null Mon 24 Dec 07:42:55 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 1vkz-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-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/1vkz-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-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 07:42:59 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/1vkz-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-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 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-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: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.6-parrot-noncs.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 7253 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.2946 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2892 (Rfree = 0.000) for 7253 atoms. Found 46 (46 requested) and removed 82 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.03 3.15 Search for helices and strands: 0 residues in 0 chains, 7344 seeds are put forward NCS extension: 0 residues added, 7344 seeds are put forward Round 1: 308 peptides, 64 chains. Longest chain 8 peptides. Score 0.282 Round 2: 420 peptides, 75 chains. Longest chain 13 peptides. Score 0.411 Round 3: 450 peptides, 75 chains. Longest chain 15 peptides. Score 0.464 Round 4: 463 peptides, 76 chains. Longest chain 14 peptides. Score 0.479 Round 5: 481 peptides, 76 chains. Longest chain 14 peptides. Score 0.509 Taking the results from Round 5 Chains 79, Residues 405, Estimated correctness of the model 0.0 % 6 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13366 restraints for refining 5976 atoms. 11683 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2454 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 55 (19 requested) atoms. Cycle 2: After refmac, R = 0.2367 (Rfree = 0.000) for 5841 atoms. Found 32 (38 requested) and removed 56 (19 requested) atoms. Cycle 3: After refmac, R = 0.2275 (Rfree = 0.000) for 5760 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. Cycle 4: After refmac, R = 0.2151 (Rfree = 0.000) for 5727 atoms. Found 34 (36 requested) and removed 35 (18 requested) atoms. Cycle 5: After refmac, R = 0.2055 (Rfree = 0.000) for 5694 atoms. Found 36 (36 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 3.15 Search for helices and strands: 0 residues in 0 chains, 5861 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5874 seeds are put forward Round 1: 388 peptides, 69 chains. Longest chain 12 peptides. Score 0.399 Round 2: 413 peptides, 62 chains. Longest chain 17 peptides. Score 0.497 Round 3: 445 peptides, 65 chains. Longest chain 17 peptides. Score 0.528 Round 4: 459 peptides, 69 chains. Longest chain 15 peptides. Score 0.522 Round 5: 455 peptides, 62 chains. Longest chain 19 peptides. Score 0.564 Taking the results from Round 5 Chains 64, Residues 393, Estimated correctness of the model 0.1 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13059 restraints for refining 5819 atoms. 11410 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2354 (Rfree = 0.000) for 5819 atoms. Found 37 (37 requested) and removed 64 (18 requested) atoms. Cycle 7: After refmac, R = 0.2265 (Rfree = 0.000) for 5726 atoms. Found 37 (37 requested) and removed 46 (18 requested) atoms. Cycle 8: After refmac, R = 0.2136 (Rfree = 0.000) for 5682 atoms. Found 36 (36 requested) and removed 30 (18 requested) atoms. Cycle 9: After refmac, R = 0.1978 (Rfree = 0.000) for 5662 atoms. Found 35 (36 requested) and removed 30 (18 requested) atoms. Cycle 10: After refmac, R = 0.1932 (Rfree = 0.000) for 5646 atoms. Found 36 (36 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.06 3.18 Search for helices and strands: 0 residues in 0 chains, 5819 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 5841 seeds are put forward Round 1: 395 peptides, 76 chains. Longest chain 13 peptides. Score 0.356 Round 2: 440 peptides, 69 chains. Longest chain 17 peptides. Score 0.491 Round 3: 447 peptides, 65 chains. Longest chain 17 peptides. Score 0.531 Round 4: 477 peptides, 76 chains. Longest chain 14 peptides. Score 0.502 Round 5: 463 peptides, 62 chains. Longest chain 23 peptides. Score 0.576 Taking the results from Round 5 Chains 67, Residues 401, Estimated correctness of the model 5.1 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13013 restraints for refining 5976 atoms. 