Sun 23 Dec 23:55:49 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 1vkz-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-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/1vkz-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-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 ============================================================ Sun 23 Dec 23:55:54 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/1vkz-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-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 652 and 0 Target number of residues in the AU: 652 Target solvent content: 0.5834 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-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: 4 Cell parameters: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.55 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: 19.959 3.600 Wilson plot Bfac: 46.03 9503 reflections ( 96.69 % complete ) and 0 restraints for refining 7273 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.2903 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2881 (Rfree = 0.000) for 7273 atoms. Found 46 (46 requested) and removed 73 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.02 3.14 Search for helices and strands: 0 residues in 0 chains, 7368 seeds are put forward NCS extension: 0 residues added, 7368 seeds are put forward Round 1: 292 peptides, 58 chains. Longest chain 10 peptides. Score 0.302 Round 2: 395 peptides, 71 chains. Longest chain 13 peptides. Score 0.397 Round 3: 424 peptides, 68 chains. Longest chain 17 peptides. Score 0.472 Round 4: 450 peptides, 69 chains. Longest chain 17 peptides. Score 0.508 Round 5: 464 peptides, 71 chains. Longest chain 15 peptides. Score 0.516 Taking the results from Round 5 Chains 73, Residues 393, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13446 restraints for refining 5974 atoms. 11868 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2451 (Rfree = 0.000) for 5974 atoms. Found 35 (38 requested) and removed 67 (19 requested) atoms. Cycle 2: After refmac, R = 0.2287 (Rfree = 0.000) for 5832 atoms. Found 38 (38 requested) and removed 55 (19 requested) atoms. Cycle 3: After refmac, R = 0.2127 (Rfree = 0.000) for 5764 atoms. Found 30 (37 requested) and removed 25 (18 requested) atoms. Cycle 4: After refmac, R = 0.2024 (Rfree = 0.000) for 5740 atoms. Found 27 (37 requested) and removed 32 (18 requested) atoms. Cycle 5: After refmac, R = 0.1993 (Rfree = 0.000) for 5712 atoms. Found 29 (36 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 3.20 Search for helices and strands: 0 residues in 0 chains, 5886 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 5899 seeds are put forward Round 1: 398 peptides, 70 chains. Longest chain 17 peptides. Score 0.410 Round 2: 447 peptides, 70 chains. Longest chain 15 peptides. Score 0.496 Round 3: 466 peptides, 69 chains. Longest chain 26 peptides. Score 0.533 Round 4: 462 peptides, 60 chains. Longest chain 20 peptides. Score 0.587 Round 5: 482 peptides, 68 chains. Longest chain 16 peptides. Score 0.564 Taking the results from Round 4 Chains 63, Residues 402, Estimated correctness of the model 9.5 % 8 chains (62 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 12537 restraints for refining 5841 atoms. 10794 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2310 (Rfree = 0.000) for 5841 atoms. Found 37 (37 requested) and removed 62 (18 requested) atoms. Cycle 7: After refmac, R = 0.2041 (Rfree = 0.000) for 5760 atoms. Found 28 (37 requested) and removed 48 (18 requested) atoms. Cycle 8: After refmac, R = 0.1882 (Rfree = 0.000) for 5716 atoms. Found 23 (36 requested) and removed 33 (18 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1771 (Rfree = 0.000) for 5691 atoms. Found 18 (36 requested) and removed 29 (18 requested) atoms. Cycle 10: After refmac, R = 0.1700 (Rfree = 0.000) for 5675 atoms. Found 11 (36 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 3.23 Search for helices and strands: 0 residues in 0 chains, 5820 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5846 seeds are put forward Round 1: 405 peptides, 71 chains. Longest chain 15 peptides. Score 0.415 Round 2: 470 peptides, 68 chains. Longest chain 19 peptides. Score 0.546 Round 3: 463 peptides, 66 chains. Longest chain 16 peptides. Score 0.549 Round 4: 485 peptides, 63 chains. Longest chain 19 peptides. Score 0.601 Round 5: 487 peptides, 68 chains. Longest chain 20 peptides. Score 0.572 Taking the results from Round 4 Chains 68, Residues 422, Estimated correctness of the model 15.0 % 7 chains (76 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 12739 restraints for refining 5976 atoms. 