Mon 24 Dec 07:57:14 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2afb-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2afb-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-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/2afb-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-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 07:57:18 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-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 497 and 0 Target number of residues in the AU: 497 Target solvent content: 0.6332 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-3.6-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 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: 97.203 3.600 Wilson plot Bfac: 68.03 Failed to save intermediate PDB 8743 reflections ( 99.44 % complete ) and 0 restraints for refining 6222 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3233 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3105 (Rfree = 0.000) for 6222 atoms. Found 39 (39 requested) and removed 54 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 6337 seeds are put forward NCS extension: 0 residues added, 6337 seeds are put forward Round 1: 270 peptides, 52 chains. Longest chain 10 peptides. Score 0.325 Round 2: 340 peptides, 54 chains. Longest chain 13 peptides. Score 0.460 Round 3: 367 peptides, 52 chains. Longest chain 21 peptides. Score 0.529 Round 4: 381 peptides, 48 chains. Longest chain 22 peptides. Score 0.585 Round 5: 401 peptides, 53 chains. Longest chain 21 peptides. Score 0.581 Taking the results from Round 4 Chains 51, Residues 333, Estimated correctness of the model 8.7 % 6 chains (41 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11432 restraints for refining 5090 atoms. 10024 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2627 (Rfree = 0.000) for 5090 atoms. Found 28 (32 requested) and removed 42 (16 requested) atoms. Cycle 2: After refmac, R = 0.2447 (Rfree = 0.000) for 4984 atoms. Found 19 (32 requested) and removed 21 (16 requested) atoms. Cycle 3: After refmac, R = 0.2400 (Rfree = 0.000) for 4938 atoms. Found 19 (31 requested) and removed 34 (15 requested) atoms. Cycle 4: After refmac, R = 0.2253 (Rfree = 0.000) for 4908 atoms. Found 20 (31 requested) and removed 21 (15 requested) atoms. Cycle 5: After refmac, R = 0.2228 (Rfree = 0.000) for 4891 atoms. Found 13 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 5079 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5093 seeds are put forward Round 1: 325 peptides, 58 chains. Longest chain 13 peptides. Score 0.392 Round 2: 386 peptides, 57 chains. Longest chain 16 peptides. Score 0.523 Round 3: 387 peptides, 57 chains. Longest chain 16 peptides. Score 0.525 Round 4: 402 peptides, 52 chains. Longest chain 26 peptides. Score 0.590 Round 5: 415 peptides, 52 chains. Longest chain 22 peptides. Score 0.611 Taking the results from Round 5 Chains 55, Residues 363, Estimated correctness of the model 18.9 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 10941 restraints for refining 5090 atoms. 9362 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2509 (Rfree = 0.000) for 5090 atoms. Found 29 (32 requested) and removed 49 (16 requested) atoms. Cycle 7: After refmac, R = 0.2200 (Rfree = 0.000) for 5017 atoms. Found 16 (32 requested) and removed 32 (16 requested) atoms. Cycle 8: After refmac, R = 0.2064 (Rfree = 0.000) for 4982 atoms. Found 10 (32 requested) and removed 20 (16 requested) atoms. Cycle 9: After refmac, R = 0.2140 (Rfree = 0.000) for 4961 atoms. Found 10 (31 requested) and removed 21 (15 requested) atoms. Cycle 10: After refmac, R = 0.2076 (Rfree = 0.000) for 4941 atoms. Found 10 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 5125 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5144 seeds are put forward Round 1: 330 peptides, 56 chains. Longest chain 12 peptides. Score 0.421 Round 2: 377 peptides, 52 chains. Longest chain 15 peptides. Score 0.547 Round 3: 388 peptides, 54 chains. Longest chain 18 peptides. Score 0.551 Round 4: 381 peptides, 52 chains. Longest chain 17 peptides. Score 0.554 Round 5: 365 peptides, 54 chains. Longest chain 16 peptides. Score 0.509 Taking the results from Round 4 Chains 54, Residues 329, Estimated correctness of the model 0.0 % 5 chains (44 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11349 restraints for refining 5091 atoms. 