Mon 24 Dec 07:26:56 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 2afb-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2afb-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2afb-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-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/2afb-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-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 07:27:01 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/2afb-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-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 479 and 0 Target number of residues in the AU: 479 Target solvent content: 0.6465 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 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: 97.203 3.800 Wilson plot Bfac: 75.97 7461 reflections ( 99.35 % complete ) and 0 restraints for refining 6218 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3367 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3373 (Rfree = 0.000) for 6218 atoms. Found 34 (34 requested) and removed 47 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 6333 seeds are put forward NCS extension: 0 residues added, 6333 seeds are put forward Round 1: 220 peptides, 47 chains. Longest chain 8 peptides. Score 0.253 Round 2: 310 peptides, 57 chains. Longest chain 16 peptides. Score 0.368 Round 3: 340 peptides, 53 chains. Longest chain 13 peptides. Score 0.469 Round 4: 371 peptides, 52 chains. Longest chain 17 peptides. Score 0.536 Round 5: 376 peptides, 50 chains. Longest chain 18 peptides. Score 0.561 Taking the results from Round 5 Chains 53, Residues 326, Estimated correctness of the model 0.0 % 9 chains (62 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11329 restraints for refining 5078 atoms. 9909 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2715 (Rfree = 0.000) for 5078 atoms. Found 22 (27 requested) and removed 38 (13 requested) atoms. Cycle 2: After refmac, R = 0.2784 (Rfree = 0.000) for 4967 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 3: After refmac, R = 0.2300 (Rfree = 0.000) for 4897 atoms. Found 16 (27 requested) and removed 29 (13 requested) atoms. Cycle 4: After refmac, R = 0.2163 (Rfree = 0.000) for 4850 atoms. Found 10 (26 requested) and removed 22 (13 requested) atoms. Cycle 5: After refmac, R = 0.2128 (Rfree = 0.000) for 4817 atoms. Found 13 (26 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 4975 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4989 seeds are put forward Round 1: 324 peptides, 58 chains. Longest chain 15 peptides. Score 0.390 Round 2: 372 peptides, 53 chains. Longest chain 18 peptides. Score 0.530 Round 3: 375 peptides, 50 chains. Longest chain 28 peptides. Score 0.559 Round 4: 392 peptides, 51 chains. Longest chain 22 peptides. Score 0.581 Round 5: 389 peptides, 50 chains. Longest chain 22 peptides. Score 0.583 Taking the results from Round 5 Chains 54, Residues 339, Estimated correctness of the model 0.0 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11306 restraints for refining 5067 atoms. 9850 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2692 (Rfree = 0.000) for 5067 atoms. Found 27 (27 requested) and removed 50 (13 requested) atoms. Cycle 7: After refmac, R = 0.2506 (Rfree = 0.000) for 5003 atoms. Found 27 (27 requested) and removed 46 (13 requested) atoms. Cycle 8: After refmac, R = 0.2488 (Rfree = 0.000) for 4949 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 9: After refmac, R = 0.1894 (Rfree = 0.000) for 4895 atoms. Found 11 (27 requested) and removed 21 (13 requested) atoms. Cycle 10: After refmac, R = 0.1847 (Rfree = 0.000) for 4871 atoms. Found 15 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 5071 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5096 seeds are put forward Round 1: 336 peptides, 63 chains. Longest chain 11 peptides. Score 0.369 Round 2: 372 peptides, 57 chains. Longest chain 21 peptides. Score 0.497 Round 3: 360 peptides, 51 chains. Longest chain 16 peptides. Score 0.524 Round 4: 369 peptides, 51 chains. Longest chain 19 peptides. Score 0.541 Round 5: 362 peptides, 52 chains. Longest chain 21 peptides. Score 0.520 Taking the results from Round 4 Chains 51, Residues 318, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11812 restraints for refining 5079 atoms. 