peptides. Score 0.433 Round 3: 392 peptides, 64 chains. Longest chain 15 peptides. Score 0.423 Round 4: 391 peptides, 60 chains. Longest chain 17 peptides. Score 0.450 Round 5: 377 peptides, 61 chains. Longest chain 16 peptides. Score 0.420 Taking the results from Round 4 Chains 62, Residues 331, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13626 restraints for refining 5933 atoms. 12305 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2160 (Rfree = 0.000) for 5933 atoms. Found 31 (32 requested) and removed 25 (16 requested) atoms. Cycle 27: After refmac, R = 0.2167 (Rfree = 0.000) for 5915 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 28: After refmac, R = 0.2101 (Rfree = 0.000) for 5893 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 29: After refmac, R = 0.2073 (Rfree = 0.000) for 5877 atoms. Found 30 (32 requested) and removed 27 (16 requested) atoms. Cycle 30: After refmac, R = 0.1696 (Rfree = 0.000) for 5867 atoms. Found 5 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 6033 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6054 seeds are put forward Round 1: 297 peptides, 63 chains. Longest chain 7 peptides. Score 0.260 Round 2: 370 peptides, 67 chains. Longest chain 12 peptides. Score 0.364 Round 3: 378 peptides, 65 chains. Longest chain 13 peptides. Score 0.393 Round 4: 385 peptides, 66 chains. Longest chain 14 peptides. Score 0.397 Round 5: 381 peptides, 64 chains. Longest chain 14 peptides. Score 0.405 Taking the results from Round 5 Chains 64, Residues 317, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13775 restraints for refining 5932 atoms. 12526 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2272 (Rfree = 0.000) for 5932 atoms. Found 21 (32 requested) and removed 21 (16 requested) atoms. Cycle 32: After refmac, R = 0.2190 (Rfree = 0.000) for 5912 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 33: After refmac, R = 0.2111 (Rfree = 0.000) for 5896 atoms. Found 29 (32 requested) and removed 25 (16 requested) atoms. Cycle 34: After refmac, R = 0.2067 (Rfree = 0.000) for 5880 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 35: After refmac, R = 0.2046 (Rfree = 0.000) for 5873 atoms. Found 26 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 6050 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6065 seeds are put forward Round 1: 302 peptides, 64 chains. Longest chain 8 peptides. Score 0.261 Round 2: 331 peptides, 59 chains. Longest chain 11 peptides. Score 0.356 Round 3: 356 peptides, 60 chains. Longest chain 13 peptides. Score 0.392 Round 4: 356 peptides, 63 chains. Longest chain 13 peptides. Score 0.369 Round 5: 367 peptides, 64 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 3 Chains 60, Residues 296, Estimated correctness of the model 0.0 % 5 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13846 restraints for refining 5933 atoms. 12673 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2117 (Rfree = 0.000) for 5933 atoms. Found 27 (32 requested) and removed 27 (16 requested) atoms. Cycle 37: After refmac, R = 0.2131 (Rfree = 0.000) for 5916 atoms. Found 32 (32 requested) and removed 25 (16 requested) atoms. Cycle 38: After refmac, R = 0.2134 (Rfree = 0.000) for 5913 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 39: After refmac, R = 0.1716 (Rfree = 0.000) for 5900 atoms. Found 7 (32 requested) and removed 19 (16 requested) atoms. Cycle 40: After refmac, R = 0.1646 (Rfree = 0.000) for 5886 atoms. Found 0 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 6035 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6051 seeds are put forward Round 1: 276 peptides, 59 chains. Longest chain 14 peptides. Score 0.251 Round 2: 318 peptides, 57 chains. Longest chain 14 peptides. Score 0.348 Round 3: 318 peptides, 55 chains. Longest chain 12 peptides. Score 0.363 Round 4: 312 peptides, 53 chains. Longest chain 14 peptides. Score 0.368 Round 5: 315 peptides, 53 chains. Longest chain 12 peptides. Score 0.374 Taking the results from Round 5 Chains 53, Residues 262, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 14008 restraints for refining 5933 atoms. 12993 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2134 (Rfree = 0.000) for 5933 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 42: After refmac, R = 0.2152 (Rfree = 0.000) for 5921 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 43: After refmac, R = 0.2120 (Rfree = 0.000) for 5923 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 44: After refmac, R = 0.2107 (Rfree = 0.000) for 5918 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 45: After refmac, R = 0.2105 (Rfree = 0.000) for 5920 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 6116 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6131 seeds are put forward Round 1: 239 peptides, 51 chains. Longest chain 8 peptides. Score 0.244 Round 2: 287 peptides, 52 chains. Longest chain 12 peptides. Score 0.330 Round 3: 275 peptides, 50 chains. Longest chain 12 peptides. Score 0.324 Round 4: 263 peptides, 48 chains. Longest chain 14 peptides. Score 0.318 Round 5: 282 peptides, 50 chains. Longest chain 12 peptides. Score 0.337 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 232, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 50 chains (232 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9324 reflections ( 99.79 % complete ) and 14193 restraints for refining 5932 atoms. 13297 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2172 (Rfree = 0.000) for 5932 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2226 (Rfree = 0.000) for 5897 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1820 (Rfree = 0.000) for 5875 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1718 (Rfree = 0.000) for 5856 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 56.18