Mon 24 Dec 07:35:25 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 1vll-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vll-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vll-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.6-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/1vll-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.6-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 07:35:30 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/1vll-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.6-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 416 and 0 Target number of residues in the AU: 416 Target solvent content: 0.6837 Checking the provided sequence file Detected sequence length: 334 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 668 Adjusted target solvent content: 0.49 Input MTZ file: 1vll-3.6-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: 19 Cell parameters: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 5344 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: 76.441 3.600 Wilson plot Bfac: 104.31 Failed to save intermediate PDB 8728 reflections ( 99.97 % complete ) and 0 restraints for refining 5890 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3730 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3277 (Rfree = 0.000) for 5890 atoms. Found 37 (37 requested) and removed 45 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.88 Search for helices and strands: 0 residues in 0 chains, 6013 seeds are put forward NCS extension: 0 residues added, 6013 seeds are put forward Round 1: 261 peptides, 50 chains. Longest chain 12 peptides. Score 0.327 Round 2: 299 peptides, 47 chains. Longest chain 21 peptides. Score 0.444 Round 3: 312 peptides, 50 chains. Longest chain 14 peptides. Score 0.444 Round 4: 330 peptides, 45 chains. Longest chain 20 peptides. Score 0.525 Round 5: 323 peptides, 48 chains. Longest chain 14 peptides. Score 0.485 Taking the results from Round 4 Chains 45, Residues 285, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11454 restraints for refining 4839 atoms. 10309 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2541 (Rfree = 0.000) for 4839 atoms. Found 15 (31 requested) and removed 33 (15 requested) atoms. Cycle 2: After refmac, R = 0.2458 (Rfree = 0.000) for 4750 atoms. Found 7 (30 requested) and removed 35 (15 requested) atoms. Cycle 3: After refmac, R = 0.2440 (Rfree = 0.000) for 4698 atoms. Found 9 (30 requested) and removed 33 (15 requested) atoms. Cycle 4: After refmac, R = 0.2377 (Rfree = 0.000) for 4654 atoms. Found 9 (29 requested) and removed 24 (14 requested) atoms. Cycle 5: After refmac, R = 0.2320 (Rfree = 0.000) for 4625 atoms. Found 9 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.85 Search for helices and strands: 0 residues in 0 chains, 4790 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 4818 seeds are put forward Round 1: 284 peptides, 49 chains. Longest chain 12 peptides. Score 0.392 Round 2: 313 peptides, 44 chains. Longest chain 20 peptides. Score 0.501 Round 3: 336 peptides, 48 chains. Longest chain 17 peptides. Score 0.511 Round 4: 317 peptides, 44 chains. Longest chain 26 peptides. Score 0.509 Round 5: 333 peptides, 44 chains. Longest chain 18 peptides. Score 0.540 Taking the results from Round 5 Chains 46, Residues 289, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11075 restraints for refining 4843 atoms. 9837 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2548 (Rfree = 0.000) for 4843 atoms. Found 9 (31 requested) and removed 51 (15 requested) atoms. Cycle 7: After refmac, R = 0.2383 (Rfree = 0.000) for 4781 atoms. Found 7 (30 requested) and removed 32 (15 requested) atoms. Cycle 8: After refmac, R = 0.2294 (Rfree = 0.000) for 4741 atoms. Found 3 (30 requested) and removed 35 (15 requested) atoms. Cycle 9: After refmac, R = 0.2289 (Rfree = 0.000) for 4700 atoms. Found 8 (30 requested) and removed 27 (15 requested) atoms. Cycle 10: After refmac, R = 0.2112 (Rfree = 0.000) for 4673 atoms. Found 5 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 4844 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 4850 seeds are put forward Round 1: 275 peptides, 49 chains. Longest chain 12 peptides. Score 0.371 Round 2: 319 peptides, 50 chains. Longest chain 22 peptides. Score 0.459 Round 3: 322 peptides, 49 chains. Longest chain 15 peptides. Score 0.474 Round 4: 313 peptides, 46 chains. Longest chain 17 peptides. Score 0.483 Round 5: 337 peptides, 50 chains. Longest chain 24 peptides. Score 0.496 Taking the results from Round 5 Chains 51, Residues 287, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11113 restraints for refining 4843 atoms. 