11262 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2308 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 60 (19 requested) atoms. Cycle 12: After refmac, R = 0.2038 (Rfree = 0.000) for 5883 atoms. Found 34 (38 requested) and removed 34 (19 requested) atoms. Cycle 13: After refmac, R = 0.1932 (Rfree = 0.000) for 5850 atoms. Found 23 (37 requested) and removed 28 (18 requested) atoms. Cycle 14: After refmac, R = 0.1890 (Rfree = 0.000) for 5820 atoms. Found 35 (37 requested) and removed 37 (18 requested) atoms. Cycle 15: After refmac, R = 0.1827 (Rfree = 0.000) for 5807 atoms. Found 22 (37 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 3.18 Search for helices and strands: 0 residues in 0 chains, 5989 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6003 seeds are put forward Round 1: 397 peptides, 72 chains. Longest chain 15 peptides. Score 0.392 Round 2: 466 peptides, 71 chains. Longest chain 16 peptides. Score 0.520 Round 3: 472 peptides, 76 chains. Longest chain 13 peptides. Score 0.494 Round 4: 488 peptides, 69 chains. Longest chain 19 peptides. Score 0.567 Round 5: 475 peptides, 69 chains. Longest chain 19 peptides. Score 0.547 Taking the results from Round 4 Chains 73, Residues 419, Estimated correctness of the model 1.3 % 7 chains (61 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 12868 restraints for refining 5975 atoms. 11039 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2363 (Rfree = 0.000) for 5975 atoms. Found 38 (38 requested) and removed 46 (19 requested) atoms. Cycle 17: After refmac, R = 0.2154 (Rfree = 0.000) for 5906 atoms. Found 34 (38 requested) and removed 35 (19 requested) atoms. Cycle 18: After refmac, R = 0.2046 (Rfree = 0.000) for 5861 atoms. Found 33 (37 requested) and removed 30 (18 requested) atoms. Cycle 19: After refmac, R = 0.1980 (Rfree = 0.000) for 5835 atoms. Found 26 (37 requested) and removed 28 (18 requested) atoms. Cycle 20: After refmac, R = 0.1912 (Rfree = 0.000) for 5817 atoms. Found 18 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 3.17 Search for helices and strands: 0 residues in 0 chains, 5980 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 5991 seeds are put forward Round 1: 385 peptides, 74 chains. Longest chain 19 peptides. Score 0.353 Round 2: 428 peptides, 66 chains. Longest chain 23 peptides. Score 0.493 Round 3: 440 peptides, 70 chains. Longest chain 16 peptides. Score 0.484 Round 4: 432 peptides, 66 chains. Longest chain 29 peptides. Score 0.500 Round 5: 427 peptides, 67 chains. Longest chain 16 peptides. Score 0.484 Taking the results from Round 4 Chains 68, Residues 366, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13102 restraints for refining 5976 atoms. 11537 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2311 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 22: After refmac, R = 0.2111 (Rfree = 0.000) for 5926 atoms. Found 33 (38 requested) and removed 42 (19 requested) atoms. Cycle 23: After refmac, R = 0.2024 (Rfree = 0.000) for 5890 atoms. Found 28 (37 requested) and removed 28 (18 requested) atoms. Cycle 24: After refmac, R = 0.1932 (Rfree = 0.000) for 5866 atoms. Found 26 (37 requested) and removed 33 (18 requested) atoms. Cycle 25: After refmac, R = 0.1910 (Rfree = 0.000) for 5841 atoms. Found 27 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.21 Search for helices and strands: 0 residues in 0 chains, 6009 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6028 seeds are put forward Round 1: 336 peptides, 66 chains. Longest chain 17 peptides. Score 0.323 Round 2: 403 peptides, 67 chains. Longest chain 19 peptides. Score 0.442 Round 3: 391 peptides, 66 chains. Longest chain 17 peptides. Score 0.429 Round 4: 412 peptides, 67 chains. Longest chain 19 peptides. Score 0.458 Round 5: 400 peptides, 68 chains. Longest chain 21 peptides. Score 0.429 Taking the results from Round 4 Chains 71, Residues 345, Estimated correctness of the model 0.0 % 6 chains (62 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 12958 restraints for refining 5976 atoms. 11449 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2085 (Rfree = 0.000) for 5976 atoms. Found 37 (38 requested) and removed 56 (19 requested) atoms. Cycle 27: After refmac, R = 0.1862 (Rfree = 0.000) for 5912 atoms. Found 16 (38 requested) and removed 35 (19 requested) atoms. Cycle 28: After refmac, R = 0.1865 (Rfree = 0.000) for 5873 atoms. Found 14 (37 requested) and removed 22 (18 requested) atoms. Cycle 29: After refmac, R = 0.1777 (Rfree = 0.000) for 5859 atoms. Found 17 (37 requested) and removed 25 (18 requested) atoms. Cycle 30: After refmac, R = 0.1746 (Rfree = 0.000) for 5838 atoms. Found 22 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.03 3.15 Search for helices and strands: 0 residues in 0 chains, 6000 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6020 seeds are put forward Round 1: 318 peptides, 65 chains. Longest chain 15 peptides. Score 0.295 Round 2: 370 peptides, 64 chains. Longest chain 13 peptides. Score 0.406 Round 3: 394 peptides, 65 chains. Longest chain 12 peptides. Score 0.442 Round 4: 385 peptides, 66 chains. Longest chain 12 peptides. Score 0.418 Round 5: 387 peptides, 64 chains. Longest chain 23 peptides. Score 0.437 Taking the results from Round 3 Chains 65, Residues 329, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13467 restraints for refining 5975 atoms. 