Mon 24 Dec 08:06:40 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 1vme-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vme-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vme-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-4.0-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/1vme-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-4.0-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 08:06:45 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/1vme-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-4.0-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 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-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: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-4.0-parrot-noncs.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 4.000 Wilson plot Bfac: 91.38 7991 reflections ( 99.75 % complete ) and 0 restraints for refining 7265 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3377 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3078 (Rfree = 0.000) for 7265 atoms. Found 34 (34 requested) and removed 357 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 3.67 Search for helices and strands: 0 residues in 0 chains, 7012 seeds are put forward NCS extension: 0 residues added, 7012 seeds are put forward Round 1: 241 peptides, 51 chains. Longest chain 10 peptides. Score 0.248 Round 2: 342 peptides, 64 chains. Longest chain 12 peptides. Score 0.337 Round 3: 377 peptides, 65 chains. Longest chain 12 peptides. Score 0.391 Round 4: 385 peptides, 67 chains. Longest chain 14 peptides. Score 0.390 Round 5: 387 peptides, 63 chains. Longest chain 13 peptides. Score 0.422 Taking the results from Round 5 Chains 63, Residues 324, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14197 restraints for refining 5923 atoms. 12910 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2867 (Rfree = 0.000) for 5923 atoms. Found 28 (28 requested) and removed 94 (14 requested) atoms. Cycle 2: After refmac, R = 0.2534 (Rfree = 0.000) for 5772 atoms. Found 27 (27 requested) and removed 58 (13 requested) atoms. Cycle 3: After refmac, R = 0.2082 (Rfree = 0.000) for 5694 atoms. Found 6 (27 requested) and removed 38 (13 requested) atoms. Cycle 4: After refmac, R = 0.2291 (Rfree = 0.000) for 5635 atoms. Found 26 (26 requested) and removed 35 (13 requested) atoms. Cycle 5: After refmac, R = 0.1921 (Rfree = 0.000) for 5610 atoms. Found 3 (26 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.67 Search for helices and strands: 0 residues in 0 chains, 5795 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 5807 seeds are put forward Round 1: 353 peptides, 67 chains. Longest chain 10 peptides. Score 0.333 Round 2: 391 peptides, 65 chains. Longest chain 13 peptides. Score 0.415 Round 3: 411 peptides, 61 chains. Longest chain 20 peptides. Score 0.475 Round 4: 416 peptides, 63 chains. Longest chain 12 peptides. Score 0.469 Round 5: 411 peptides, 60 chains. Longest chain 14 peptides. Score 0.482 Taking the results from Round 5 Chains 60, Residues 351, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13961 restraints for refining 5921 atoms. 12617 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2593 (Rfree = 0.000) for 5921 atoms. Found 21 (28 requested) and removed 54 (14 requested) atoms. Cycle 7: After refmac, R = 0.2335 (Rfree = 0.000) for 5824 atoms. Found 22 (27 requested) and removed 42 (13 requested) atoms. Cycle 8: After refmac, R = 0.2362 (Rfree = 0.000) for 5775 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 9: After refmac, R = 0.2077 (Rfree = 0.000) for 5751 atoms. Found 2 (27 requested) and removed 30 (13 requested) atoms. Cycle 10: After refmac, R = 0.2198 (Rfree = 0.000) for 5715 atoms. Found 11 (27 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 3.69 Search for helices and strands: 0 residues in 0 chains, 5882 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5896 seeds are put forward Round 1: 348 peptides, 68 chains. Longest chain 10 peptides. Score 0.317 Round 2: 390 peptides, 62 chains. Longest chain 14 peptides. Score 0.435 Round 3: 377 peptides, 61 chains. Longest chain 12 peptides. Score 0.420 Round 4: 385 peptides, 57 chains. Longest chain 17 peptides. Score 0.462 Round 5: 382 peptides, 55 chains. Longest chain 19 peptides. Score 0.471 Taking the results from Round 5 Chains 55, Residues 327, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14137 restraints for refining 5923 atoms. 