Mon 24 Dec 07:45:06 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vll-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vll-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-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 07:45:10 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-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 405 and 0 Target number of residues in the AU: 405 Target solvent content: 0.6921 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-3.8-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-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 5344 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: 76.441 3.800 Wilson plot Bfac: 112.68 7455 reflections ( 99.96 % complete ) and 0 restraints for refining 5934 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3827 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3556 (Rfree = 0.000) for 5934 atoms. Found 32 (32 requested) and removed 98 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.97 4.02 Search for helices and strands: 0 residues in 0 chains, 5988 seeds are put forward NCS extension: 0 residues added, 5988 seeds are put forward Round 1: 184 peptides, 38 chains. Longest chain 11 peptides. Score 0.260 Round 2: 234 peptides, 47 chains. Longest chain 12 peptides. Score 0.292 Round 3: 245 peptides, 45 chains. Longest chain 12 peptides. Score 0.340 Round 4: 257 peptides, 46 chains. Longest chain 15 peptides. Score 0.359 Round 5: 269 peptides, 45 chains. Longest chain 16 peptides. Score 0.397 Taking the results from Round 5 Chains 47, Residues 224, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 12127 restraints for refining 4832 atoms. 11245 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2936 (Rfree = 0.000) for 4832 atoms. Found 18 (26 requested) and removed 41 (13 requested) atoms. Cycle 2: After refmac, R = 0.2841 (Rfree = 0.000) for 4731 atoms. Found 12 (26 requested) and removed 44 (13 requested) atoms. Cycle 3: After refmac, R = 0.2633 (Rfree = 0.000) for 4655 atoms. Found 18 (25 requested) and removed 27 (12 requested) atoms. Cycle 4: After refmac, R = 0.2600 (Rfree = 0.000) for 4607 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 5: After refmac, R = 0.2353 (Rfree = 0.000) for 4594 atoms. Found 13 (25 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.96 4.01 Search for helices and strands: 0 residues in 0 chains, 4784 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4796 seeds are put forward Round 1: 243 peptides, 48 chains. Longest chain 9 peptides. Score 0.304 Round 2: 286 peptides, 45 chains. Longest chain 14 peptides. Score 0.435 Round 3: 311 peptides, 45 chains. Longest chain 14 peptides. Score 0.488 Round 4: 310 peptides, 42 chains. Longest chain 17 peptides. Score 0.513 Round 5: 333 peptides, 49 chains. Longest chain 14 peptides. Score 0.496 Taking the results from Round 4 Chains 42, Residues 268, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 10913 restraints for refining 4592 atoms. 9883 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2593 (Rfree = 0.000) for 4592 atoms. Found 13 (25 requested) and removed 48 (12 requested) atoms. Cycle 7: After refmac, R = 0.2383 (Rfree = 0.000) for 4519 atoms. Found 17 (25 requested) and removed 22 (12 requested) atoms. Cycle 8: After refmac, R = 0.2412 (Rfree = 0.000) for 4488 atoms. Found 16 (24 requested) and removed 29 (12 requested) atoms. Cycle 9: After refmac, R = 0.2277 (Rfree = 0.000) for 4464 atoms. Found 13 (24 requested) and removed 21 (12 requested) atoms. Cycle 10: After refmac, R = 0.2223 (Rfree = 0.000) for 4444 atoms. Found 9 (24 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.93 3.98 Search for helices and strands: 0 residues in 0 chains, 4639 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4659 seeds are put forward Round 1: 236 peptides, 45 chains. Longest chain 9 peptides. Score 0.318 Round 2: 276 peptides, 42 chains. Longest chain 13 peptides. Score 0.442 Round 3: 293 peptides, 38 chains. Longest chain 17 peptides. Score 0.515 Round 4: 297 peptides, 38 chains. Longest chain 15 peptides. Score 0.523 Round 5: 305 peptides, 45 chains. Longest chain 16 peptides. Score 0.475 Taking the results from Round 4 Chains 38, Residues 259, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 10949 restraints for refining 4668 atoms. 