Mon 24 Dec 00:32:42 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 1vky-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-4.0-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/1vky-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-4.0-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 00:32:47 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/1vky-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-4.0-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 666 and 0 Target number of residues in the AU: 666 Target solvent content: 0.6264 Checking the provided sequence file Detected sequence length: 347 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 694 Adjusted target solvent content: 0.61 Input MTZ file: 1vky-4.0-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: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5552 target number of atoms Had to go as low as 0.80 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: 41.380 4.000 Wilson plot Bfac: 64.68 8439 reflections ( 99.70 % complete ) and 0 restraints for refining 6141 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3297 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3138 (Rfree = 0.000) for 6141 atoms. Found 29 (29 requested) and removed 69 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.02 Search for helices and strands: 0 residues in 0 chains, 6180 seeds are put forward NCS extension: 0 residues added, 6180 seeds are put forward Round 1: 292 peptides, 52 chains. Longest chain 14 peptides. Score 0.338 Round 2: 349 peptides, 50 chains. Longest chain 17 peptides. Score 0.452 Round 3: 379 peptides, 43 chains. Longest chain 21 peptides. Score 0.545 Round 4: 371 peptides, 48 chains. Longest chain 17 peptides. Score 0.500 Round 5: 374 peptides, 45 chains. Longest chain 29 peptides. Score 0.525 Taking the results from Round 3 Chains 44, Residues 336, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11662 restraints for refining 5013 atoms. 10338 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2589 (Rfree = 0.000) for 5013 atoms. Found 23 (23 requested) and removed 41 (11 requested) atoms. Cycle 2: After refmac, R = 0.2418 (Rfree = 0.000) for 4883 atoms. Found 23 (23 requested) and removed 43 (11 requested) atoms. Cycle 3: After refmac, R = 0.2202 (Rfree = 0.000) for 4810 atoms. Found 23 (23 requested) and removed 36 (11 requested) atoms. Cycle 4: After refmac, R = 0.1921 (Rfree = 0.000) for 4764 atoms. Found 12 (22 requested) and removed 35 (11 requested) atoms. Cycle 5: After refmac, R = 0.1870 (Rfree = 0.000) for 4731 atoms. Found 8 (22 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 4884 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4902 seeds are put forward Round 1: 326 peptides, 44 chains. Longest chain 23 peptides. Score 0.458 Round 2: 355 peptides, 44 chains. Longest chain 21 peptides. Score 0.503 Round 3: 345 peptides, 45 chains. Longest chain 21 peptides. Score 0.481 Round 4: 358 peptides, 38 chains. Longest chain 30 peptides. Score 0.549 Round 5: 366 peptides, 40 chains. Longest chain 24 peptides. Score 0.547 Taking the results from Round 4 Chains 44, Residues 320, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 10905 restraints for refining 5012 atoms. 9503 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2323 (Rfree = 0.000) for 5012 atoms. Found 23 (23 requested) and removed 58 (11 requested) atoms. Cycle 7: After refmac, R = 0.2147 (Rfree = 0.000) for 4898 atoms. Found 23 (23 requested) and removed 80 (11 requested) atoms. Cycle 8: After refmac, R = 0.2078 (Rfree = 0.000) for 4810 atoms. Found 23 (23 requested) and removed 62 (11 requested) atoms. Cycle 9: After refmac, R = 0.2104 (Rfree = 0.000) for 4734 atoms. Found 22 (22 requested) and removed 59 (11 requested) atoms. Cycle 10: After refmac, R = 0.2054 (Rfree = 0.000) for 4678 atoms. Found 22 (22 requested) and removed 47 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 2.90 Search for helices and strands: 0 residues in 0 chains, 4804 seeds are put forward NCS extension: 40 residues added (7 deleted due to clashes), 4844 seeds are put forward Round 1: 342 peptides, 55 chains. Longest chain 13 peptides. Score 0.403 Round 2: 377 peptides, 47 chains. Longest chain 24 peptides. Score 0.516 Round 3: 376 peptides, 46 chains. Longest chain 22 peptides. Score 0.521 Round 4: 361 peptides, 45 chains. Longest chain 33 peptides. Score 0.506 Round 5: 376 peptides, 42 chains. Longest chain 22 peptides. Score 0.548 Taking the results from Round 5 Chains 43, Residues 334, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11239 restraints for refining 5013 atoms. 