10577 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2744 (Rfree = 0.000) for 5079 atoms. Found 26 (27 requested) and removed 35 (13 requested) atoms. Cycle 12: After refmac, R = 0.2606 (Rfree = 0.000) for 5016 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 13: After refmac, R = 0.2418 (Rfree = 0.000) for 4973 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 14: After refmac, R = 0.2347 (Rfree = 0.000) for 4942 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 15: After refmac, R = 0.1814 (Rfree = 0.000) for 4917 atoms. Found 8 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 5090 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5112 seeds are put forward Round 1: 292 peptides, 61 chains. Longest chain 10 peptides. Score 0.287 Round 2: 321 peptides, 56 chains. Longest chain 16 peptides. Score 0.402 Round 3: 338 peptides, 53 chains. Longest chain 13 peptides. Score 0.465 Round 4: 356 peptides, 55 chains. Longest chain 16 peptides. Score 0.483 Round 5: 356 peptides, 57 chains. Longest chain 18 peptides. Score 0.466 Taking the results from Round 4 Chains 56, Residues 301, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11610 restraints for refining 5048 atoms. 10427 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2574 (Rfree = 0.000) for 5048 atoms. Found 27 (27 requested) and removed 49 (13 requested) atoms. Cycle 17: After refmac, R = 0.2380 (Rfree = 0.000) for 4995 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 18: After refmac, R = 0.1778 (Rfree = 0.000) for 4949 atoms. Found 12 (27 requested) and removed 21 (13 requested) atoms. Cycle 19: After refmac, R = 0.1689 (Rfree = 0.000) for 4918 atoms. Found 14 (27 requested) and removed 18 (13 requested) atoms. Cycle 20: After refmac, R = 0.1705 (Rfree = 0.000) for 4905 atoms. Found 7 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 5064 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 5089 seeds are put forward Round 1: 283 peptides, 52 chains. Longest chain 11 peptides. Score 0.355 Round 2: 331 peptides, 51 chains. Longest chain 16 peptides. Score 0.468 Round 3: 333 peptides, 52 chains. Longest chain 14 peptides. Score 0.463 Round 4: 339 peptides, 51 chains. Longest chain 14 peptides. Score 0.484 Round 5: 336 peptides, 52 chains. Longest chain 15 peptides. Score 0.469 Taking the results from Round 4 Chains 52, Residues 288, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11765 restraints for refining 5079 atoms. 10602 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2603 (Rfree = 0.000) for 5079 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 22: After refmac, R = 0.2467 (Rfree = 0.000) for 5038 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 23: After refmac, R = 0.2461 (Rfree = 0.000) for 5014 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 24: After refmac, R = 0.1859 (Rfree = 0.000) for 5002 atoms. Found 19 (27 requested) and removed 20 (13 requested) atoms. Cycle 25: After refmac, R = 0.1825 (Rfree = 0.000) for 4994 atoms. Found 17 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 5156 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5169 seeds are put forward Round 1: 269 peptides, 57 chains. Longest chain 10 peptides. Score 0.272 Round 2: 296 peptides, 53 chains. Longest chain 11 peptides. Score 0.375 Round 3: 307 peptides, 56 chains. Longest chain 13 peptides. Score 0.371 Round 4: 324 peptides, 51 chains. Longest chain 13 peptides. Score 0.454 Round 5: 327 peptides, 55 chains. Longest chain 17 peptides. Score 0.424 Taking the results from Round 4 Chains 51, Residues 273, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 12153 restraints for refining 5080 atoms. 11112 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2614 (Rfree = 0.000) for 5080 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 27: After refmac, R = 0.2458 (Rfree = 0.000) for 5043 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 28: After refmac, R = 0.2396 (Rfree = 0.000) for 5016 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 29: After refmac, R = 0.1789 (Rfree = 0.000) for 4986 atoms. Found 26 (27 requested) and removed 20 (13 requested) atoms. Cycle 30: After refmac, R = 0.1654 (Rfree = 0.000) for 4978 atoms. Found 11 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 5154 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5172 seeds are put forward Round 1: 265 peptides, 53 chains. Longest chain 11 peptides. Score 0.303 Round 2: 317 peptides, 54 chains. Longest chain 15 peptides. Score 0.412 Round 3: 330 peptides, 55 chains. Longest chain 17 peptides. Score 0.430 Round 4: 328 peptides, 53 chains. Longest chain 13 peptides. Score 0.444 Round 5: 309 peptides, 48 chains. Longest chain 12 peptides. Score 0.450 Taking the results from Round 5 Chains 48, Residues 261, Estimated correctness of the model 0.0 % 4 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 12012 restraints for refining 5080 atoms. 