9958 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2207 (Rfree = 0.000) for 4843 atoms. Found 4 (31 requested) and removed 34 (15 requested) atoms. Cycle 12: After refmac, R = 0.2065 (Rfree = 0.000) for 4791 atoms. Found 0 (30 requested) and removed 25 (15 requested) atoms. Cycle 13: After refmac, R = 0.2116 (Rfree = 0.000) for 4756 atoms. Found 1 (30 requested) and removed 27 (15 requested) atoms. Cycle 14: After refmac, R = 0.2141 (Rfree = 0.000) for 4725 atoms. Found 4 (30 requested) and removed 31 (15 requested) atoms. Cycle 15: After refmac, R = 0.2063 (Rfree = 0.000) for 4690 atoms. Found 2 (30 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 4818 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 4844 seeds are put forward Round 1: 261 peptides, 48 chains. Longest chain 14 peptides. Score 0.348 Round 2: 290 peptides, 40 chains. Longest chain 16 peptides. Score 0.490 Round 3: 301 peptides, 45 chains. Longest chain 17 peptides. Score 0.467 Round 4: 299 peptides, 42 chains. Longest chain 17 peptides. Score 0.491 Round 5: 308 peptides, 48 chains. Longest chain 14 peptides. Score 0.454 Taking the results from Round 4 Chains 44, Residues 257, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11399 restraints for refining 4843 atoms. 10360 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2246 (Rfree = 0.000) for 4843 atoms. Found 11 (31 requested) and removed 32 (15 requested) atoms. Cycle 17: After refmac, R = 0.2143 (Rfree = 0.000) for 4799 atoms. Found 1 (30 requested) and removed 24 (15 requested) atoms. Cycle 18: After refmac, R = 0.2097 (Rfree = 0.000) for 4767 atoms. Found 15 (30 requested) and removed 19 (15 requested) atoms. Cycle 19: After refmac, R = 0.2029 (Rfree = 0.000) for 4750 atoms. Found 2 (30 requested) and removed 23 (15 requested) atoms. Cycle 20: After refmac, R = 0.1993 (Rfree = 0.000) for 4723 atoms. Found 13 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 4894 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4908 seeds are put forward Round 1: 277 peptides, 50 chains. Longest chain 18 peptides. Score 0.365 Round 2: 297 peptides, 43 chains. Longest chain 22 peptides. Score 0.477 Round 3: 288 peptides, 41 chains. Longest chain 31 peptides. Score 0.477 Round 4: 312 peptides, 37 chains. Longest chain 31 peptides. Score 0.560 Round 5: 302 peptides, 43 chains. Longest chain 31 peptides. Score 0.488 Taking the results from Round 4 Chains 39, Residues 275, Estimated correctness of the model 0.0 % 6 chains (54 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 10655 restraints for refining 4844 atoms. 9396 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2298 (Rfree = 0.000) for 4844 atoms. Found 5 (31 requested) and removed 36 (15 requested) atoms. Cycle 22: After refmac, R = 0.2192 (Rfree = 0.000) for 4792 atoms. Found 2 (30 requested) and removed 28 (15 requested) atoms. Cycle 23: After refmac, R = 0.2136 (Rfree = 0.000) for 4757 atoms. Found 5 (30 requested) and removed 20 (15 requested) atoms. Cycle 24: After refmac, R = 0.2108 (Rfree = 0.000) for 4734 atoms. Found 4 (30 requested) and removed 19 (15 requested) atoms. Cycle 25: After refmac, R = 0.2037 (Rfree = 0.000) for 4710 atoms. Found 10 (30 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 4849 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 4876 seeds are put forward Round 1: 253 peptides, 46 chains. Longest chain 26 peptides. Score 0.349 Round 2: 272 peptides, 41 chains. Longest chain 24 peptides. Score 0.443 Round 3: 276 peptides, 42 chains. Longest chain 26 peptides. Score 0.442 Round 4: 272 peptides, 42 chains. Longest chain 28 peptides. Score 0.433 Round 5: 285 peptides, 41 chains. Longest chain 29 peptides. Score 0.471 Taking the results from Round 5 Chains 41, Residues 244, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11275 restraints for refining 4843 atoms. 10244 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2137 (Rfree = 0.000) for 4843 atoms. Found 20 (31 requested) and removed 30 (15 requested) atoms. Cycle 27: After refmac, R = 0.1972 (Rfree = 0.000) for 4819 atoms. Found 5 (31 requested) and removed 18 (15 requested) atoms. Cycle 28: After refmac, R = 0.2004 (Rfree = 0.000) for 4797 atoms. Found 9 (30 requested) and removed 18 (15 requested) atoms. Cycle 29: After refmac, R = 0.1976 (Rfree = 0.000) for 4782 atoms. Found 16 (30 requested) and removed 20 (15 requested) atoms. Cycle 30: After refmac, R = 0.1957 (Rfree = 0.000) for 4767 atoms. Found 7 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 4929 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 4964 seeds are put forward Round 1: 267 peptides, 54 chains. Longest chain 10 peptides. Score 0.300 Round 2: 283 peptides, 47 chains. Longest chain 21 peptides. Score 0.409 Round 3: 294 peptides, 47 chains. Longest chain 23 peptides. Score 0.433 Round 4: 295 peptides, 47 chains. Longest chain 23 peptides. Score 0.435 Round 5: 277 peptides, 45 chains. Longest chain 14 peptides. Score 0.415 Taking the results from Round 4 Chains 48, Residues 248, Estimated correctness of the model 0.0 % 6 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11152 restraints for refining 4844 atoms. 