9932 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2221 (Rfree = 0.000) for 4668 atoms. Found 8 (25 requested) and removed 46 (12 requested) atoms. Cycle 12: After refmac, R = 0.2072 (Rfree = 0.000) for 4606 atoms. Found 21 (25 requested) and removed 26 (12 requested) atoms. Cycle 13: After refmac, R = 0.2206 (Rfree = 0.000) for 4588 atoms. Found 20 (25 requested) and removed 28 (12 requested) atoms. Cycle 14: After refmac, R = 0.2079 (Rfree = 0.000) for 4572 atoms. Found 21 (25 requested) and removed 24 (12 requested) atoms. Cycle 15: After refmac, R = 0.1654 (Rfree = 0.000) for 4564 atoms. Found 4 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.96 4.01 Search for helices and strands: 0 residues in 0 chains, 4735 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 4754 seeds are put forward Round 1: 230 peptides, 44 chains. Longest chain 10 peptides. Score 0.314 Round 2: 282 peptides, 43 chains. Longest chain 14 peptides. Score 0.445 Round 3: 294 peptides, 43 chains. Longest chain 21 peptides. Score 0.471 Round 4: 293 peptides, 39 chains. Longest chain 25 peptides. Score 0.506 Round 5: 301 peptides, 44 chains. Longest chain 16 peptides. Score 0.476 Taking the results from Round 4 Chains 42, Residues 254, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 10909 restraints for refining 4832 atoms. 9805 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2467 (Rfree = 0.000) for 4832 atoms. Found 21 (26 requested) and removed 51 (13 requested) atoms. Cycle 17: After refmac, R = 0.2226 (Rfree = 0.000) for 4779 atoms. Found 15 (26 requested) and removed 34 (13 requested) atoms. Cycle 18: After refmac, R = 0.2211 (Rfree = 0.000) for 4742 atoms. Found 18 (26 requested) and removed 32 (13 requested) atoms. Cycle 19: After refmac, R = 0.2140 (Rfree = 0.000) for 4717 atoms. Found 15 (26 requested) and removed 20 (13 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2145 (Rfree = 0.000) for 4702 atoms. Found 16 (25 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.94 3.99 Search for helices and strands: 0 residues in 0 chains, 4877 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 4898 seeds are put forward Round 1: 249 peptides, 48 chains. Longest chain 12 peptides. Score 0.319 Round 2: 268 peptides, 38 chains. Longest chain 13 peptides. Score 0.463 Round 3: 272 peptides, 41 chains. Longest chain 13 peptides. Score 0.443 Round 4: 288 peptides, 34 chains. Longest chain 22 peptides. Score 0.541 Round 5: 267 peptides, 39 chains. Longest chain 15 peptides. Score 0.451 Taking the results from Round 4 Chains 37, Residues 254, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11084 restraints for refining 4832 atoms. 10002 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2351 (Rfree = 0.000) for 4832 atoms. Found 8 (26 requested) and removed 50 (13 requested) atoms. Cycle 22: After refmac, R = 0.2302 (Rfree = 0.000) for 4764 atoms. Found 6 (26 requested) and removed 27 (13 requested) atoms. Cycle 23: After refmac, R = 0.2232 (Rfree = 0.000) for 4727 atoms. Found 8 (26 requested) and removed 25 (13 requested) atoms. Cycle 24: After refmac, R = 0.2174 (Rfree = 0.000) for 4683 atoms. Found 8 (25 requested) and removed 22 (12 requested) atoms. Cycle 25: After refmac, R = 0.1741 (Rfree = 0.000) for 4645 atoms. Found 2 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.93 3.98 Search for helices and strands: 0 residues in 0 chains, 4774 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4792 seeds are put forward Round 1: 227 peptides, 44 chains. Longest chain 13 peptides. Score 0.306 Round 2: 281 peptides, 45 chains. Longest chain 15 peptides. Score 0.424 Round 3: 269 peptides, 39 chains. Longest chain 15 peptides. Score 0.456 Round 4: 248 peptides, 36 chains. Longest chain 15 peptides. Score 0.439 Round 5: 265 peptides, 40 chains. Longest chain 15 peptides. Score 0.437 Taking the results from Round 3 Chains 42, Residues 230, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11039 restraints for refining 4807 atoms. 10053 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2436 (Rfree = 0.000) for 4807 atoms. Found 24 (26 requested) and removed 38 (13 requested) atoms. Cycle 27: After refmac, R = 0.2404 (Rfree = 0.000) for 4762 atoms. Found 21 (26 requested) and removed 30 (13 requested) atoms. Cycle 28: After refmac, R = 0.2144 (Rfree = 0.000) for 4723 atoms. Found 12 (26 requested) and removed 22 (13 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2376 (Rfree = 0.000) for 4697 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. Cycle 30: After refmac, R = 0.2260 (Rfree = 0.000) for 4687 atoms. Found 8 (25 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.95 4.00 Search for helices and strands: 0 residues in 0 chains, 4854 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4867 seeds are put forward Round 1: 207 peptides, 44 chains. Longest chain 7 peptides. Score 0.254 Round 2: 254 peptides, 44 chains. Longest chain 19 peptides. Score 0.372 Round 3: 269 peptides, 45 chains. Longest chain 15 peptides. Score 0.397 Round 4: 266 peptides, 42 chains. Longest chain 12 peptides. Score 0.420 Round 5: 262 peptides, 42 chains. Longest chain 20 peptides. Score 0.411 Taking the results from Round 4 Chains 42, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 10894 restraints for refining 4675 atoms. 