10978 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2867 (Rfree = 0.000) for 5080 atoms. Found 27 (27 requested) and removed 35 (13 requested) atoms. Cycle 32: After refmac, R = 0.2486 (Rfree = 0.000) for 5032 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 33: After refmac, R = 0.1869 (Rfree = 0.000) for 5012 atoms. Found 21 (27 requested) and removed 19 (13 requested) atoms. Cycle 34: After refmac, R = 0.2364 (Rfree = 0.000) for 4998 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 35: After refmac, R = 0.1662 (Rfree = 0.000) for 4986 atoms. Found 11 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 5175 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5187 seeds are put forward Round 1: 226 peptides, 47 chains. Longest chain 11 peptides. Score 0.269 Round 2: 295 peptides, 52 chains. Longest chain 13 peptides. Score 0.382 Round 3: 316 peptides, 56 chains. Longest chain 14 peptides. Score 0.391 Round 4: 302 peptides, 49 chains. Longest chain 13 peptides. Score 0.426 Round 5: 287 peptides, 50 chains. Longest chain 12 peptides. Score 0.384 Taking the results from Round 4 Chains 51, Residues 253, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11950 restraints for refining 5079 atoms. 10926 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2613 (Rfree = 0.000) for 5079 atoms. Found 27 (27 requested) and removed 133 (13 requested) atoms. Cycle 37: After refmac, R = 0.2436 (Rfree = 0.000) for 4943 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 38: After refmac, R = 0.1773 (Rfree = 0.000) for 4927 atoms. Found 21 (27 requested) and removed 18 (13 requested) atoms. Cycle 39: After refmac, R = 0.1641 (Rfree = 0.000) for 4916 atoms. Found 15 (27 requested) and removed 16 (13 requested) atoms. Cycle 40: After refmac, R = 0.1542 (Rfree = 0.000) for 4907 atoms. Found 11 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 5094 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5107 seeds are put forward Round 1: 268 peptides, 54 chains. Longest chain 10 peptides. Score 0.300 Round 2: 276 peptides, 49 chains. Longest chain 11 peptides. Score 0.369 Round 3: 293 peptides, 51 chains. Longest chain 12 peptides. Score 0.387 Round 4: 284 peptides, 50 chains. Longest chain 11 peptides. Score 0.377 Round 5: 279 peptides, 47 chains. Longest chain 11 peptides. Score 0.395 Taking the results from Round 5 Chains 47, Residues 232, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11913 restraints for refining 5078 atoms. 11008 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2681 (Rfree = 0.000) for 5078 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 42: After refmac, R = 0.2432 (Rfree = 0.000) for 5033 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 43: After refmac, R = 0.2447 (Rfree = 0.000) for 5010 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 44: After refmac, R = 0.1833 (Rfree = 0.000) for 4992 atoms. Found 25 (27 requested) and removed 19 (13 requested) atoms. Cycle 45: After refmac, R = 0.1719 (Rfree = 0.000) for 4984 atoms. Found 18 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 5165 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5177 seeds are put forward Round 1: 208 peptides, 43 chains. Longest chain 8 peptides. Score 0.266 Round 2: 241 peptides, 43 chains. Longest chain 12 peptides. Score 0.347 Round 3: 244 peptides, 45 chains. Longest chain 14 peptides. Score 0.334 Round 4: 258 peptides, 43 chains. Longest chain 15 peptides. Score 0.387 Round 5: 254 peptides, 44 chains. Longest chain 15 peptides. Score 0.368 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 215, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2afb-3_warpNtrace.pdb as input Building loops using Loopy2018 43 chains (215 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7461 reflections ( 99.35 % complete ) and 12016 restraints for refining 5079 atoms. 11168 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2687 (Rfree = 0.000) for 5079 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2530 (Rfree = 0.000) for 5035 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1778 (Rfree = 0.000) for 5000 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2329 (Rfree = 0.000) for 4964 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... TimeTaking 62.43