null Mon 24 Dec 00:38:12 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 1vme-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-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/1vme-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-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 ============================================================ Mon 24 Dec 00:38:17 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/1vme-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-3.8-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 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-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: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-3.8-parrot-mrncs.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 7264 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3261 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3122 (Rfree = 0.000) for 7264 atoms. Found 39 (39 requested) and removed 60 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 7386 seeds are put forward NCS extension: 0 residues added, 7386 seeds are put forward Round 1: 373 peptides, 65 chains. Longest chain 17 peptides. Score 0.384 Round 2: 432 peptides, 57 chains. Longest chain 21 peptides. Score 0.533 Round 3: 448 peptides, 65 chains. Longest chain 14 peptides. Score 0.504 Round 4: 487 peptides, 62 chains. Longest chain 20 peptides. Score 0.577 Round 5: 469 peptides, 58 chains. Longest chain 25 peptides. Score 0.578 Taking the results from Round 5 Chains 59, Residues 411, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13525 restraints for refining 5929 atoms. 11906 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2386 (Rfree = 0.000) for 5929 atoms. Found 19 (32 requested) and removed 39 (16 requested) atoms. Cycle 2: After refmac, R = 0.2359 (Rfree = 0.000) for 5821 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 3: After refmac, R = 0.2176 (Rfree = 0.000) for 5778 atoms. Found 17 (31 requested) and removed 37 (15 requested) atoms. Cycle 4: After refmac, R = 0.2132 (Rfree = 0.000) for 5740 atoms. Found 28 (31 requested) and removed 24 (15 requested) atoms. Cycle 5: After refmac, R = 0.2054 (Rfree = 0.000) for 5725 atoms. Found 30 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 5977 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6001 seeds are put forward Round 1: 445 peptides, 71 chains. Longest chain 23 peptides. Score 0.460 Round 2: 472 peptides, 64 chains. Longest chain 26 peptides. Score 0.545 Round 3: 486 peptides, 58 chains. Longest chain 34 peptides. Score 0.600 Round 4: 491 peptides, 63 chains. Longest chain 18 peptides. Score 0.577 Round 5: 522 peptides, 66 chains. Longest chain 23 peptides. Score 0.599 Taking the results from Round 3 Chains 61, Residues 428, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13000 restraints for refining 5929 atoms. 11235 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2167 (Rfree = 0.000) for 5929 atoms. Found 30 (32 requested) and removed 41 (16 requested) atoms. Cycle 7: After refmac, R = 0.2093 (Rfree = 0.000) for 5882 atoms. Found 21 (32 requested) and removed 41 (16 requested) atoms. Cycle 8: After refmac, R = 0.2058 (Rfree = 0.000) for 5848 atoms. Found 19 (32 requested) and removed 31 (16 requested) atoms. Cycle 9: After refmac, R = 0.2015 (Rfree = 0.000) for 5824 atoms. Found 22 (32 requested) and removed 28 (16 requested) atoms. Cycle 10: After refmac, R = 0.1913 (Rfree = 0.000) for 5809 atoms. Found 26 (31 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.56 Search for helices and strands: 0 residues in 0 chains, 5990 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6010 seeds are put forward Round 1: 402 peptides, 63 chains. Longest chain 16 peptides. Score 0.447 Round 2: 464 peptides, 65 chains. Longest chain 15 peptides. Score 0.527 Round 3: 473 peptides, 65 chains. Longest chain 20 peptides. Score 0.540 Round 4: 471 peptides, 64 chains. Longest chain 14 peptides. Score 0.544 Round 5: 481 peptides, 65 chains. Longest chain 19 peptides. Score 0.551 Taking the results from Round 5 Chains 66, Residues 416, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13499 restraints for refining 5932 atoms. 