12878 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2524 (Rfree = 0.000) for 5923 atoms. Found 17 (28 requested) and removed 39 (14 requested) atoms. Cycle 12: After refmac, R = 0.2415 (Rfree = 0.000) for 5858 atoms. Found 25 (28 requested) and removed 39 (14 requested) atoms. Cycle 13: After refmac, R = 0.2280 (Rfree = 0.000) for 5812 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 14: After refmac, R = 0.1897 (Rfree = 0.000) for 5776 atoms. Found 6 (27 requested) and removed 23 (13 requested) atoms. Cycle 15: After refmac, R = 0.1782 (Rfree = 0.000) for 5742 atoms. Found 4 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 3.67 Search for helices and strands: 0 residues in 0 chains, 5903 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5924 seeds are put forward Round 1: 335 peptides, 64 chains. Longest chain 12 peptides. Score 0.324 Round 2: 382 peptides, 63 chains. Longest chain 17 peptides. Score 0.414 Round 3: 384 peptides, 61 chains. Longest chain 16 peptides. Score 0.432 Round 4: 408 peptides, 63 chains. Longest chain 19 peptides. Score 0.456 Round 5: 397 peptides, 61 chains. Longest chain 15 peptides. Score 0.453 Taking the results from Round 4 Chains 63, Residues 345, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13674 restraints for refining 5923 atoms. 12340 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2358 (Rfree = 0.000) for 5923 atoms. Found 17 (28 requested) and removed 60 (14 requested) atoms. Cycle 17: After refmac, R = 0.2278 (Rfree = 0.000) for 5839 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 18: After refmac, R = 0.1819 (Rfree = 0.000) for 5806 atoms. Found 9 (27 requested) and removed 31 (13 requested) atoms. Cycle 19: After refmac, R = 0.1701 (Rfree = 0.000) for 5769 atoms. Found 1 (27 requested) and removed 24 (13 requested) atoms. Cycle 20: After refmac, R = 0.1701 (Rfree = 0.000) for 5740 atoms. Found 4 (27 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 5882 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5904 seeds are put forward Round 1: 331 peptides, 69 chains. Longest chain 9 peptides. Score 0.277 Round 2: 349 peptides, 63 chains. Longest chain 13 peptides. Score 0.357 Round 3: 359 peptides, 62 chains. Longest chain 12 peptides. Score 0.382 Round 4: 353 peptides, 60 chains. Longest chain 12 peptides. Score 0.387 Round 5: 369 peptides, 60 chains. Longest chain 13 peptides. Score 0.414 Taking the results from Round 5 Chains 60, Residues 309, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14032 restraints for refining 5924 atoms. 12817 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2373 (Rfree = 0.000) for 5924 atoms. Found 28 (28 requested) and removed 42 (14 requested) atoms. Cycle 22: After refmac, R = 0.2424 (Rfree = 0.000) for 5871 atoms. Found 28 (28 requested) and removed 53 (14 requested) atoms. Cycle 23: After refmac, R = 0.2246 (Rfree = 0.000) for 5823 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 24: After refmac, R = 0.2195 (Rfree = 0.000) for 5796 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 25: After refmac, R = 0.2079 (Rfree = 0.000) for 5782 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 5965 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5982 seeds are put forward Round 1: 307 peptides, 66 chains. Longest chain 8 peptides. Score 0.255 Round 2: 328 peptides, 59 chains. Longest chain 10 peptides. Score 0.350 Round 3: 342 peptides, 59 chains. Longest chain 11 peptides. Score 0.375 Round 4: 349 peptides, 59 chains. Longest chain 13 peptides. Score 0.387 Round 5: 353 peptides, 54 chains. Longest chain 12 peptides. Score 0.432 Taking the results from Round 5 Chains 54, Residues 299, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14283 restraints for refining 5923 atoms. 13113 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2208 (Rfree = 0.000) for 5923 atoms. Found 28 (28 requested) and removed 38 (14 requested) atoms. Cycle 27: After refmac, R = 0.2131 (Rfree = 0.000) for 5878 atoms. Found 28 (28 requested) and removed 31 (14 requested) atoms. Cycle 28: After refmac, R = 0.1723 (Rfree = 0.000) for 5853 atoms. Found 6 (27 requested) and removed 28 (13 requested) atoms. Cycle 29: After refmac, R = 0.1649 (Rfree = 0.000) for 5820 atoms. Found 8 (27 requested) and removed 17 (13 requested) atoms. Cycle 30: After refmac, R = 0.1608 (Rfree = 0.000) for 5803 atoms. Found 8 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 5949 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5963 seeds are put forward Round 1: 315 peptides, 67 chains. Longest chain 10 peptides. Score 0.262 Round 2: 369 peptides, 70 chains. Longest chain 12 peptides. Score 0.339 Round 3: 355 peptides, 62 chains. Longest chain 14 peptides. Score 0.375 Round 4: 359 peptides, 62 chains. Longest chain 10 peptides. Score 0.382 Round 5: 351 peptides, 58 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 5 Chains 58, Residues 293, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14309 restraints for refining 5923 atoms. 