null Mon 24 Dec 00:35:43 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 1vqr-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.6-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/1vqr-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.6-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 00:35:47 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/1vqr-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.6-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 885 and 0 Target number of residues in the AU: 885 Target solvent content: 0.6181 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.49 Input MTZ file: 1vqr-3.6-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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9504 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: 83.418 3.600 Wilson plot Bfac: 60.50 12846 reflections ( 89.37 % complete ) and 0 restraints for refining 10473 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3622 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3136 (Rfree = 0.000) for 10473 atoms. Found 59 (67 requested) and removed 121 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 10540 seeds are put forward NCS extension: 0 residues added, 10540 seeds are put forward Round 1: 257 peptides, 58 chains. Longest chain 9 peptides. Score 0.211 Round 2: 359 peptides, 77 chains. Longest chain 10 peptides. Score 0.249 Round 3: 382 peptides, 79 chains. Longest chain 10 peptides. Score 0.271 Round 4: 404 peptides, 81 chains. Longest chain 9 peptides. Score 0.291 Round 5: 446 peptides, 86 chains. Longest chain 11 peptides. Score 0.320 Taking the results from Round 5 Chains 86, Residues 360, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 21227 restraints for refining 8610 atoms. 19836 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2576 (Rfree = 0.000) for 8610 atoms. Found 31 (55 requested) and removed 56 (27 requested) atoms. Cycle 2: After refmac, R = 0.2514 (Rfree = 0.000) for 8475 atoms. Found 29 (55 requested) and removed 47 (27 requested) atoms. Cycle 3: After refmac, R = 0.2092 (Rfree = 0.000) for 8409 atoms. Found 9 (54 requested) and removed 44 (27 requested) atoms. Cycle 4: After refmac, R = 0.2178 (Rfree = 0.000) for 8343 atoms. Found 19 (53 requested) and removed 39 (26 requested) atoms. Cycle 5: After refmac, R = 0.2194 (Rfree = 0.000) for 8310 atoms. Found 35 (53 requested) and removed 42 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.22 Search for helices and strands: 0 residues in 0 chains, 8467 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8479 seeds are put forward Round 1: 412 peptides, 88 chains. Longest chain 11 peptides. Score 0.259 Round 2: 467 peptides, 84 chains. Longest chain 12 peptides. Score 0.361 Round 3: 463 peptides, 82 chains. Longest chain 15 peptides. Score 0.367 Round 4: 461 peptides, 77 chains. Longest chain 15 peptides. Score 0.393 Round 5: 461 peptides, 79 chains. Longest chain 13 peptides. Score 0.382 Taking the results from Round 4 Chains 77, Residues 384, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20243 restraints for refining 8370 atoms. 18765 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2347 (Rfree = 0.000) for 8370 atoms. Found 32 (53 requested) and removed 49 (26 requested) atoms. Cycle 7: After refmac, R = 0.2180 (Rfree = 0.000) for 8297 atoms. Found 33 (53 requested) and removed 51 (26 requested) atoms. Cycle 8: After refmac, R = 0.1845 (Rfree = 0.000) for 8263 atoms. Found 8 (53 requested) and removed 40 (26 requested) atoms. Cycle 9: After refmac, R = 0.1768 (Rfree = 0.000) for 8215 atoms. Found 8 (52 requested) and removed 34 (26 requested) atoms. Cycle 10: After refmac, R = 0.1865 (Rfree = 0.000) for 8178 atoms. Found 14 (52 requested) and removed 35 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 8362 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 8384 seeds are put forward Round 1: 414 peptides, 83 chains. Longest chain 12 peptides. Score 0.293 Round 2: 442 peptides, 75 chains. Longest chain 15 peptides. Score 0.379 Round 3: 466 peptides, 85 chains. Longest chain 11 peptides. Score 0.354 Round 4: 461 peptides, 78 chains. Longest chain 18 peptides. Score 0.387 Round 5: 454 peptides, 78 chains. Longest chain 12 peptides. Score 0.378 Taking the results from Round 4 Chains 78, Residues 383, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20286 restraints for refining 8441 atoms. 