Mon 24 Dec 08:00:52 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vme-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vme-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-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/1vme-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-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 08:00:57 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/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-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 607 and 0 Target number of residues in the AU: 607 Target solvent content: 0.6542 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-3.6-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: 4 Cell parameters: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-3.6-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 3.600 Wilson plot Bfac: 80.80 10948 reflections ( 99.82 % complete ) and 0 restraints for refining 7330 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3250 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3015 (Rfree = 0.000) for 7330 atoms. Found 47 (47 requested) and removed 65 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 7462 seeds are put forward NCS extension: 0 residues added, 7462 seeds are put forward Round 1: 383 peptides, 71 chains. Longest chain 14 peptides. Score 0.357 Round 2: 443 peptides, 67 chains. Longest chain 12 peptides. Score 0.483 Round 3: 468 peptides, 71 chains. Longest chain 18 peptides. Score 0.495 Round 4: 488 peptides, 66 chains. Longest chain 23 peptides. Score 0.555 Round 5: 511 peptides, 69 chains. Longest chain 25 peptides. Score 0.568 Taking the results from Round 5 Chains 69, Residues 442, Estimated correctness of the model 1.7 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13002 restraints for refining 5943 atoms. 11162 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2668 (Rfree = 0.000) for 5943 atoms. Found 27 (38 requested) and removed 43 (19 requested) atoms. Cycle 2: After refmac, R = 0.2644 (Rfree = 0.000) for 5845 atoms. Found 23 (38 requested) and removed 49 (19 requested) atoms. Cycle 3: After refmac, R = 0.2535 (Rfree = 0.000) for 5773 atoms. Found 15 (37 requested) and removed 38 (18 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2478 (Rfree = 0.000) for 5724 atoms. Found 23 (36 requested) and removed 36 (18 requested) atoms. Cycle 5: After refmac, R = 0.2405 (Rfree = 0.000) for 5692 atoms. Found 18 (36 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 5884 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 5909 seeds are put forward Round 1: 418 peptides, 71 chains. Longest chain 14 peptides. Score 0.416 Round 2: 453 peptides, 62 chains. Longest chain 19 peptides. Score 0.531 Round 3: 510 peptides, 67 chains. Longest chain 19 peptides. Score 0.578 Round 4: 491 peptides, 63 chains. Longest chain 22 peptides. Score 0.577 Round 5: 470 peptides, 61 chains. Longest chain 17 peptides. Score 0.561 Taking the results from Round 3 Chains 69, Residues 443, Estimated correctness of the model 5.9 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 12849 restraints for refining 5945 atoms. 11036 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2475 (Rfree = 0.000) for 5945 atoms. Found 22 (38 requested) and removed 72 (19 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2503 (Rfree = 0.000) for 5861 atoms. Found 28 (37 requested) and removed 46 (18 requested) atoms. Cycle 8: After refmac, R = 0.2419 (Rfree = 0.000) for 5821 atoms. Found 29 (37 requested) and removed 32 (18 requested) atoms. Cycle 9: After refmac, R = 0.2124 (Rfree = 0.000) for 5796 atoms. Found 13 (37 requested) and removed 21 (18 requested) atoms. Cycle 10: After refmac, R = 0.2087 (Rfree = 0.000) for 5779 atoms. Found 5 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 5936 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 5957 seeds are put forward Round 1: 419 peptides, 71 chains. Longest chain 14 peptides. Score 0.418 Round 2: 477 peptides, 64 chains. Longest chain 21 peptides. Score 0.552 Round 3: 488 peptides, 69 chains. Longest chain 18 peptides. Score 0.536 Round 4: 475 peptides, 66 chains. Longest chain 15 peptides. Score 0.537 Round 5: 481 peptides, 63 chains. Longest chain 19 peptides. Score 0.563 Taking the results from Round 5 Chains 63, Residues 418, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13234 restraints for refining 5944 atoms. 