null Sun 23 Dec 22:22:49 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vme-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vme-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-4.0-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 22:22:58 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-4.0-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 581 and 0 Target number of residues in the AU: 581 Target solvent content: 0.6690 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 6560 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: 48.998 4.000 Wilson plot Bfac: 91.38 7991 reflections ( 99.75 % complete ) and 0 restraints for refining 7217 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3327 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3179 (Rfree = 0.000) for 7217 atoms. Found 34 (34 requested) and removed 49 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 7340 seeds are put forward NCS extension: 0 residues added, 7340 seeds are put forward Round 1: 318 peptides, 58 chains. Longest chain 11 peptides. Score 0.340 Round 2: 375 peptides, 60 chains. Longest chain 12 peptides. Score 0.424 Round 3: 403 peptides, 61 chains. Longest chain 13 peptides. Score 0.462 Round 4: 397 peptides, 57 chains. Longest chain 17 peptides. Score 0.481 Round 5: 426 peptides, 60 chains. Longest chain 19 peptides. Score 0.505 Taking the results from Round 5 Chains 60, Residues 366, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13882 restraints for refining 5921 atoms. 12455 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2827 (Rfree = 0.000) for 5921 atoms. Found 26 (28 requested) and removed 42 (14 requested) atoms. Cycle 2: After refmac, R = 0.2372 (Rfree = 0.000) for 5819 atoms. Found 24 (28 requested) and removed 30 (14 requested) atoms. Cycle 3: After refmac, R = 0.2224 (Rfree = 0.000) for 5769 atoms. Found 13 (27 requested) and removed 37 (13 requested) atoms. Cycle 4: After refmac, R = 0.1933 (Rfree = 0.000) for 5723 atoms. Found 8 (27 requested) and removed 22 (13 requested) atoms. Cycle 5: After refmac, R = 0.1822 (Rfree = 0.000) for 5692 atoms. Found 5 (27 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 5892 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 5919 seeds are put forward Round 1: 368 peptides, 65 chains. Longest chain 16 peptides. Score 0.375 Round 2: 412 peptides, 63 chains. Longest chain 18 peptides. Score 0.463 Round 3: 431 peptides, 62 chains. Longest chain 17 peptides. Score 0.499 Round 4: 429 peptides, 64 chains. Longest chain 21 peptides. Score 0.482 Round 5: 421 peptides, 59 chains. Longest chain 18 peptides. Score 0.504 Taking the results from Round 5 Chains 60, Residues 362, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13674 restraints for refining 5923 atoms. 12220 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2378 (Rfree = 0.000) for 5923 atoms. Found 24 (28 requested) and removed 36 (14 requested) atoms. Cycle 7: After refmac, R = 0.2357 (Rfree = 0.000) for 5860 atoms. Found 28 (28 requested) and removed 48 (14 requested) atoms. Cycle 8: After refmac, R = 0.2255 (Rfree = 0.000) for 5796 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 9: After refmac, R = 0.1855 (Rfree = 0.000) for 5748 atoms. Found 11 (27 requested) and removed 26 (13 requested) atoms. Cycle 10: After refmac, R = 0.1736 (Rfree = 0.000) for 5719 atoms. Found 4 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 5904 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5918 seeds are put forward Round 1: 369 peptides, 73 chains. Longest chain 10 peptides. Score 0.316 Round 2: 421 peptides, 68 chains. Longest chain 16 peptides. Score 0.442 Round 3: 431 peptides, 70 chains. Longest chain 14 peptides. Score 0.444 Round 4: 441 peptides, 66 chains. Longest chain 17 peptides. Score 0.487 Round 5: 418 peptides, 64 chains. Longest chain 12 peptides. Score 0.465 Taking the results from Round 4 Chains 67, Residues 375, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13823 restraints for refining 5923 atoms. 