13195 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2217 (Rfree = 0.000) for 5923 atoms. Found 25 (28 requested) and removed 32 (14 requested) atoms. Cycle 32: After refmac, R = 0.2253 (Rfree = 0.000) for 5880 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 33: After refmac, R = 0.2218 (Rfree = 0.000) for 5864 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 34: After refmac, R = 0.2233 (Rfree = 0.000) for 5840 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 35: After refmac, R = 0.2300 (Rfree = 0.000) for 5830 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 5992 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6004 seeds are put forward Round 1: 257 peptides, 57 chains. Longest chain 8 peptides. Score 0.229 Round 2: 302 peptides, 57 chains. Longest chain 10 peptides. Score 0.318 Round 3: 316 peptides, 57 chains. Longest chain 12 peptides. Score 0.344 Round 4: 296 peptides, 52 chains. Longest chain 12 peptides. Score 0.347 Round 5: 312 peptides, 54 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 5 Chains 54, Residues 258, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14096 restraints for refining 5924 atoms. 13095 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2266 (Rfree = 0.000) for 5924 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 37: After refmac, R = 0.2392 (Rfree = 0.000) for 5890 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 38: After refmac, R = 0.2338 (Rfree = 0.000) for 5865 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 39: After refmac, R = 0.1807 (Rfree = 0.000) for 5842 atoms. Found 9 (27 requested) and removed 25 (13 requested) atoms. Cycle 40: After refmac, R = 0.1653 (Rfree = 0.000) for 5821 atoms. Found 7 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 5950 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 5960 seeds are put forward Round 1: 260 peptides, 58 chains. Longest chain 10 peptides. Score 0.227 Round 2: 308 peptides, 57 chains. Longest chain 10 peptides. Score 0.329 Round 3: 312 peptides, 59 chains. Longest chain 10 peptides. Score 0.321 Round 4: 322 peptides, 57 chains. Longest chain 11 peptides. Score 0.355 Round 5: 321 peptides, 58 chains. Longest chain 14 peptides. Score 0.345 Taking the results from Round 4 Chains 57, Residues 265, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14163 restraints for refining 5923 atoms. 13153 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2253 (Rfree = 0.000) for 5923 atoms. Found 28 (28 requested) and removed 37 (14 requested) atoms. Cycle 42: After refmac, R = 0.2120 (Rfree = 0.000) for 5894 atoms. Found 28 (28 requested) and removed 33 (14 requested) atoms. Cycle 43: After refmac, R = 0.2176 (Rfree = 0.000) for 5879 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 44: After refmac, R = 0.1629 (Rfree = 0.000) for 5871 atoms. Found 11 (27 requested) and removed 17 (13 requested) atoms. Cycle 45: After refmac, R = 0.1507 (Rfree = 0.000) for 5854 atoms. Found 6 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 5972 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5986 seeds are put forward Round 1: 226 peptides, 52 chains. Longest chain 7 peptides. Score 0.207 Round 2: 238 peptides, 50 chains. Longest chain 8 peptides. Score 0.250 Round 3: 228 peptides, 44 chains. Longest chain 10 peptides. Score 0.283 Round 4: 243 peptides, 44 chains. Longest chain 11 peptides. Score 0.313 Round 5: 241 peptides, 43 chains. Longest chain 11 peptides. Score 0.318 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 198, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vme-4_warpNtrace.pdb as input Building loops using Loopy2018 43 chains (198 residues) following loop building 3 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7991 reflections ( 99.75 % complete ) and 14500 restraints for refining 5924 atoms. 13729 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2395 (Rfree = 0.000) for 5924 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2352 (Rfree = 0.000) for 5892 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1897 (Rfree = 0.000) for 5859 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1718 (Rfree = 0.000) for 5832 atoms. TimeTaking 63.32