Mon 24 Dec 08:00:23 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 1vl4-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl4-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl4-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-4.0-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/1vl4-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-4.0-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 08:00:28 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/1vl4-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-4.0-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 688 and 0 Target number of residues in the AU: 688 Target solvent content: 0.6382 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-4.0-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: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 7152 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: 79.862 4.000 Wilson plot Bfac: 70.96 9072 reflections ( 99.17 % complete ) and 0 restraints for refining 7944 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3203 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3290 (Rfree = 0.000) for 7944 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.51 Search for helices and strands: 0 residues in 0 chains, 8052 seeds are put forward NCS extension: 0 residues added, 8052 seeds are put forward Round 1: 332 peptides, 69 chains. Longest chain 8 peptides. Score 0.272 Round 2: 443 peptides, 69 chains. Longest chain 15 peptides. Score 0.453 Round 3: 492 peptides, 70 chains. Longest chain 20 peptides. Score 0.516 Round 4: 506 peptides, 62 chains. Longest chain 34 peptides. Score 0.580 Round 5: 510 peptides, 68 chains. Longest chain 23 peptides. Score 0.551 Taking the results from Round 4 Chains 65, Residues 444, Estimated correctness of the model 0.0 % 7 chains (80 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14090 restraints for refining 6455 atoms. 12103 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2750 (Rfree = 0.000) for 6455 atoms. Found 28 (30 requested) and removed 58 (15 requested) atoms. Cycle 2: After refmac, R = 0.2492 (Rfree = 0.000) for 6267 atoms. Found 21 (30 requested) and removed 52 (15 requested) atoms. Cycle 3: After refmac, R = 0.2355 (Rfree = 0.000) for 6184 atoms. Found 9 (29 requested) and removed 42 (14 requested) atoms. Cycle 4: After refmac, R = 0.2281 (Rfree = 0.000) for 6125 atoms. Found 17 (29 requested) and removed 38 (14 requested) atoms. Cycle 5: After refmac, R = 0.2242 (Rfree = 0.000) for 6087 atoms. Found 9 (29 requested) and removed 26 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.37 Search for helices and strands: 0 residues in 0 chains, 6257 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 6281 seeds are put forward Round 1: 421 peptides, 78 chains. Longest chain 13 peptides. Score 0.359 Round 2: 479 peptides, 67 chains. Longest chain 32 peptides. Score 0.516 Round 3: 450 peptides, 66 chains. Longest chain 20 peptides. Score 0.482 Round 4: 470 peptides, 60 chains. Longest chain 31 peptides. Score 0.546 Round 5: 486 peptides, 64 chains. Longest chain 24 peptides. Score 0.543 Taking the results from Round 4 Chains 66, Residues 410, Estimated correctness of the model 0.0 % 7 chains (72 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14495 restraints for refining 6458 atoms. 12660 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2435 (Rfree = 0.000) for 6458 atoms. Found 24 (30 requested) and removed 66 (15 requested) atoms. Cycle 7: After refmac, R = 0.2169 (Rfree = 0.000) for 6347 atoms. Found 13 (30 requested) and removed 65 (15 requested) atoms. Cycle 8: After refmac, R = 0.2085 (Rfree = 0.000) for 6268 atoms. Found 6 (29 requested) and removed 27 (14 requested) atoms. Cycle 9: After refmac, R = 0.2082 (Rfree = 0.000) for 6235 atoms. Found 10 (29 requested) and removed 20 (14 requested) atoms. Cycle 10: After refmac, R = 0.2072 (Rfree = 0.000) for 6222 atoms. Found 3 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 6358 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6383 seeds are put forward Round 1: 422 peptides, 72 chains. Longest chain 16 peptides. Score 0.402 Round 2: 442 peptides, 64 chains. Longest chain 19 peptides. Score 0.484 Round 3: 455 peptides, 60 chains. Longest chain 20 peptides. Score 0.526 Round 4: 450 peptides, 66 chains. Longest chain 27 peptides. Score 0.482 Round 5: 450 peptides, 58 chains. Longest chain 20 peptides. Score 0.532 Taking the results from Round 5 Chains 62, Residues 392, Estimated correctness of the model 0.0 % 7 chains (67 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14389 restraints for refining 6459 atoms. 