11866 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2238 (Rfree = 0.000) for 5932 atoms. Found 31 (32 requested) and removed 35 (16 requested) atoms. Cycle 12: After refmac, R = 0.2109 (Rfree = 0.000) for 5892 atoms. Found 27 (32 requested) and removed 32 (16 requested) atoms. Cycle 13: After refmac, R = 0.1804 (Rfree = 0.000) for 5860 atoms. Found 8 (32 requested) and removed 23 (16 requested) atoms. Cycle 14: After refmac, R = 0.1717 (Rfree = 0.000) for 5833 atoms. Found 8 (32 requested) and removed 16 (16 requested) atoms. Cycle 15: After refmac, R = 0.1671 (Rfree = 0.000) for 5819 atoms. Found 4 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 5998 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 6018 seeds are put forward Round 1: 401 peptides, 67 chains. Longest chain 14 peptides. Score 0.417 Round 2: 449 peptides, 62 chains. Longest chain 29 peptides. Score 0.525 Round 3: 450 peptides, 65 chains. Longest chain 20 peptides. Score 0.507 Round 4: 459 peptides, 67 chains. Longest chain 17 peptides. Score 0.507 Round 5: 457 peptides, 63 chains. Longest chain 24 peptides. Score 0.530 Taking the results from Round 5 Chains 65, Residues 394, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13383 restraints for refining 5932 atoms. 11805 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2317 (Rfree = 0.000) for 5932 atoms. Found 26 (32 requested) and removed 26 (16 requested) atoms. Cycle 17: After refmac, R = 0.2253 (Rfree = 0.000) for 5892 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 18: After refmac, R = 0.2109 (Rfree = 0.000) for 5870 atoms. Found 26 (32 requested) and removed 25 (16 requested) atoms. Cycle 19: After refmac, R = 0.2085 (Rfree = 0.000) for 5855 atoms. Found 32 (32 requested) and removed 25 (16 requested) atoms. Cycle 20: After refmac, R = 0.1686 (Rfree = 0.000) for 5849 atoms. Found 6 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.57 Search for helices and strands: 0 residues in 0 chains, 6030 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6048 seeds are put forward Round 1: 396 peptides, 72 chains. Longest chain 13 peptides. Score 0.372 Round 2: 434 peptides, 72 chains. Longest chain 13 peptides. Score 0.435 Round 3: 435 peptides, 60 chains. Longest chain 16 peptides. Score 0.518 Round 4: 441 peptides, 67 chains. Longest chain 14 peptides. Score 0.480 Round 5: 435 peptides, 66 chains. Longest chain 15 peptides. Score 0.478 Taking the results from Round 3 Chains 60, Residues 375, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13524 restraints for refining 5932 atoms. 12025 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2054 (Rfree = 0.000) for 5932 atoms. Found 18 (32 requested) and removed 31 (16 requested) atoms. Cycle 22: After refmac, R = 0.2162 (Rfree = 0.000) for 5880 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 23: After refmac, R = 0.2145 (Rfree = 0.000) for 5863 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 24: After refmac, R = 0.2134 (Rfree = 0.000) for 5853 atoms. Found 32 (32 requested) and removed 26 (16 requested) atoms. Cycle 25: After refmac, R = 0.2028 (Rfree = 0.000) for 5841 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 6049 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6065 seeds are put forward Round 1: 357 peptides, 69 chains. Longest chain 11 peptides. Score 0.325 Round 2: 397 peptides, 65 chains. Longest chain 14 peptides. Score 0.424 Round 3: 402 peptides, 68 chains. Longest chain 15 peptides. Score 0.411 Round 4: 402 peptides, 66 chains. Longest chain 19 peptides. Score 0.426 Round 5: 404 peptides, 62 chains. Longest chain 15 peptides. Score 0.457 Taking the results from Round 5 Chains 63, Residues 342, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13719 restraints for refining 5933 atoms. 12342 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2385 (Rfree = 0.000) for 5933 atoms. Found 31 (32 requested) and removed 38 (16 requested) atoms. Cycle 27: After refmac, R = 0.2238 (Rfree = 0.000) for 5885 atoms. Found 24 (32 requested) and removed 25 (16 requested) atoms. Cycle 28: After refmac, R = 0.2081 (Rfree = 0.000) for 5866 atoms. Found 12 (32 requested) and removed 27 (16 requested) atoms. Cycle 29: After refmac, R = 0.2074 (Rfree = 0.000) for 5837 atoms. Found 26 (32 requested) and removed 22 (16 requested) atoms. Cycle 30: After refmac, R = 0.2021 (Rfree = 0.000) for 5832 atoms. Found 27 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 6000 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 6011 seeds are put forward Round 1: 313 peptides, 61 chains. Longest chain 12 peptides. Score 0.307 Round 2: 356 peptides, 60 chains. Longest chain 18 peptides. Score 0.392 Round 3: 358 peptides, 59 chains. Longest chain 18 peptides. Score 0.403 Round 4: 384 peptides, 58 chains. Longest chain 19 peptides. Score 0.453 Round 5: 367 peptides, 58 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 4 Chains 58, Residues 326, Estimated correctness of the model 0.0 % 4 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13764 restraints for refining 5932 atoms. 