12354 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2305 (Rfree = 0.000) for 5923 atoms. Found 25 (28 requested) and removed 39 (14 requested) atoms. Cycle 12: After refmac, R = 0.2272 (Rfree = 0.000) for 5856 atoms. Found 28 (28 requested) and removed 36 (14 requested) atoms. Cycle 13: After refmac, R = 0.2272 (Rfree = 0.000) for 5827 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 14: After refmac, R = 0.2204 (Rfree = 0.000) for 5789 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 15: After refmac, R = 0.1802 (Rfree = 0.000) for 5767 atoms. Found 12 (27 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 5952 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 5980 seeds are put forward Round 1: 361 peptides, 69 chains. Longest chain 13 peptides. Score 0.333 Round 2: 368 peptides, 60 chains. Longest chain 15 peptides. Score 0.413 Round 3: 389 peptides, 59 chains. Longest chain 17 peptides. Score 0.454 Round 4: 370 peptides, 57 chains. Longest chain 14 peptides. Score 0.438 Round 5: 360 peptides, 55 chains. Longest chain 16 peptides. Score 0.436 Taking the results from Round 3 Chains 59, Residues 330, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13936 restraints for refining 5924 atoms. 12645 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2477 (Rfree = 0.000) for 5924 atoms. Found 28 (28 requested) and removed 37 (14 requested) atoms. Cycle 17: After refmac, R = 0.2316 (Rfree = 0.000) for 5867 atoms. Found 28 (28 requested) and removed 46 (14 requested) atoms. Cycle 18: After refmac, R = 0.2270 (Rfree = 0.000) for 5828 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 19: After refmac, R = 0.2198 (Rfree = 0.000) for 5805 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 20: After refmac, R = 0.2274 (Rfree = 0.000) for 5787 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.75 3.60 Search for helices and strands: 0 residues in 0 chains, 5929 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 5944 seeds are put forward Round 1: 296 peptides, 58 chains. Longest chain 12 peptides. Score 0.299 Round 2: 346 peptides, 58 chains. Longest chain 13 peptides. Score 0.390 Round 3: 356 peptides, 55 chains. Longest chain 16 peptides. Score 0.429 Round 4: 362 peptides, 56 chains. Longest chain 16 peptides. Score 0.432 Round 5: 357 peptides, 56 chains. Longest chain 16 peptides. Score 0.424 Taking the results from Round 4 Chains 56, Residues 306, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14118 restraints for refining 5923 atoms. 12923 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2423 (Rfree = 0.000) for 5923 atoms. Found 22 (28 requested) and removed 61 (14 requested) atoms. Cycle 22: After refmac, R = 0.2392 (Rfree = 0.000) for 5849 atoms. Found 27 (27 requested) and removed 41 (13 requested) atoms. Cycle 23: After refmac, R = 0.2191 (Rfree = 0.000) for 5812 atoms. Found 27 (27 requested) and removed 43 (13 requested) atoms. Cycle 24: After refmac, R = 0.1803 (Rfree = 0.000) for 5784 atoms. Found 13 (27 requested) and removed 27 (13 requested) atoms. Cycle 25: After refmac, R = 0.1702 (Rfree = 0.000) for 5764 atoms. Found 7 (27 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 5948 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5967 seeds are put forward Round 1: 335 peptides, 66 chains. Longest chain 11 peptides. Score 0.308 Round 2: 350 peptides, 60 chains. Longest chain 15 peptides. Score 0.382 Round 3: 348 peptides, 61 chains. Longest chain 20 peptides. Score 0.370 Round 4: 351 peptides, 54 chains. Longest chain 19 peptides. Score 0.428 Round 5: 360 peptides, 60 chains. Longest chain 17 peptides. Score 0.399 Taking the results from Round 4 Chains 55, Residues 297, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13846 restraints for refining 5924 atoms. 12664 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2218 (Rfree = 0.000) for 5924 atoms. Found 24 (28 requested) and removed 44 (14 requested) atoms. Cycle 27: After refmac, R = 0.2313 (Rfree = 0.000) for 5872 atoms. Found 28 (28 requested) and removed 41 (14 requested) atoms. Cycle 28: After refmac, R = 0.2217 (Rfree = 0.000) for 5844 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 29: After refmac, R = 0.1716 (Rfree = 0.000) for 5826 atoms. Found 8 (27 requested) and removed 26 (13 requested) atoms. Cycle 30: After refmac, R = 0.1583 (Rfree = 0.000) for 5803 atoms. Found 4 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.63 Search for helices and strands: 0 residues in 0 chains, 5951 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5965 seeds are put forward Round 1: 277 peptides, 54 chains. Longest chain 13 peptides. Score 0.295 Round 2: 317 peptides, 53 chains. Longest chain 17 peptides. Score 0.377 Round 3: 320 peptides, 52 chains. Longest chain 14 peptides. Score 0.390 Round 4: 320 peptides, 51 chains. Longest chain 15 peptides. Score 0.398 Round 5: 318 peptides, 51 chains. Longest chain 14 peptides. Score 0.395 Taking the results from Round 4 Chains 52, Residues 269, Estimated correctness of the model 0.0 % 5 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13719 restraints for refining 5923 atoms. 