10040 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2543 (Rfree = 0.000) for 4675 atoms. Found 6 (25 requested) and removed 50 (12 requested) atoms. Cycle 32: After refmac, R = 0.2349 (Rfree = 0.000) for 4605 atoms. Found 9 (25 requested) and removed 26 (12 requested) atoms. Cycle 33: After refmac, R = 0.2363 (Rfree = 0.000) for 4575 atoms. Found 8 (25 requested) and removed 24 (12 requested) atoms. Cycle 34: After refmac, R = 0.1880 (Rfree = 0.000) for 4542 atoms. Found 2 (25 requested) and removed 15 (12 requested) atoms. Cycle 35: After refmac, R = 0.1976 (Rfree = 0.000) for 4519 atoms. Found 3 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.97 4.02 Search for helices and strands: 0 residues in 0 chains, 4653 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 4665 seeds are put forward Round 1: 202 peptides, 41 chains. Longest chain 8 peptides. Score 0.274 Round 2: 238 peptides, 39 chains. Longest chain 12 peptides. Score 0.386 Round 3: 240 peptides, 41 chains. Longest chain 10 peptides. Score 0.370 Round 4: 252 peptides, 40 chains. Longest chain 12 peptides. Score 0.408 Round 5: 252 peptides, 43 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 4 Chains 40, Residues 212, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 10704 restraints for refining 4672 atoms. 9850 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2398 (Rfree = 0.000) for 4672 atoms. Found 18 (25 requested) and removed 38 (12 requested) atoms. Cycle 37: After refmac, R = 0.2228 (Rfree = 0.000) for 4630 atoms. Found 13 (25 requested) and removed 24 (12 requested) atoms. Cycle 38: After refmac, R = 0.2271 (Rfree = 0.000) for 4603 atoms. Found 14 (25 requested) and removed 28 (12 requested) atoms. Cycle 39: After refmac, R = 0.2123 (Rfree = 0.000) for 4576 atoms. Found 6 (25 requested) and removed 24 (12 requested) atoms. Cycle 40: After refmac, R = 0.2193 (Rfree = 0.000) for 4544 atoms. Found 6 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.93 3.98 Search for helices and strands: 0 residues in 0 chains, 4686 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4699 seeds are put forward Round 1: 208 peptides, 42 chains. Longest chain 10 peptides. Score 0.279 Round 2: 214 peptides, 36 chains. Longest chain 13 peptides. Score 0.360 Round 3: 233 peptides, 41 chains. Longest chain 15 peptides. Score 0.353 Round 4: 233 peptides, 41 chains. Longest chain 16 peptides. Score 0.353 Round 5: 249 peptides, 40 chains. Longest chain 13 peptides. Score 0.401 Taking the results from Round 5 Chains 41, Residues 209, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 10858 restraints for refining 4719 atoms. 10003 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2383 (Rfree = 0.000) for 4719 atoms. Found 8 (25 requested) and removed 43 (12 requested) atoms. Cycle 42: After refmac, R = 0.2206 (Rfree = 0.000) for 4660 atoms. Found 7 (25 requested) and removed 22 (12 requested) atoms. Cycle 43: After refmac, R = 0.2230 (Rfree = 0.000) for 4631 atoms. Found 5 (25 requested) and removed 26 (12 requested) atoms. Cycle 44: After refmac, R = 0.2071 (Rfree = 0.000) for 4606 atoms. Found 5 (25 requested) and removed 20 (12 requested) atoms. Cycle 45: After refmac, R = 0.2142 (Rfree = 0.000) for 4585 atoms. Found 6 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.92 3.97 Search for helices and strands: 0 residues in 0 chains, 4719 seeds are put forward NCS extension: 0 residues added, 4719 seeds are put forward Round 1: 160 peptides, 36 chains. Longest chain 7 peptides. Score 0.216 Round 2: 214 peptides, 41 chains. Longest chain 10 peptides. Score 0.306 Round 3: 206 peptides, 40 chains. Longest chain 10 peptides. Score 0.296 Round 4: 234 peptides, 43 chains. Longest chain 11 peptides. Score 0.334 Round 5: 205 peptides, 37 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 191, 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 1vll-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7455 reflections ( 99.96 % complete ) and 11094 restraints for refining 4685 atoms. 10373 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2579 (Rfree = 0.000) for 4685 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2489 (Rfree = 0.000) for 4651 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2313 (Rfree = 0.000) for 4626 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2181 (Rfree = 0.000) for 4600 atoms. TimeTaking 48.8