12492 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2112 (Rfree = 0.000) for 5932 atoms. Found 22 (32 requested) and removed 28 (16 requested) atoms. Cycle 32: After refmac, R = 0.2116 (Rfree = 0.000) for 5891 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 33: After refmac, R = 0.1707 (Rfree = 0.000) for 5879 atoms. Found 6 (32 requested) and removed 21 (16 requested) atoms. Cycle 34: After refmac, R = 0.1607 (Rfree = 0.000) for 5857 atoms. Found 4 (32 requested) and removed 19 (16 requested) atoms. Cycle 35: After refmac, R = 0.1585 (Rfree = 0.000) for 5834 atoms. Found 7 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 5976 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 6003 seeds are put forward Round 1: 304 peptides, 60 chains. Longest chain 11 peptides. Score 0.298 Round 2: 356 peptides, 60 chains. Longest chain 18 peptides. Score 0.392 Round 3: 351 peptides, 53 chains. Longest chain 18 peptides. Score 0.436 Round 4: 362 peptides, 58 chains. Longest chain 16 peptides. Score 0.417 Round 5: 352 peptides, 56 chains. Longest chain 15 peptides. Score 0.415 Taking the results from Round 3 Chains 54, Residues 298, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 13807 restraints for refining 5933 atoms. 12620 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2044 (Rfree = 0.000) for 5933 atoms. Found 28 (32 requested) and removed 33 (16 requested) atoms. Cycle 37: After refmac, R = 0.2043 (Rfree = 0.000) for 5912 atoms. Found 31 (32 requested) and removed 28 (16 requested) atoms. Cycle 38: After refmac, R = 0.2034 (Rfree = 0.000) for 5901 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 39: After refmac, R = 0.1928 (Rfree = 0.000) for 5894 atoms. Found 30 (32 requested) and removed 26 (16 requested) atoms. Cycle 40: After refmac, R = 0.1522 (Rfree = 0.000) for 5889 atoms. Found 5 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 6061 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6076 seeds are put forward Round 1: 294 peptides, 63 chains. Longest chain 10 peptides. Score 0.254 Round 2: 315 peptides, 58 chains. Longest chain 13 peptides. Score 0.334 Round 3: 316 peptides, 58 chains. Longest chain 10 peptides. Score 0.336 Round 4: 327 peptides, 60 chains. Longest chain 10 peptides. Score 0.341 Round 5: 327 peptides, 53 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 5 Chains 53, Residues 274, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9324 reflections ( 99.79 % complete ) and 14079 restraints for refining 5933 atoms. 12997 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2206 (Rfree = 0.000) for 5933 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 42: After refmac, R = 0.2126 (Rfree = 0.000) for 5922 atoms. Found 31 (32 requested) and removed 29 (16 requested) atoms. Cycle 43: After refmac, R = 0.2039 (Rfree = 0.000) for 5905 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 44: After refmac, R = 0.1989 (Rfree = 0.000) for 5899 atoms. Found 27 (32 requested) and removed 23 (16 requested) atoms. Cycle 45: After refmac, R = 0.1578 (Rfree = 0.000) for 5889 atoms. Found 8 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 6051 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6067 seeds are put forward Round 1: 267 peptides, 58 chains. Longest chain 8 peptides. Score 0.241 Round 2: 314 peptides, 64 chains. Longest chain 10 peptides. Score 0.284 Round 3: 317 peptides, 57 chains. Longest chain 13 peptides. Score 0.346 Round 4: 316 peptides, 57 chains. Longest chain 13 peptides. Score 0.344 Round 5: 314 peptides, 54 chains. Longest chain 13 peptides. Score 0.364 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 260, Estimated correctness of the model 0.0 % 7 chains (27 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 54 chains (260 residues) following loop building 7 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9324 reflections ( 99.79 % complete ) and 13925 restraints for refining 5932 atoms. 12866 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2076 (Rfree = 0.000) for 5932 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2041 (Rfree = 0.000) for 5889 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2086 (Rfree = 0.000) for 5858 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1988 (Rfree = 0.000) for 5836 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:50:07 GMT 2018 Job finished. TimeTaking 71.91 Used memory is bytes: 7006040