12614 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2223 (Rfree = 0.000) for 5923 atoms. Found 28 (28 requested) and removed 35 (14 requested) atoms. Cycle 32: After refmac, R = 0.2353 (Rfree = 0.000) for 5887 atoms. Found 28 (28 requested) and removed 33 (14 requested) atoms. Cycle 33: After refmac, R = 0.2227 (Rfree = 0.000) for 5865 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 34: After refmac, R = 0.1788 (Rfree = 0.000) for 5852 atoms. Found 13 (27 requested) and removed 15 (13 requested) atoms. Cycle 35: After refmac, R = 0.1624 (Rfree = 0.000) for 5844 atoms. Found 10 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 6006 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6028 seeds are put forward Round 1: 218 peptides, 45 chains. Longest chain 13 peptides. Score 0.253 Round 2: 282 peptides, 53 chains. Longest chain 10 peptides. Score 0.313 Round 3: 285 peptides, 52 chains. Longest chain 9 peptides. Score 0.327 Round 4: 277 peptides, 48 chains. Longest chain 16 peptides. Score 0.344 Round 5: 294 peptides, 48 chains. Longest chain 14 peptides. Score 0.376 Taking the results from Round 5 Chains 48, Residues 246, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14161 restraints for refining 5923 atoms. 13208 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2383 (Rfree = 0.000) for 5923 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. Cycle 37: After refmac, R = 0.2385 (Rfree = 0.000) for 5898 atoms. Found 28 (28 requested) and removed 35 (14 requested) atoms. Cycle 38: After refmac, R = 0.1842 (Rfree = 0.000) for 5874 atoms. Found 16 (27 requested) and removed 27 (13 requested) atoms. Cycle 39: After refmac, R = 0.1668 (Rfree = 0.000) for 5853 atoms. Found 14 (27 requested) and removed 17 (13 requested) atoms. Cycle 40: After refmac, R = 0.1664 (Rfree = 0.000) for 5845 atoms. Found 8 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 5986 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6000 seeds are put forward Round 1: 232 peptides, 48 chains. Longest chain 13 peptides. Score 0.256 Round 2: 290 peptides, 55 chains. Longest chain 15 peptides. Score 0.312 Round 3: 283 peptides, 52 chains. Longest chain 14 peptides. Score 0.323 Round 4: 303 peptides, 52 chains. Longest chain 14 peptides. Score 0.360 Round 5: 292 peptides, 47 chains. Longest chain 15 peptides. Score 0.380 Taking the results from Round 5 Chains 47, Residues 245, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14160 restraints for refining 5922 atoms. 13227 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2437 (Rfree = 0.000) for 5922 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 42: After refmac, R = 0.2497 (Rfree = 0.000) for 5900 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 43: After refmac, R = 0.2382 (Rfree = 0.000) for 5881 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 44: After refmac, R = 0.1991 (Rfree = 0.000) for 5873 atoms. Found 18 (27 requested) and removed 16 (13 requested) atoms. Cycle 45: After refmac, R = 0.1797 (Rfree = 0.000) for 5862 atoms. Found 14 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 5976 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6000 seeds are put forward Round 1: 217 peptides, 45 chains. Longest chain 8 peptides. Score 0.251 Round 2: 264 peptides, 51 chains. Longest chain 15 peptides. Score 0.294 Round 3: 292 peptides, 56 chains. Longest chain 15 peptides. Score 0.307 Round 4: 287 peptides, 53 chains. Longest chain 11 peptides. Score 0.322 Round 5: 295 peptides, 55 chains. Longest chain 14 peptides. Score 0.321 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 234, 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 1vme-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7991 reflections ( 99.75 % complete ) and 13982 restraints for refining 5888 atoms. 13099 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2319 (Rfree = 0.000) for 5888 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2408 (Rfree = 0.000) for 5847 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2365 (Rfree = 0.000) for 5809 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2412 (Rfree = 0.000) for 5782 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:40:31 GMT 2018 Job finished. TimeTaking 77.7 Used memory is bytes: 10678896