null Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vme-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vme-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vme-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-parrot-hancs ############### 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 22:23:15 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/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-parrot-hancs/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 593 and 0 Target number of residues in the AU: 593 Target solvent content: 0.6622 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-3.8-parrot-hancs.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-3.8-parrot-hancs.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 3.800 Wilson plot Bfac: 86.28 9324 reflections ( 99.79 % complete ) and 0 restraints for refining 7260 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3269 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3099 (Rfree = 0.000) for 7260 atoms. Found 39 (39 requested) and removed 62 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 7396 seeds are put forward NCS extension: 0 residues added, 7396 seeds are put forward Round 1: 354 peptides, 67 chains. Longest chain 14 peptides. Score 0.335 Round 2: 448 peptides, 70 chains. Longest chain 15 peptides. Score 0.471 Round 3: 478 peptides, 69 chains. Longest chain 17 peptides. Score 0.522 Round 4: 486 peptides, 64 chains. Longest chain 20 peptides. Score 0.564 Round 5: 492 peptides, 66 chains. Longest chain 23 peptides. Score 0.560 Taking the results from Round 4 Chains 65, Residues 422, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13495 restraints for refining 5928 atoms. 11813 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2372 (Rfree = 0.000) for 5928 atoms. Found 23 (32 requested) and removed 36 (16 requested) atoms. Cycle 2: After refmac, R = 0.2273 (Rfree = 0.000) for 5838 atoms. Found 15 (32 requested) and removed 37 (16 requested) atoms. Cycle 3: After refmac, R = 0.2153 (Rfree = 0.000) for 5784 atoms. Found 10 (31 requested) and removed 30 (15 requested) atoms. Cycle 4: After refmac, R = 0.2110 (Rfree = 0.000) for 5743 atoms. Found 20 (31 requested) and removed 32 (15 requested) atoms. Cycle 5: After refmac, R = 0.2015 (Rfree = 0.000) for 5720 atoms. Found 8 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 5910 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5928 seeds are put forward Round 1: 428 peptides, 69 chains. Longest chain 16 peptides. Score 0.446 Round 2: 453 peptides, 63 chains. Longest chain 21 peptides. Score 0.525 Round 3: 465 peptides, 62 chains. Longest chain 20 peptides. Score 0.548 Round 4: 470 peptides, 64 chains. Longest chain 18 peptides. Score 0.542 Round 5: 453 peptides, 60 chains. Longest chain 19 peptides. Score 0.544 Taking the results from Round 3 Chains 63, Residues 403, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13367 restraints for refining 5932 atoms. 11776 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2256 (Rfree = 0.000) for 5932 atoms. Found 25 (32 requested) and removed 50 (16 requested) atoms. Cycle 7: After refmac, R = 0.2144 (Rfree = 0.000) for 5871 atoms. Found 13 (32 requested) and removed 35 (16 requested) atoms. Cycle 8: After refmac, R = 0.2165 (Rfree = 0.000) for 5837 atoms. Found 18 (32 requested) and removed 43 (16 requested) atoms. Cycle 9: After refmac, R = 0.1995 (Rfree = 0.000) for 5798 atoms. Found 11 (31 requested) and removed 27 (15 requested) atoms. Cycle 10: After refmac, R = 0.1992 (Rfree = 0.000) for 5767 atoms. Found 14 (31 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 5976 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 6003 seeds are put forward Round 1: 407 peptides, 69 chains. Longest chain 16 peptides. Score 0.412 Round 2: 443 peptides, 65 chains. Longest chain 17 peptides. Score 0.497 Round 3: 465 peptides, 60 chains. Longest chain 20 peptides. Score 0.560 Round 4: 452 peptides, 65 chains. Longest chain 27 peptides. Score 0.510 Round 5: 464 peptides, 64 chains. Longest chain 20 peptides. Score 0.534 Taking the results from Round 3 Chains 62, Residues 405, Estimated correctness of the model 0.0 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13035 restraints for refining 5932 atoms. 