11564 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2542 (Rfree = 0.000) for 5944 atoms. Found 30 (38 requested) and removed 47 (19 requested) atoms. Cycle 12: After refmac, R = 0.2470 (Rfree = 0.000) for 5891 atoms. Found 18 (38 requested) and removed 32 (19 requested) atoms. Cycle 13: After refmac, R = 0.2356 (Rfree = 0.000) for 5857 atoms. Found 30 (37 requested) and removed 30 (18 requested) atoms. Cycle 14: After refmac, R = 0.2349 (Rfree = 0.000) for 5839 atoms. Found 27 (37 requested) and removed 31 (18 requested) atoms. Cycle 15: After refmac, R = 0.2303 (Rfree = 0.000) for 5821 atoms. Found 30 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 6010 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 6020 seeds are put forward Round 1: 398 peptides, 72 chains. Longest chain 14 peptides. Score 0.375 Round 2: 442 peptides, 68 chains. Longest chain 15 peptides. Score 0.475 Round 3: 438 peptides, 61 chains. Longest chain 16 peptides. Score 0.516 Round 4: 446 peptides, 60 chains. Longest chain 17 peptides. Score 0.534 Round 5: 453 peptides, 64 chains. Longest chain 14 peptides. Score 0.518 Taking the results from Round 4 Chains 60, Residues 386, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13365 restraints for refining 5946 atoms. 11824 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2481 (Rfree = 0.000) for 5946 atoms. Found 28 (38 requested) and removed 33 (19 requested) atoms. Cycle 17: After refmac, R = 0.2413 (Rfree = 0.000) for 5903 atoms. Found 37 (38 requested) and removed 34 (19 requested) atoms. Cycle 18: After refmac, R = 0.2366 (Rfree = 0.000) for 5869 atoms. Found 32 (37 requested) and removed 26 (18 requested) atoms. Cycle 19: After refmac, R = 0.2318 (Rfree = 0.000) for 5860 atoms. Found 37 (37 requested) and removed 27 (18 requested) atoms. Cycle 20: After refmac, R = 0.2277 (Rfree = 0.000) for 5850 atoms. Found 26 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 6019 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6038 seeds are put forward Round 1: 366 peptides, 70 chains. Longest chain 13 peptides. Score 0.334 Round 2: 398 peptides, 65 chains. Longest chain 13 peptides. Score 0.426 Round 3: 401 peptides, 63 chains. Longest chain 17 peptides. Score 0.445 Round 4: 418 peptides, 64 chains. Longest chain 13 peptides. Score 0.465 Round 5: 448 peptides, 63 chains. Longest chain 14 peptides. Score 0.517 Taking the results from Round 5 Chains 63, Residues 385, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13430 restraints for refining 5946 atoms. 11898 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2372 (Rfree = 0.000) for 5946 atoms. Found 18 (38 requested) and removed 42 (19 requested) atoms. Cycle 22: After refmac, R = 0.2276 (Rfree = 0.000) for 5889 atoms. Found 23 (37 requested) and removed 28 (18 requested) atoms. Cycle 23: After refmac, R = 0.2183 (Rfree = 0.000) for 5865 atoms. Found 21 (37 requested) and removed 32 (18 requested) atoms. Cycle 24: After refmac, R = 0.2167 (Rfree = 0.000) for 5839 atoms. Found 28 (37 requested) and removed 29 (18 requested) atoms. Cycle 25: After refmac, R = 0.2191 (Rfree = 0.000) for 5831 atoms. Found 33 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 6015 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6030 seeds are put forward Round 1: 396 peptides, 76 chains. Longest chain 13 peptides. Score 0.342 Round 2: 439 peptides, 72 chains. Longest chain 14 peptides. Score 0.443 Round 3: 433 peptides, 66 chains. Longest chain 16 peptides. Score 0.475 Round 4: 456 peptides, 66 chains. Longest chain 17 peptides. Score 0.509 Round 5: 431 peptides, 67 chains. Longest chain 19 peptides. Score 0.465 Taking the results from Round 4 Chains 67, Residues 390, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13099 restraints for refining 5945 atoms. 11470 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2343 (Rfree = 0.000) for 5945 atoms. Found 22 (38 requested) and removed 34 (19 requested) atoms. Cycle 27: After refmac, R = 0.2309 (Rfree = 0.000) for 5889 atoms. Found 27 (38 requested) and removed 41 (19 requested) atoms. Cycle 28: After refmac, R = 0.2272 (Rfree = 0.000) for 5863 atoms. Found 32 (37 requested) and removed 32 (18 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2266 (Rfree = 0.000) for 5844 atoms. Found 29 (37 requested) and removed 27 (18 requested) atoms. Cycle 30: After refmac, R = 0.2231 (Rfree = 0.000) for 5836 atoms. Found 35 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 5993 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6013 seeds are put forward Round 1: 363 peptides, 71 chains. Longest chain 9 peptides. Score 0.321 Round 2: 397 peptides, 68 chains. Longest chain 14 peptides. Score 0.403 Round 3: 421 peptides, 69 chains. Longest chain 21 peptides. Score 0.435 Round 4: 405 peptides, 65 chains. Longest chain 13 peptides. Score 0.438 Round 5: 428 peptides, 65 chains. Longest chain 22 peptides. Score 0.474 Taking the results from Round 5 Chains 68, Residues 363, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13355 restraints for refining 5946 atoms. 