12167 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1961 (Rfree = 0.000) for 5975 atoms. Found 30 (38 requested) and removed 46 (19 requested) atoms. Cycle 32: After refmac, R = 0.1807 (Rfree = 0.000) for 5928 atoms. Found 32 (38 requested) and removed 31 (19 requested) atoms. Cycle 33: After refmac, R = 0.1757 (Rfree = 0.000) for 5914 atoms. Found 23 (38 requested) and removed 25 (19 requested) atoms. Cycle 34: After refmac, R = 0.1706 (Rfree = 0.000) for 5905 atoms. Found 22 (37 requested) and removed 23 (18 requested) atoms. Cycle 35: After refmac, R = 0.1683 (Rfree = 0.000) for 5893 atoms. Found 23 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 3.15 Search for helices and strands: 0 residues in 0 chains, 6039 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6052 seeds are put forward Round 1: 339 peptides, 68 chains. Longest chain 12 peptides. Score 0.312 Round 2: 381 peptides, 68 chains. Longest chain 12 peptides. Score 0.394 Round 3: 371 peptides, 60 chains. Longest chain 20 peptides. Score 0.439 Round 4: 379 peptides, 61 chains. Longest chain 13 peptides. Score 0.446 Round 5: 377 peptides, 59 chains. Longest chain 14 peptides. Score 0.458 Taking the results from Round 5 Chains 60, Residues 318, Estimated correctness of the model 0.0 % 10 chains (46 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13355 restraints for refining 5976 atoms. 11999 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2099 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 41 (19 requested) atoms. Cycle 37: After refmac, R = 0.1909 (Rfree = 0.000) for 5934 atoms. Found 36 (38 requested) and removed 33 (19 requested) atoms. Cycle 38: After refmac, R = 0.1857 (Rfree = 0.000) for 5918 atoms. Found 32 (38 requested) and removed 28 (19 requested) atoms. Cycle 39: After refmac, R = 0.1711 (Rfree = 0.000) for 5908 atoms. Found 24 (37 requested) and removed 20 (18 requested) atoms. Cycle 40: After refmac, R = 0.1719 (Rfree = 0.000) for 5896 atoms. Found 33 (37 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 3.15 Search for helices and strands: 0 residues in 0 chains, 6057 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 6068 seeds are put forward Round 1: 276 peptides, 55 chains. Longest chain 11 peptides. Score 0.295 Round 2: 328 peptides, 60 chains. Longest chain 11 peptides. Score 0.358 Round 3: 341 peptides, 56 chains. Longest chain 13 peptides. Score 0.416 Round 4: 356 peptides, 60 chains. Longest chain 12 peptides. Score 0.412 Round 5: 337 peptides, 54 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 5 Chains 54, Residues 283, Estimated correctness of the model 0.0 % 6 chains (37 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13522 restraints for refining 5976 atoms. 12336 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2076 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 32 (19 requested) atoms. Cycle 42: After refmac, R = 0.1817 (Rfree = 0.000) for 5953 atoms. Found 33 (38 requested) and removed 34 (19 requested) atoms. Cycle 43: After refmac, R = 0.1793 (Rfree = 0.000) for 5942 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. Cycle 44: After refmac, R = 0.1797 (Rfree = 0.000) for 5940 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 45: After refmac, R = 0.1768 (Rfree = 0.000) for 5939 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.04 3.16 Search for helices and strands: 0 residues in 0 chains, 6086 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 6101 seeds are put forward Round 1: 276 peptides, 58 chains. Longest chain 10 peptides. Score 0.267 Round 2: 335 peptides, 62 chains. Longest chain 12 peptides. Score 0.355 Round 3: 360 peptides, 61 chains. Longest chain 16 peptides. Score 0.411 Round 4: 355 peptides, 58 chains. Longest chain 15 peptides. Score 0.426 Round 5: 362 peptides, 58 chains. Longest chain 14 peptides. Score 0.439 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 59, Residues 304, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 59 chains (304 residues) following loop building 4 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9503 reflections ( 96.69 % complete ) and 13260 restraints for refining 5976 atoms. 12022 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2111 (Rfree = 0.000) for 5976 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1959 (Rfree = 0.000) for 5933 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1911 (Rfree = 0.000) for 5896 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1856 (Rfree = 0.000) for 5867 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:38:56 GMT 2018 Job finished. TimeTaking 56.02 Used memory is bytes: 20706296