9872 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2252 (Rfree = 0.000) for 5013 atoms. Found 23 (23 requested) and removed 55 (11 requested) atoms. Cycle 12: After refmac, R = 0.2142 (Rfree = 0.000) for 4931 atoms. Found 23 (23 requested) and removed 62 (11 requested) atoms. Cycle 13: After refmac, R = 0.2069 (Rfree = 0.000) for 4870 atoms. Found 20 (23 requested) and removed 39 (11 requested) atoms. Cycle 14: After refmac, R = 0.1973 (Rfree = 0.000) for 4831 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 15: After refmac, R = 0.1960 (Rfree = 0.000) for 4807 atoms. Found 22 (22 requested) and removed 41 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 4919 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 4946 seeds are put forward Round 1: 347 peptides, 53 chains. Longest chain 19 peptides. Score 0.426 Round 2: 354 peptides, 43 chains. Longest chain 20 peptides. Score 0.509 Round 3: 366 peptides, 41 chains. Longest chain 23 peptides. Score 0.540 Round 4: 352 peptides, 45 chains. Longest chain 19 peptides. Score 0.492 Round 5: 358 peptides, 43 chains. Longest chain 19 peptides. Score 0.515 Taking the results from Round 3 Chains 44, Residues 325, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11041 restraints for refining 5011 atoms. 9711 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2392 (Rfree = 0.000) for 5011 atoms. Found 23 (23 requested) and removed 49 (11 requested) atoms. Cycle 17: After refmac, R = 0.2390 (Rfree = 0.000) for 4936 atoms. Found 23 (23 requested) and removed 44 (11 requested) atoms. Cycle 18: After refmac, R = 0.2314 (Rfree = 0.000) for 4891 atoms. Found 23 (23 requested) and removed 42 (11 requested) atoms. Cycle 19: After refmac, R = 0.2196 (Rfree = 0.000) for 4841 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 20: After refmac, R = 0.2232 (Rfree = 0.000) for 4813 atoms. Found 22 (22 requested) and removed 33 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.01 Search for helices and strands: 0 residues in 0 chains, 4945 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 4970 seeds are put forward Round 1: 335 peptides, 55 chains. Longest chain 13 peptides. Score 0.391 Round 2: 354 peptides, 49 chains. Longest chain 18 peptides. Score 0.467 Round 3: 369 peptides, 51 chains. Longest chain 19 peptides. Score 0.476 Round 4: 371 peptides, 42 chains. Longest chain 28 peptides. Score 0.541 Round 5: 373 peptides, 50 chains. Longest chain 23 peptides. Score 0.489 Taking the results from Round 4 Chains 43, Residues 329, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11362 restraints for refining 5012 atoms. 10035 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2549 (Rfree = 0.000) for 5012 atoms. Found 23 (23 requested) and removed 43 (11 requested) atoms. Cycle 22: After refmac, R = 0.2461 (Rfree = 0.000) for 4943 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 23: After refmac, R = 0.2156 (Rfree = 0.000) for 4909 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 24: After refmac, R = 0.2211 (Rfree = 0.000) for 4889 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 25: After refmac, R = 0.2097 (Rfree = 0.000) for 4867 atoms. Found 23 (23 requested) and removed 41 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 2.94 Search for helices and strands: 0 residues in 0 chains, 4998 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5013 seeds are put forward Round 1: 313 peptides, 52 chains. Longest chain 15 peptides. Score 0.376 Round 2: 335 peptides, 47 chains. Longest chain 19 peptides. Score 0.451 Round 3: 341 peptides, 52 chains. Longest chain 17 peptides. Score 0.424 Round 4: 353 peptides, 50 chains. Longest chain 21 peptides. Score 0.458 Round 5: 348 peptides, 49 chains. Longest chain 17 peptides. Score 0.457 Taking the results from Round 4 Chains 51, Residues 303, Estimated correctness of the model 0.0 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 10952 restraints for refining 5011 atoms. 9573 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2469 (Rfree = 0.000) for 5011 atoms. Found 23 (23 requested) and removed 42 (11 requested) atoms. Cycle 27: After refmac, R = 0.2245 (Rfree = 0.000) for 4942 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 28: After refmac, R = 0.2157 (Rfree = 0.000) for 4903 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 29: After refmac, R = 0.2015 (Rfree = 0.000) for 4866 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 30: After refmac, R = 0.2053 (Rfree = 0.000) for 4847 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 2.97 Search for helices and strands: 0 residues in 0 chains, 4974 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 4989 seeds are put forward Round 1: 317 peptides, 57 chains. Longest chain 15 peptides. Score 0.344 Round 2: 353 peptides, 51 chains. Longest chain 19 peptides. Score 0.451 Round 3: 362 peptides, 50 chains. Longest chain 21 peptides. Score 0.472 Round 4: 361 peptides, 51 chains. Longest chain 18 peptides. Score 0.463 Round 5: 360 peptides, 50 chains. Longest chain 14 peptides. Score 0.469 Taking the results from Round 3 Chains 54, Residues 312, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11220 restraints for refining 5011 atoms. 