11313 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2199 (Rfree = 0.000) for 5932 atoms. Found 15 (32 requested) and removed 39 (16 requested) atoms. Cycle 12: After refmac, R = 0.2127 (Rfree = 0.000) for 5872 atoms. Found 13 (32 requested) and removed 33 (16 requested) atoms. Cycle 13: After refmac, R = 0.2003 (Rfree = 0.000) for 5831 atoms. Found 10 (32 requested) and removed 34 (16 requested) atoms. Cycle 14: After refmac, R = 0.1944 (Rfree = 0.000) for 5791 atoms. Found 13 (31 requested) and removed 34 (15 requested) atoms. Cycle 15: After refmac, R = 0.1893 (Rfree = 0.000) for 5756 atoms. Found 9 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 3.51 Search for helices and strands: 0 residues in 0 chains, 5929 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 5950 seeds are put forward Round 1: 385 peptides, 71 chains. Longest chain 11 peptides. Score 0.360 Round 2: 432 peptides, 65 chains. Longest chain 15 peptides. Score 0.480 Round 3: 422 peptides, 62 chains. Longest chain 15 peptides. Score 0.485 Round 4: 442 peptides, 62 chains. Longest chain 19 peptides. Score 0.515 Round 5: 438 peptides, 65 chains. Longest chain 15 peptides. Score 0.489 Taking the results from Round 4 Chains 63, Residues 380, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13368 restraints for refining 5932 atoms. 11841 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2069 (Rfree = 0.000) for 5932 atoms. Found 28 (32 requested) and removed 40 (16 requested) atoms. Cycle 17: After refmac, R = 0.1983 (Rfree = 0.000) for 5887 atoms. Found 14 (32 requested) and removed 35 (16 requested) atoms. Cycle 18: After refmac, R = 0.1962 (Rfree = 0.000) for 5847 atoms. Found 18 (32 requested) and removed 27 (16 requested) atoms. Cycle 19: After refmac, R = 0.1987 (Rfree = 0.000) for 5825 atoms. Found 22 (32 requested) and removed 28 (16 requested) atoms. Cycle 20: After refmac, R = 0.1654 (Rfree = 0.000) for 5807 atoms. Found 5 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 5967 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 5991 seeds are put forward Round 1: 378 peptides, 71 chains. Longest chain 14 peptides. Score 0.348 Round 2: 437 peptides, 67 chains. Longest chain 17 peptides. Score 0.474 Round 3: 430 peptides, 68 chains. Longest chain 14 peptides. Score 0.457 Round 4: 433 peptides, 62 chains. Longest chain 16 peptides. Score 0.502 Round 5: 431 peptides, 69 chains. Longest chain 13 peptides. Score 0.451 Taking the results from Round 4 Chains 63, Residues 371, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13356 restraints for refining 5932 atoms. 11851 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2092 (Rfree = 0.000) for 5932 atoms. Found 26 (32 requested) and removed 31 (16 requested) atoms. Cycle 22: After refmac, R = 0.2067 (Rfree = 0.000) for 5900 atoms. Found 24 (32 requested) and removed 27 (16 requested) atoms. Cycle 23: After refmac, R = 0.2054 (Rfree = 0.000) for 5878 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 24: After refmac, R = 0.1960 (Rfree = 0.000) for 5862 atoms. Found 31 (32 requested) and removed 24 (16 requested) atoms. Cycle 25: After refmac, R = 0.1864 (Rfree = 0.000) for 5854 atoms. Found 20 (32 requested) and removed 29 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.49 Search for helices and strands: 0 residues in 0 chains, 6056 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 6077 seeds are put forward Round 1: 348 peptides, 68 chains. Longest chain 10 peptides. Score 0.317 Round 2: 390 peptides, 60 chains. Longest chain 15 peptides. Score 0.449 Round 3: 397 peptides, 64 chains. Longest chain 13 peptides. Score 0.432 Round 4: 406 peptides, 67 chains. Longest chain 14 peptides. Score 0.425 Round 5: 402 peptides, 61 chains. Longest chain 13 peptides. Score 0.461 Taking the results from Round 5 Chains 61, Residues 341, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13707 restraints for refining 5932 atoms. 12333 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2136 (Rfree = 0.000) for 5932 atoms. Found 24 (32 requested) and removed 30 (16 requested) atoms. Cycle 27: After refmac, R = 0.2171 (Rfree = 0.000) for 5899 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 28: After refmac, R = 0.2170 (Rfree = 0.000) for 5892 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 29: After refmac, R = 0.1811 (Rfree = 0.000) for 5873 atoms. Found 4 (32 requested) and removed 23 (16 requested) atoms. Cycle 30: After refmac, R = 0.1763 (Rfree = 0.000) for 5847 atoms. Found 3 (32 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 6006 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 6018 seeds are put forward Round 1: 319 peptides, 60 chains. Longest chain 10 peptides. Score 0.326 Round 2: 354 peptides, 57 chains. Longest chain 13 peptides. Score 0.411 Round 3: 362 peptides, 56 chains. Longest chain 15 peptides. Score 0.432 Round 4: 371 peptides, 57 chains. Longest chain 13 peptides. Score 0.439 Round 5: 362 peptides, 55 chains. Longest chain 14 peptides. Score 0.439 Taking the results from Round 5 Chains 55, Residues 307, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13933 restraints for refining 5931 atoms. 