18812 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2069 (Rfree = 0.000) for 8441 atoms. Found 35 (54 requested) and removed 52 (27 requested) atoms. Cycle 12: After refmac, R = 0.2025 (Rfree = 0.000) for 8391 atoms. Found 31 (54 requested) and removed 36 (27 requested) atoms. Cycle 13: After refmac, R = 0.1976 (Rfree = 0.000) for 8366 atoms. Found 41 (53 requested) and removed 54 (26 requested) atoms. Cycle 14: After refmac, R = 0.1906 (Rfree = 0.000) for 8339 atoms. Found 33 (53 requested) and removed 36 (26 requested) atoms. Cycle 15: After refmac, R = 0.1878 (Rfree = 0.000) for 8324 atoms. Found 42 (53 requested) and removed 37 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 8552 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8570 seeds are put forward Round 1: 375 peptides, 80 chains. Longest chain 8 peptides. Score 0.254 Round 2: 430 peptides, 78 chains. Longest chain 12 peptides. Score 0.346 Round 3: 443 peptides, 75 chains. Longest chain 16 peptides. Score 0.381 Round 4: 456 peptides, 74 chains. Longest chain 16 peptides. Score 0.404 Round 5: 462 peptides, 74 chains. Longest chain 17 peptides. Score 0.411 Taking the results from Round 5 Chains 74, Residues 388, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20805 restraints for refining 8613 atoms. 19298 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2052 (Rfree = 0.000) for 8613 atoms. Found 38 (55 requested) and removed 52 (27 requested) atoms. Cycle 17: After refmac, R = 0.1940 (Rfree = 0.000) for 8572 atoms. Found 22 (55 requested) and removed 40 (27 requested) atoms. Cycle 18: After refmac, R = 0.1866 (Rfree = 0.000) for 8539 atoms. Found 34 (54 requested) and removed 42 (27 requested) atoms. Cycle 19: After refmac, R = 0.1861 (Rfree = 0.000) for 8511 atoms. Found 36 (54 requested) and removed 33 (27 requested) atoms. Cycle 20: After refmac, R = 0.1811 (Rfree = 0.000) for 8504 atoms. Found 33 (54 requested) and removed 38 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 8695 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 8718 seeds are put forward Round 1: 406 peptides, 83 chains. Longest chain 11 peptides. Score 0.281 Round 2: 448 peptides, 76 chains. Longest chain 15 peptides. Score 0.382 Round 3: 436 peptides, 72 chains. Longest chain 12 peptides. Score 0.389 Round 4: 425 peptides, 71 chains. Longest chain 15 peptides. Score 0.380 Round 5: 445 peptides, 73 chains. Longest chain 16 peptides. Score 0.395 Taking the results from Round 5 Chains 74, Residues 372, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20640 restraints for refining 8615 atoms. 19162 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2092 (Rfree = 0.000) for 8615 atoms. Found 34 (55 requested) and removed 59 (27 requested) atoms. Cycle 22: After refmac, R = 0.1979 (Rfree = 0.000) for 8569 atoms. Found 37 (55 requested) and removed 46 (27 requested) atoms. Cycle 23: After refmac, R = 0.1884 (Rfree = 0.000) for 8532 atoms. Found 22 (54 requested) and removed 36 (27 requested) atoms. Cycle 24: After refmac, R = 0.1863 (Rfree = 0.000) for 8503 atoms. Found 27 (54 requested) and removed 40 (27 requested) atoms. Cycle 25: After refmac, R = 0.1654 (Rfree = 0.000) for 8477 atoms. Found 7 (54 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 8656 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8673 seeds are put forward Round 1: 378 peptides, 76 chains. Longest chain 9 peptides. Score 0.284 Round 2: 415 peptides, 69 chains. Longest chain 18 peptides. Score 0.379 Round 3: 451 peptides, 75 chains. Longest chain 14 peptides. Score 0.391 Round 4: 422 peptides, 72 chains. Longest chain 18 peptides. Score 0.370 Round 5: 441 peptides, 71 chains. Longest chain 12 peptides. Score 0.401 Taking the results from Round 5 Chains 71, Residues 370, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20904 restraints for refining 8613 atoms. 19466 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1967 (Rfree = 0.000) for 8613 atoms. Found 21 (55 requested) and removed 40 (27 requested) atoms. Cycle 27: After refmac, R = 0.1887 (Rfree = 0.000) for 8573 atoms. Found 15 (55 requested) and removed 35 (27 requested) atoms. Cycle 28: After refmac, R = 0.1944 (Rfree = 0.000) for 8547 atoms. Found 28 (54 requested) and removed 35 (27 requested) atoms. Cycle 29: After refmac, R = 0.1956 (Rfree = 0.000) for 8531 atoms. Found 34 (54 requested) and removed 43 (27 requested) atoms. Cycle 30: After refmac, R = 0.1949 (Rfree = 0.000) for 8513 atoms. Found 37 (54 requested) and removed 39 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 8698 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 8708 seeds are put forward Round 1: 409 peptides, 89 chains. Longest chain 9 peptides. Score 0.249 Round 2: 457 peptides, 85 chains. Longest chain 12 peptides. Score 0.341 Round 3: 453 peptides, 87 chains. Longest chain 12 peptides. Score 0.324 Round 4: 439 peptides, 80 chains. Longest chain 12 peptides. Score 0.346 Round 5: 437 peptides, 78 chains. Longest chain 13 peptides. Score 0.355 Taking the results from Round 5 Chains 78, Residues 359, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20700 restraints for refining 8614 atoms. 