11819 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2416 (Rfree = 0.000) for 5946 atoms. Found 25 (38 requested) and removed 35 (19 requested) atoms. Cycle 32: After refmac, R = 0.2320 (Rfree = 0.000) for 5904 atoms. Found 23 (38 requested) and removed 28 (19 requested) atoms. Cycle 33: After refmac, R = 0.2231 (Rfree = 0.000) for 5881 atoms. Found 22 (37 requested) and removed 30 (18 requested) atoms. Cycle 34: After refmac, R = 0.2180 (Rfree = 0.000) for 5857 atoms. Found 21 (37 requested) and removed 25 (18 requested) atoms. Cycle 35: After refmac, R = 0.2140 (Rfree = 0.000) for 5840 atoms. Found 24 (37 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 5997 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6023 seeds are put forward Round 1: 318 peptides, 62 chains. Longest chain 10 peptides. Score 0.308 Round 2: 361 peptides, 59 chains. Longest chain 12 peptides. Score 0.408 Round 3: 375 peptides, 58 chains. Longest chain 15 peptides. Score 0.439 Round 4: 376 peptides, 61 chains. Longest chain 12 peptides. Score 0.419 Round 5: 382 peptides, 58 chains. Longest chain 17 peptides. Score 0.450 Taking the results from Round 5 Chains 59, Residues 324, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13764 restraints for refining 5946 atoms. 12461 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2371 (Rfree = 0.000) for 5946 atoms. Found 22 (38 requested) and removed 33 (19 requested) atoms. Cycle 37: After refmac, R = 0.2274 (Rfree = 0.000) for 5922 atoms. Found 28 (38 requested) and removed 29 (19 requested) atoms. Cycle 38: After refmac, R = 0.1925 (Rfree = 0.000) for 5906 atoms. Found 9 (37 requested) and removed 27 (18 requested) atoms. Cycle 39: After refmac, R = 0.1867 (Rfree = 0.000) for 5877 atoms. Found 7 (37 requested) and removed 24 (18 requested) atoms. Cycle 40: After refmac, R = 0.1845 (Rfree = 0.000) for 5857 atoms. Found 6 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 5978 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5994 seeds are put forward Round 1: 322 peptides, 64 chains. Longest chain 11 peptides. Score 0.300 Round 2: 366 peptides, 61 chains. Longest chain 14 peptides. Score 0.402 Round 3: 380 peptides, 61 chains. Longest chain 15 peptides. Score 0.425 Round 4: 365 peptides, 57 chains. Longest chain 16 peptides. Score 0.429 Round 5: 375 peptides, 61 chains. Longest chain 15 peptides. Score 0.417 Taking the results from Round 4 Chains 57, Residues 308, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13868 restraints for refining 5946 atoms. 12645 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2418 (Rfree = 0.000) for 5946 atoms. Found 38 (38 requested) and removed 28 (19 requested) atoms. Cycle 42: After refmac, R = 0.2390 (Rfree = 0.000) for 5937 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. Cycle 43: After refmac, R = 0.2332 (Rfree = 0.000) for 5942 atoms. Found 38 (38 requested) and removed 29 (19 requested) atoms. Cycle 44: After refmac, R = 0.2352 (Rfree = 0.000) for 5939 atoms. Found 38 (38 requested) and removed 30 (19 requested) atoms. Cycle 45: After refmac, R = 0.2307 (Rfree = 0.000) for 5945 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.48 Search for helices and strands: 0 residues in 0 chains, 6090 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 6116 seeds are put forward Round 1: 279 peptides, 58 chains. Longest chain 8 peptides. Score 0.265 Round 2: 305 peptides, 51 chains. Longest chain 13 peptides. Score 0.372 Round 3: 330 peptides, 54 chains. Longest chain 16 peptides. Score 0.392 Round 4: 322 peptides, 54 chains. Longest chain 14 peptides. Score 0.378 Round 5: 308 peptides, 51 chains. Longest chain 16 peptides. Score 0.377 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 276, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 54 chains (276 residues) following loop building 4 chains (26 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10948 reflections ( 99.82 % complete ) and 13889 restraints for refining 5946 atoms. 12748 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2286 (Rfree = 0.000) for 5946 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2340 (Rfree = 0.000) for 5909 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2269 (Rfree = 0.000) for 5874 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2203 (Rfree = 0.000) for 5848 atoms. TimeTaking 59.9