12638 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2254 (Rfree = 0.000) for 6459 atoms. Found 16 (30 requested) and removed 50 (15 requested) atoms. Cycle 12: After refmac, R = 0.2124 (Rfree = 0.000) for 6379 atoms. Found 9 (30 requested) and removed 29 (15 requested) atoms. Cycle 13: After refmac, R = 0.2166 (Rfree = 0.000) for 6333 atoms. Found 13 (30 requested) and removed 25 (15 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1973 (Rfree = 0.000) for 6299 atoms. Found 3 (30 requested) and removed 25 (15 requested) atoms. Cycle 15: After refmac, R = 0.2034 (Rfree = 0.000) for 6255 atoms. Found 5 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 6393 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6408 seeds are put forward Round 1: 403 peptides, 75 chains. Longest chain 21 peptides. Score 0.351 Round 2: 457 peptides, 69 chains. Longest chain 22 peptides. Score 0.473 Round 3: 479 peptides, 67 chains. Longest chain 33 peptides. Score 0.516 Round 4: 469 peptides, 64 chains. Longest chain 29 peptides. Score 0.521 Round 5: 473 peptides, 66 chains. Longest chain 27 peptides. Score 0.514 Taking the results from Round 4 Chains 66, Residues 405, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14788 restraints for refining 6458 atoms. 13122 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2499 (Rfree = 0.000) for 6458 atoms. Found 30 (30 requested) and removed 51 (15 requested) atoms. Cycle 17: After refmac, R = 0.2257 (Rfree = 0.000) for 6369 atoms. Found 30 (30 requested) and removed 44 (15 requested) atoms. Cycle 18: After refmac, R = 0.1934 (Rfree = 0.000) for 6312 atoms. Found 11 (30 requested) and removed 29 (15 requested) atoms. Cycle 19: After refmac, R = 0.1857 (Rfree = 0.000) for 6266 atoms. Found 9 (29 requested) and removed 23 (14 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1830 (Rfree = 0.000) for 6234 atoms. Found 5 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.49 Search for helices and strands: 0 residues in 0 chains, 6370 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 6397 seeds are put forward Round 1: 364 peptides, 66 chains. Longest chain 13 peptides. Score 0.350 Round 2: 435 peptides, 68 chains. Longest chain 22 peptides. Score 0.448 Round 3: 422 peptides, 64 chains. Longest chain 18 peptides. Score 0.455 Round 4: 421 peptides, 60 chains. Longest chain 16 peptides. Score 0.479 Round 5: 443 peptides, 62 chains. Longest chain 18 peptides. Score 0.498 Taking the results from Round 5 Chains 62, Residues 381, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14952 restraints for refining 6457 atoms. 13411 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2333 (Rfree = 0.000) for 6457 atoms. Found 28 (30 requested) and removed 63 (15 requested) atoms. Cycle 22: After refmac, R = 0.2058 (Rfree = 0.000) for 6371 atoms. Found 23 (30 requested) and removed 30 (15 requested) atoms. Cycle 23: After refmac, R = 0.1954 (Rfree = 0.000) for 6340 atoms. Found 9 (30 requested) and removed 22 (15 requested) atoms. Cycle 24: After refmac, R = 0.1910 (Rfree = 0.000) for 6314 atoms. Found 6 (30 requested) and removed 18 (15 requested) atoms. Cycle 25: After refmac, R = 0.1885 (Rfree = 0.000) for 6295 atoms. Found 7 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.46 Search for helices and strands: 0 residues in 0 chains, 6441 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6463 seeds are put forward Round 1: 332 peptides, 64 chains. Longest chain 15 peptides. Score 0.310 Round 2: 382 peptides, 63 chains. Longest chain 12 peptides. Score 0.400 Round 3: 399 peptides, 65 chains. Longest chain 20 peptides. Score 0.413 Round 4: 402 peptides, 59 chains. Longest chain 16 peptides. Score 0.458 Round 5: 402 peptides, 58 chains. Longest chain 16 peptides. Score 0.464 Taking the results from Round 5 Chains 58, Residues 344, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15133 restraints for refining 6459 atoms. 13715 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2505 (Rfree = 0.000) for 6459 atoms. Found 30 (30 requested) and removed 56 (15 requested) atoms. Cycle 27: After refmac, R = 0.2036 (Rfree = 0.000) for 6374 atoms. Found 19 (30 requested) and removed 19 (15 requested) atoms. Cycle 28: After refmac, R = 0.1955 (Rfree = 0.000) for 6358 atoms. Found 9 (30 requested) and removed 22 (15 requested) atoms. Cycle 29: After refmac, R = 0.1953 (Rfree = 0.000) for 6336 atoms. Found 3 (30 requested) and removed 20 (15 requested) atoms. Cycle 30: After refmac, R = 0.1946 (Rfree = 0.000) for 6317 atoms. Found 3 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 6444 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6460 seeds are put forward Round 1: 355 peptides, 72 chains. Longest chain 12 peptides. Score 0.291 Round 2: 394 peptides, 67 chains. Longest chain 16 peptides. Score 0.392 Round 3: 394 peptides, 62 chains. Longest chain 25 peptides. Score 0.426 Round 4: 374 peptides, 57 chains. Longest chain 17 peptides. Score 0.429 Round 5: 380 peptides, 58 chains. Longest chain 18 peptides. Score 0.431 Taking the results from Round 5 Chains 58, Residues 322, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15309 restraints for refining 6458 atoms. 