19319 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2098 (Rfree = 0.000) for 8614 atoms. Found 38 (55 requested) and removed 45 (27 requested) atoms. Cycle 32: After refmac, R = 0.1952 (Rfree = 0.000) for 8590 atoms. Found 36 (55 requested) and removed 39 (27 requested) atoms. Cycle 33: After refmac, R = 0.1931 (Rfree = 0.000) for 8584 atoms. Found 36 (55 requested) and removed 34 (27 requested) atoms. Cycle 34: After refmac, R = 0.1973 (Rfree = 0.000) for 8574 atoms. Found 45 (55 requested) and removed 39 (27 requested) atoms. Cycle 35: After refmac, R = 0.1945 (Rfree = 0.000) for 8571 atoms. Found 55 (55 requested) and removed 37 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 8761 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8775 seeds are put forward Round 1: 338 peptides, 74 chains. Longest chain 9 peptides. Score 0.235 Round 2: 387 peptides, 72 chains. Longest chain 12 peptides. Score 0.321 Round 3: 390 peptides, 72 chains. Longest chain 11 peptides. Score 0.326 Round 4: 399 peptides, 72 chains. Longest chain 13 peptides. Score 0.338 Round 5: 381 peptides, 69 chains. Longest chain 11 peptides. Score 0.331 Taking the results from Round 4 Chains 72, Residues 327, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 21107 restraints for refining 8615 atoms. 19871 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1979 (Rfree = 0.000) for 8615 atoms. Found 44 (55 requested) and removed 35 (27 requested) atoms. Cycle 37: After refmac, R = 0.1970 (Rfree = 0.000) for 8587 atoms. Found 47 (55 requested) and removed 33 (27 requested) atoms. Cycle 38: After refmac, R = 0.1926 (Rfree = 0.000) for 8583 atoms. Found 35 (55 requested) and removed 31 (27 requested) atoms. Cycle 39: After refmac, R = 0.1886 (Rfree = 0.000) for 8578 atoms. Found 34 (55 requested) and removed 32 (27 requested) atoms. Cycle 40: After refmac, R = 0.1885 (Rfree = 0.000) for 8568 atoms. Found 42 (55 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 8738 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 8749 seeds are put forward Round 1: 318 peptides, 69 chains. Longest chain 12 peptides. Score 0.237 Round 2: 351 peptides, 69 chains. Longest chain 12 peptides. Score 0.288 Round 3: 362 peptides, 62 chains. Longest chain 13 peptides. Score 0.348 Round 4: 344 peptides, 65 chains. Longest chain 12 peptides. Score 0.303 Round 5: 361 peptides, 64 chains. Longest chain 12 peptides. Score 0.334 Taking the results from Round 3 Chains 62, Residues 300, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 21237 restraints for refining 8615 atoms. 20099 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1958 (Rfree = 0.000) for 8615 atoms. Found 45 (55 requested) and removed 39 (27 requested) atoms. Cycle 42: After refmac, R = 0.1900 (Rfree = 0.000) for 8606 atoms. Found 44 (55 requested) and removed 32 (27 requested) atoms. Cycle 43: After refmac, R = 0.1921 (Rfree = 0.000) for 8604 atoms. Found 50 (55 requested) and removed 39 (27 requested) atoms. Cycle 44: After refmac, R = 0.1835 (Rfree = 0.000) for 8604 atoms. Found 41 (55 requested) and removed 33 (27 requested) atoms. Cycle 45: After refmac, R = 0.1899 (Rfree = 0.000) for 8605 atoms. Found 49 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 8778 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8796 seeds are put forward Round 1: 319 peptides, 68 chains. Longest chain 10 peptides. Score 0.245 Round 2: 347 peptides, 68 chains. Longest chain 12 peptides. Score 0.288 Round 3: 366 peptides, 65 chains. Longest chain 16 peptides. Score 0.335 Round 4: 359 peptides, 65 chains. Longest chain 15 peptides. Score 0.325 Round 5: 338 peptides, 61 chains. Longest chain 13 peptides. Score 0.320 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 301, 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 1vqr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12846 reflections ( 89.37 % complete ) and 20850 restraints for refining 8615 atoms. 19711 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1910 (Rfree = 0.000) for 8615 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.1986 (Rfree = 0.000) for 8579 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1936 (Rfree = 0.000) for 8546 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1860 (Rfree = 0.000) for 8515 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:03:27 GMT 2018 Job finished. TimeTaking 87.73 Used memory is bytes: 22465480