10844 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2256 (Rfree = 0.000) for 5976 atoms. Found 33 (38 requested) and removed 54 (19 requested) atoms. Cycle 12: After refmac, R = 0.2132 (Rfree = 0.000) for 5888 atoms. Found 33 (38 requested) and removed 42 (19 requested) atoms. Cycle 13: After refmac, R = 0.2004 (Rfree = 0.000) for 5849 atoms. Found 29 (37 requested) and removed 37 (18 requested) atoms. Cycle 14: After refmac, R = 0.1854 (Rfree = 0.000) for 5813 atoms. Found 21 (37 requested) and removed 34 (18 requested) atoms. Cycle 15: After refmac, R = 0.1815 (Rfree = 0.000) for 5787 atoms. Found 21 (37 requested) and removed 35 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 3.17 Search for helices and strands: 0 residues in 0 chains, 5916 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 5927 seeds are put forward Round 1: 418 peptides, 74 chains. Longest chain 18 peptides. Score 0.415 Round 2: 433 peptides, 66 chains. Longest chain 15 peptides. Score 0.501 Round 3: 452 peptides, 64 chains. Longest chain 15 peptides. Score 0.546 Round 4: 463 peptides, 64 chains. Longest chain 20 peptides. Score 0.562 Round 5: 471 peptides, 63 chains. Longest chain 19 peptides. Score 0.581 Taking the results from Round 5 Chains 65, Residues 408, Estimated correctness of the model 7.1 % 8 chains (54 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13011 restraints for refining 5976 atoms. 11260 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2294 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 64 (19 requested) atoms. Cycle 17: After refmac, R = 0.2056 (Rfree = 0.000) for 5903 atoms. Found 33 (38 requested) and removed 39 (19 requested) atoms. Cycle 18: After refmac, R = 0.1978 (Rfree = 0.000) for 5863 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. Cycle 19: After refmac, R = 0.1762 (Rfree = 0.000) for 5846 atoms. Found 15 (37 requested) and removed 27 (18 requested) atoms. Cycle 20: After refmac, R = 0.1725 (Rfree = 0.000) for 5819 atoms. Found 16 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 3.17 Search for helices and strands: 0 residues in 0 chains, 5945 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5960 seeds are put forward Round 1: 381 peptides, 68 chains. Longest chain 13 peptides. Score 0.394 Round 2: 428 peptides, 64 chains. Longest chain 15 peptides. Score 0.507 Round 3: 440 peptides, 63 chains. Longest chain 18 peptides. Score 0.534 Round 4: 427 peptides, 63 chains. Longest chain 17 peptides. Score 0.513 Round 5: 423 peptides, 60 chains. Longest chain 22 peptides. Score 0.528 Taking the results from Round 3 Chains 64, Residues 377, Estimated correctness of the model 0.0 % 7 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13270 restraints for refining 5976 atoms. 11698 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2093 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 39 (19 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1942 (Rfree = 0.000) for 5947 atoms. Found 17 (38 requested) and removed 34 (19 requested) atoms. Cycle 23: After refmac, R = 0.1883 (Rfree = 0.000) for 5904 atoms. Found 27 (38 requested) and removed 30 (19 requested) atoms. Cycle 24: After refmac, R = 0.1791 (Rfree = 0.000) for 5890 atoms. Found 15 (37 requested) and removed 27 (18 requested) atoms. Cycle 25: After refmac, R = 0.1781 (Rfree = 0.000) for 5868 atoms. Found 23 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.22 Search for helices and strands: 0 residues in 0 chains, 6014 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6030 seeds are put forward Round 1: 367 peptides, 65 chains. Longest chain 18 peptides. Score 0.392 Round 2: 423 peptides, 64 chains. Longest chain 19 peptides. Score 0.499 Round 3: 444 peptides, 62 chains. Longest chain 19 peptides. Score 0.547 Round 4: 442 peptides, 65 chains. Longest chain 19 peptides. Score 0.523 Round 5: 414 peptides, 59 chains. Longest chain 18 peptides. Score 0.521 Taking the results from Round 3 Chains 64, Residues 382, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13071 restraints for refining 5976 atoms. 11447 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2232 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 46 (19 requested) atoms. Cycle 27: After refmac, R = 0.2016 (Rfree = 0.000) for 5938 atoms. Found 35 (38 requested) and removed 30 (19 requested) atoms. Cycle 28: After refmac, R = 0.1857 (Rfree = 0.000) for 5923 atoms. Found 26 (38 requested) and removed 31 (19 requested) atoms. Cycle 29: After refmac, R = 0.1837 (Rfree = 0.000) for 5898 atoms. Found 26 (37 requested) and removed 35 (18 requested) atoms. Cycle 30: After refmac, R = 0.1783 (Rfree = 0.000) for 5876 atoms. Found 24 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.20 Search for helices and strands: 0 residues in 0 chains, 6038 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6054 seeds are put forward Round 1: 374 peptides, 73 chains. Longest chain 11 peptides. Score 0.340 Round 2: 385 peptides, 61 chains. Longest chain 22 peptides. Score 0.457 Round 3: 400 peptides, 62 chains. Longest chain 22 peptides. Score 0.475 Round 4: 403 peptides, 58 chains. Longest chain 22 peptides. Score 0.510 Round 5: 385 peptides, 58 chains. Longest chain 23 peptides. Score 0.479 Taking the results from Round 4 Chains 60, Residues 345, Estimated correctness of the model 0.0 % 8 chains (50 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13082 restraints for refining 5976 atoms. 