12736 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2136 (Rfree = 0.000) for 5931 atoms. Found 24 (32 requested) and removed 34 (16 requested) atoms. Cycle 32: After refmac, R = 0.2188 (Rfree = 0.000) for 5910 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 33: After refmac, R = 0.2061 (Rfree = 0.000) for 5901 atoms. Found 28 (32 requested) and removed 31 (16 requested) atoms. Cycle 34: After refmac, R = 0.1719 (Rfree = 0.000) for 5889 atoms. Found 8 (32 requested) and removed 22 (16 requested) atoms. Cycle 35: After refmac, R = 0.1666 (Rfree = 0.000) for 5872 atoms. Found 10 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 6027 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6048 seeds are put forward Round 1: 281 peptides, 53 chains. Longest chain 11 peptides. Score 0.311 Round 2: 330 peptides, 54 chains. Longest chain 13 peptides. Score 0.392 Round 3: 323 peptides, 51 chains. Longest chain 14 peptides. Score 0.403 Round 4: 323 peptides, 49 chains. Longest chain 24 peptides. Score 0.419 Round 5: 311 peptides, 51 chains. Longest chain 18 peptides. Score 0.382 Taking the results from Round 4 Chains 50, Residues 274, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 14104 restraints for refining 5933 atoms. 13014 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2074 (Rfree = 0.000) for 5933 atoms. Found 19 (32 requested) and removed 39 (16 requested) atoms. Cycle 37: After refmac, R = 0.2085 (Rfree = 0.000) for 5891 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 38: After refmac, R = 0.2019 (Rfree = 0.000) for 5896 atoms. Found 32 (32 requested) and removed 26 (16 requested) atoms. Cycle 39: After refmac, R = 0.1617 (Rfree = 0.000) for 5898 atoms. Found 3 (32 requested) and removed 23 (16 requested) atoms. Cycle 40: After refmac, R = 0.1585 (Rfree = 0.000) for 5870 atoms. Found 6 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 6044 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 6058 seeds are put forward Round 1: 288 peptides, 55 chains. Longest chain 16 peptides. Score 0.308 Round 2: 330 peptides, 57 chains. Longest chain 11 peptides. Score 0.369 Round 3: 343 peptides, 56 chains. Longest chain 13 peptides. Score 0.400 Round 4: 326 peptides, 54 chains. Longest chain 11 peptides. Score 0.385 Round 5: 335 peptides, 53 chains. Longest chain 16 peptides. Score 0.409 Taking the results from Round 5 Chains 53, Residues 282, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 14250 restraints for refining 5933 atoms. 13164 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2056 (Rfree = 0.000) for 5933 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 42: After refmac, R = 0.2054 (Rfree = 0.000) for 5928 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 43: After refmac, R = 0.1655 (Rfree = 0.000) for 5931 atoms. Found 5 (32 requested) and removed 20 (16 requested) atoms. Cycle 44: After refmac, R = 0.1565 (Rfree = 0.000) for 5908 atoms. Found 3 (32 requested) and removed 24 (16 requested) atoms. Cycle 45: After refmac, R = 0.1560 (Rfree = 0.000) for 5886 atoms. Found 4 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 6054 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6077 seeds are put forward Round 1: 284 peptides, 58 chains. Longest chain 11 peptides. Score 0.275 Round 2: 312 peptides, 55 chains. Longest chain 12 peptides. Score 0.353 Round 3: 312 peptides, 52 chains. Longest chain 12 peptides. Score 0.376 Round 4: 317 peptides, 54 chains. Longest chain 12 peptides. Score 0.369 Round 5: 313 peptides, 48 chains. Longest chain 15 peptides. Score 0.409 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 265, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9324 reflections ( 99.79 % complete ) and 14244 restraints for refining 5933 atoms. 13206 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2112 (Rfree = 0.000) for 5933 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2153 (Rfree = 0.000) for 5898 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2046 (Rfree = 0.000) for 5876 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2032 (Rfree = 0.000) for 5850 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:38:07 GMT 2018 Job finished. TimeTaking 75.04 Used memory is bytes: 14716232