13958 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2330 (Rfree = 0.000) for 6458 atoms. Found 29 (30 requested) and removed 36 (15 requested) atoms. Cycle 32: After refmac, R = 0.2133 (Rfree = 0.000) for 6422 atoms. Found 15 (30 requested) and removed 26 (15 requested) atoms. Cycle 33: After refmac, R = 0.2074 (Rfree = 0.000) for 6396 atoms. Found 13 (30 requested) and removed 23 (15 requested) atoms. Cycle 34: After refmac, R = 0.2093 (Rfree = 0.000) for 6375 atoms. Found 11 (30 requested) and removed 19 (15 requested) atoms. Cycle 35: After refmac, R = 0.2089 (Rfree = 0.000) for 6358 atoms. Found 16 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.50 Search for helices and strands: 0 residues in 0 chains, 6488 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6503 seeds are put forward Round 1: 321 peptides, 64 chains. Longest chain 15 peptides. Score 0.290 Round 2: 369 peptides, 65 chains. Longest chain 14 peptides. Score 0.365 Round 3: 373 peptides, 64 chains. Longest chain 16 peptides. Score 0.379 Round 4: 378 peptides, 61 chains. Longest chain 18 peptides. Score 0.408 Round 5: 380 peptides, 62 chains. Longest chain 15 peptides. Score 0.404 Taking the results from Round 4 Chains 62, Residues 317, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15314 restraints for refining 6458 atoms. 14015 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2195 (Rfree = 0.000) for 6458 atoms. Found 16 (30 requested) and removed 21 (15 requested) atoms. Cycle 37: After refmac, R = 0.2055 (Rfree = 0.000) for 6437 atoms. Found 12 (30 requested) and removed 26 (15 requested) atoms. Cycle 38: After refmac, R = 0.1989 (Rfree = 0.000) for 6415 atoms. Found 6 (30 requested) and removed 17 (15 requested) atoms. Cycle 39: After refmac, R = 0.1978 (Rfree = 0.000) for 6393 atoms. Found 5 (30 requested) and removed 17 (15 requested) atoms. Cycle 40: After refmac, R = 0.1968 (Rfree = 0.000) for 6378 atoms. Found 5 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 6488 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 6513 seeds are put forward Round 1: 314 peptides, 68 chains. Longest chain 8 peptides. Score 0.247 Round 2: 340 peptides, 64 chains. Longest chain 10 peptides. Score 0.324 Round 3: 351 peptides, 67 chains. Longest chain 12 peptides. Score 0.321 Round 4: 343 peptides, 58 chains. Longest chain 17 peptides. Score 0.373 Round 5: 339 peptides, 58 chains. Longest chain 14 peptides. Score 0.366 Taking the results from Round 4 Chains 58, Residues 285, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15754 restraints for refining 6457 atoms. 14672 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2129 (Rfree = 0.000) for 6457 atoms. Found 13 (30 requested) and removed 20 (15 requested) atoms. Cycle 42: After refmac, R = 0.2029 (Rfree = 0.000) for 6436 atoms. Found 7 (30 requested) and removed 15 (15 requested) atoms. Cycle 43: After refmac, R = 0.2042 (Rfree = 0.000) for 6422 atoms. Found 5 (30 requested) and removed 16 (15 requested) atoms. Cycle 44: After refmac, R = 0.2075 (Rfree = 0.000) for 6407 atoms. Found 11 (30 requested) and removed 17 (15 requested) atoms. Cycle 45: After refmac, R = 0.2160 (Rfree = 0.000) for 6397 atoms. Found 22 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 6556 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6571 seeds are put forward Round 1: 259 peptides, 57 chains. Longest chain 9 peptides. Score 0.230 Round 2: 305 peptides, 58 chains. Longest chain 11 peptides. Score 0.308 Round 3: 287 peptides, 56 chains. Longest chain 11 peptides. Score 0.291 Round 4: 304 peptides, 55 chains. Longest chain 12 peptides. Score 0.329 Round 5: 312 peptides, 53 chains. Longest chain 12 peptides. Score 0.357 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 259, 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 1vl4-4_warpNtrace.pdb as input Building loops using Loopy2018 53 chains (259 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9072 reflections ( 99.17 % complete ) and 16084 restraints for refining 6459 atoms. 15080 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2224 (Rfree = 0.000) for 6459 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2179 (Rfree = 0.000) for 6420 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2154 (Rfree = 0.000) for 6391 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2056 (Rfree = 0.000) for 6365 atoms. TimeTaking 62.6