11584 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2076 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. Cycle 32: After refmac, R = 0.2001 (Rfree = 0.000) for 5939 atoms. Found 38 (38 requested) and removed 34 (19 requested) atoms. Cycle 33: After refmac, R = 0.1931 (Rfree = 0.000) for 5922 atoms. Found 28 (38 requested) and removed 31 (19 requested) atoms. Cycle 34: After refmac, R = 0.1934 (Rfree = 0.000) for 5904 atoms. Found 37 (37 requested) and removed 30 (18 requested) atoms. Cycle 35: After refmac, R = 0.1926 (Rfree = 0.000) for 5891 atoms. Found 37 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 3.21 Search for helices and strands: 0 residues in 0 chains, 6033 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6045 seeds are put forward Round 1: 342 peptides, 66 chains. Longest chain 10 peptides. Score 0.335 Round 2: 372 peptides, 60 chains. Longest chain 14 peptides. Score 0.441 Round 3: 390 peptides, 62 chains. Longest chain 20 peptides. Score 0.458 Round 4: 396 peptides, 59 chains. Longest chain 21 peptides. Score 0.491 Round 5: 370 peptides, 56 chains. Longest chain 22 peptides. Score 0.469 Taking the results from Round 4 Chains 60, Residues 337, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13399 restraints for refining 5976 atoms. 11953 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2273 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. Cycle 37: After refmac, R = 0.2000 (Rfree = 0.000) for 5942 atoms. Found 34 (38 requested) and removed 40 (19 requested) atoms. Cycle 38: After refmac, R = 0.1913 (Rfree = 0.000) for 5909 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 39: After refmac, R = 0.1821 (Rfree = 0.000) for 5902 atoms. Found 30 (37 requested) and removed 28 (18 requested) atoms. Cycle 40: After refmac, R = 0.1675 (Rfree = 0.000) for 5897 atoms. Found 11 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 3.22 Search for helices and strands: 0 residues in 0 chains, 6033 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6049 seeds are put forward Round 1: 303 peptides, 59 chains. Longest chain 9 peptides. Score 0.316 Round 2: 365 peptides, 65 chains. Longest chain 14 peptides. Score 0.388 Round 3: 360 peptides, 62 chains. Longest chain 20 peptides. Score 0.403 Round 4: 357 peptides, 59 chains. Longest chain 18 peptides. Score 0.422 Round 5: 344 peptides, 53 chains. Longest chain 20 peptides. Score 0.446 Taking the results from Round 5 Chains 56, Residues 291, Estimated correctness of the model 0.0 % 7 chains (46 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13520 restraints for refining 5976 atoms. 12225 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2237 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. Cycle 42: After refmac, R = 0.2011 (Rfree = 0.000) for 5938 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 43: After refmac, R = 0.1856 (Rfree = 0.000) for 5917 atoms. Found 36 (38 requested) and removed 23 (19 requested) atoms. Cycle 44: After refmac, R = 0.1768 (Rfree = 0.000) for 5909 atoms. Found 27 (38 requested) and removed 27 (19 requested) atoms. Cycle 45: After refmac, R = 0.1758 (Rfree = 0.000) for 5901 atoms. Found 26 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 3.17 Search for helices and strands: 0 residues in 0 chains, 6036 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6056 seeds are put forward Round 1: 265 peptides, 55 chains. Longest chain 11 peptides. Score 0.271 Round 2: 327 peptides, 59 chains. Longest chain 11 peptides. Score 0.364 Round 3: 322 peptides, 56 chains. Longest chain 13 peptides. Score 0.380 Round 4: 323 peptides, 57 chains. Longest chain 17 peptides. Score 0.373 Round 5: 333 peptides, 53 chains. Longest chain 17 peptides. Score 0.426 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 280, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 55 chains (280 residues) following loop building 4 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9503 reflections ( 96.69 % complete ) and 13789 restraints for refining 5963 atoms. 12602 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2171 (Rfree = 0.000) for 5963 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2072 (Rfree = 0.000) for 5920 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1980 (Rfree = 0.000) for 5885 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1902 (Rfree = 0.000) for 5859 atoms. TimeTaking 67.27