9926 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2444 (Rfree = 0.000) for 5011 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 32: After refmac, R = 0.2353 (Rfree = 0.000) for 4950 atoms. Found 23 (23 requested) and removed 43 (11 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2180 (Rfree = 0.000) for 4884 atoms. Found 23 (23 requested) and removed 39 (11 requested) atoms. Cycle 34: After refmac, R = 0.2161 (Rfree = 0.000) for 4835 atoms. Found 23 (23 requested) and removed 45 (11 requested) atoms. Cycle 35: After refmac, R = 0.2068 (Rfree = 0.000) for 4794 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.02 Search for helices and strands: 0 residues in 0 chains, 4907 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4925 seeds are put forward Round 1: 309 peptides, 56 chains. Longest chain 11 peptides. Score 0.337 Round 2: 307 peptides, 47 chains. Longest chain 16 peptides. Score 0.404 Round 3: 326 peptides, 49 chains. Longest chain 23 peptides. Score 0.421 Round 4: 332 peptides, 49 chains. Longest chain 15 peptides. Score 0.431 Round 5: 341 peptides, 52 chains. Longest chain 19 peptides. Score 0.424 Taking the results from Round 4 Chains 49, Residues 283, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11370 restraints for refining 5013 atoms. 10202 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2404 (Rfree = 0.000) for 5013 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 37: After refmac, R = 0.2175 (Rfree = 0.000) for 4964 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 38: After refmac, R = 0.2093 (Rfree = 0.000) for 4947 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 39: After refmac, R = 0.2058 (Rfree = 0.000) for 4922 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 40: After refmac, R = 0.1757 (Rfree = 0.000) for 4902 atoms. Found 9 (23 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 5025 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5044 seeds are put forward Round 1: 302 peptides, 55 chains. Longest chain 12 peptides. Score 0.332 Round 2: 328 peptides, 53 chains. Longest chain 23 peptides. Score 0.394 Round 3: 338 peptides, 51 chains. Longest chain 13 peptides. Score 0.426 Round 4: 317 peptides, 47 chains. Longest chain 14 peptides. Score 0.421 Round 5: 331 peptides, 46 chains. Longest chain 18 peptides. Score 0.452 Taking the results from Round 5 Chains 46, Residues 285, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11498 restraints for refining 5013 atoms. 10382 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2282 (Rfree = 0.000) for 5013 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Cycle 42: After refmac, R = 0.2104 (Rfree = 0.000) for 4967 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 43: After refmac, R = 0.2255 (Rfree = 0.000) for 4942 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 44: After refmac, R = 0.2133 (Rfree = 0.000) for 4905 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 45: After refmac, R = 0.2199 (Rfree = 0.000) for 4882 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 5008 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 5019 seeds are put forward Round 1: 263 peptides, 52 chains. Longest chain 10 peptides. Score 0.283 Round 2: 309 peptides, 49 chains. Longest chain 16 peptides. Score 0.392 Round 3: 317 peptides, 53 chains. Longest chain 19 peptides. Score 0.375 Round 4: 328 peptides, 44 chains. Longest chain 18 peptides. Score 0.462 Round 5: 321 peptides, 48 chains. Longest chain 18 peptides. Score 0.420 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 284, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vky-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8439 reflections ( 99.70 % complete ) and 11300 restraints for refining 5013 atoms. 10168 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2289 (Rfree = 0.000) for 5013 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2154 (Rfree = 0.000) for 4966 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2192 (Rfree = 0.000) for 4937 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2054 (Rfree = 0.000) for 4912 atoms. TimeTaking 55.67