10015 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2174 (Rfree = 0.000) for 4844 atoms. Found 9 (31 requested) and removed 30 (15 requested) atoms. Cycle 32: After refmac, R = 0.2090 (Rfree = 0.000) for 4807 atoms. Found 6 (30 requested) and removed 19 (15 requested) atoms. Cycle 33: After refmac, R = 0.2084 (Rfree = 0.000) for 4785 atoms. Found 6 (30 requested) and removed 26 (15 requested) atoms. Cycle 34: After refmac, R = 0.2081 (Rfree = 0.000) for 4756 atoms. Found 8 (30 requested) and removed 21 (15 requested) atoms. Cycle 35: After refmac, R = 0.2061 (Rfree = 0.000) for 4740 atoms. Found 2 (30 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 3.82 Search for helices and strands: 0 residues in 0 chains, 4857 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4869 seeds are put forward Round 1: 230 peptides, 48 chains. Longest chain 10 peptides. Score 0.270 Round 2: 272 peptides, 46 chains. Longest chain 11 peptides. Score 0.394 Round 3: 269 peptides, 45 chains. Longest chain 13 peptides. Score 0.397 Round 4: 261 peptides, 41 chains. Longest chain 18 peptides. Score 0.419 Round 5: 270 peptides, 40 chains. Longest chain 20 peptides. Score 0.448 Taking the results from Round 5 Chains 43, Residues 230, Estimated correctness of the model 0.0 % 7 chains (56 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11103 restraints for refining 4843 atoms. 10058 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2243 (Rfree = 0.000) for 4843 atoms. Found 13 (31 requested) and removed 33 (15 requested) atoms. Cycle 37: After refmac, R = 0.2142 (Rfree = 0.000) for 4810 atoms. Found 16 (30 requested) and removed 26 (15 requested) atoms. Cycle 38: After refmac, R = 0.2078 (Rfree = 0.000) for 4793 atoms. Found 11 (30 requested) and removed 21 (15 requested) atoms. Cycle 39: After refmac, R = 0.2145 (Rfree = 0.000) for 4777 atoms. Found 21 (30 requested) and removed 20 (15 requested) atoms. Cycle 40: After refmac, R = 0.2014 (Rfree = 0.000) for 4767 atoms. Found 10 (30 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 4931 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 4959 seeds are put forward Round 1: 214 peptides, 45 chains. Longest chain 12 peptides. Score 0.261 Round 2: 246 peptides, 43 chains. Longest chain 16 peptides. Score 0.363 Round 3: 263 peptides, 47 chains. Longest chain 16 peptides. Score 0.363 Round 4: 260 peptides, 42 chains. Longest chain 14 peptides. Score 0.406 Round 5: 262 peptides, 42 chains. Longest chain 19 peptides. Score 0.411 Taking the results from Round 5 Chains 43, Residues 220, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11431 restraints for refining 4844 atoms. 10539 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2194 (Rfree = 0.000) for 4844 atoms. Found 11 (31 requested) and removed 24 (15 requested) atoms. Cycle 42: After refmac, R = 0.2109 (Rfree = 0.000) for 4814 atoms. Found 12 (30 requested) and removed 22 (15 requested) atoms. Cycle 43: After refmac, R = 0.2063 (Rfree = 0.000) for 4791 atoms. Found 10 (30 requested) and removed 19 (15 requested) atoms. Cycle 44: After refmac, R = 0.2016 (Rfree = 0.000) for 4777 atoms. Found 11 (30 requested) and removed 18 (15 requested) atoms. Cycle 45: After refmac, R = 0.2009 (Rfree = 0.000) for 4767 atoms. Found 13 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 4883 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4903 seeds are put forward Round 1: 190 peptides, 41 chains. Longest chain 7 peptides. Score 0.242 Round 2: 244 peptides, 45 chains. Longest chain 13 peptides. Score 0.338 Round 3: 247 peptides, 45 chains. Longest chain 22 peptides. Score 0.345 Round 4: 246 peptides, 44 chains. Longest chain 13 peptides. Score 0.353 Round 5: 248 peptides, 41 chains. Longest chain 17 peptides. Score 0.389 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 207, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input Building loops using Loopy2018 42 chains (207 residues) following loop building 4 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8728 reflections ( 99.97 % complete ) and 11356 restraints for refining 4842 atoms. 10481 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2074 (Rfree = 0.000) for 4842 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.1938 (Rfree = 0.000) for 4821 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1974 (Rfree = 0.000) for 4798 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1929 (Rfree = 0.000) for 4779 atoms. TimeTaking 53.57