9913 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2371 (Rfree = 0.000) for 5091 atoms. Found 25 (32 requested) and removed 32 (16 requested) atoms. Cycle 12: After refmac, R = 0.2140 (Rfree = 0.000) for 5048 atoms. Found 17 (32 requested) and removed 26 (16 requested) atoms. Cycle 13: After refmac, R = 0.1847 (Rfree = 0.000) for 5021 atoms. Found 7 (32 requested) and removed 21 (16 requested) atoms. Cycle 14: After refmac, R = 0.1977 (Rfree = 0.000) for 5001 atoms. Found 20 (32 requested) and removed 19 (16 requested) atoms. Cycle 15: After refmac, R = 0.2013 (Rfree = 0.000) for 4997 atoms. Found 18 (32 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 5188 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5204 seeds are put forward Round 1: 290 peptides, 50 chains. Longest chain 13 peptides. Score 0.390 Round 2: 361 peptides, 52 chains. Longest chain 15 peptides. Score 0.518 Round 3: 367 peptides, 52 chains. Longest chain 21 peptides. Score 0.529 Round 4: 359 peptides, 49 chains. Longest chain 23 peptides. Score 0.539 Round 5: 374 peptides, 53 chains. Longest chain 17 peptides. Score 0.534 Taking the results from Round 4 Chains 50, Residues 310, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11750 restraints for refining 5090 atoms. 10513 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2301 (Rfree = 0.000) for 5090 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 17: After refmac, R = 0.2121 (Rfree = 0.000) for 5064 atoms. Found 26 (32 requested) and removed 21 (16 requested) atoms. Cycle 18: After refmac, R = 0.2058 (Rfree = 0.000) for 5050 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 19: After refmac, R = 0.1676 (Rfree = 0.000) for 5047 atoms. Found 10 (32 requested) and removed 20 (16 requested) atoms. Cycle 20: After refmac, R = 0.1622 (Rfree = 0.000) for 5025 atoms. Found 6 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 5218 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 5244 seeds are put forward Round 1: 276 peptides, 53 chains. Longest chain 11 peptides. Score 0.329 Round 2: 338 peptides, 55 chains. Longest chain 16 peptides. Score 0.447 Round 3: 346 peptides, 56 chains. Longest chain 18 peptides. Score 0.454 Round 4: 364 peptides, 51 chains. Longest chain 20 peptides. Score 0.532 Round 5: 354 peptides, 49 chains. Longest chain 20 peptides. Score 0.530 Taking the results from Round 4 Chains 55, Residues 313, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11520 restraints for refining 5091 atoms. 10232 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2231 (Rfree = 0.000) for 5091 atoms. Found 28 (32 requested) and removed 26 (16 requested) atoms. Cycle 22: After refmac, R = 0.2036 (Rfree = 0.000) for 5071 atoms. Found 15 (32 requested) and removed 26 (16 requested) atoms. Cycle 23: After refmac, R = 0.1997 (Rfree = 0.000) for 5051 atoms. Found 30 (32 requested) and removed 22 (16 requested) atoms. Cycle 24: After refmac, R = 0.1851 (Rfree = 0.000) for 5049 atoms. Found 15 (32 requested) and removed 28 (16 requested) atoms. Cycle 25: After refmac, R = 0.1909 (Rfree = 0.000) for 5031 atoms. Found 20 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 5214 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5228 seeds are put forward Round 1: 280 peptides, 51 chains. Longest chain 11 peptides. Score 0.358 Round 2: 320 peptides, 51 chains. Longest chain 14 peptides. Score 0.445 Round 3: 345 peptides, 52 chains. Longest chain 13 peptides. Score 0.487 Round 4: 344 peptides, 56 chains. Longest chain 14 peptides. Score 0.450 Round 5: 345 peptides, 55 chains. Longest chain 16 peptides. Score 0.461 Taking the results from Round 3 Chains 54, Residues 293, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11820 restraints for refining 5090 atoms. 10587 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2210 (Rfree = 0.000) for 5090 atoms. Found 23 (32 requested) and removed 32 (16 requested) atoms. Cycle 27: After refmac, R = 0.1998 (Rfree = 0.000) for 5058 atoms. Found 21 (32 requested) and removed 20 (16 requested) atoms. Cycle 28: After refmac, R = 0.1958 (Rfree = 0.000) for 5046 atoms. Found 20 (32 requested) and removed 24 (16 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1873 (Rfree = 0.000) for 5035 atoms. Found 22 (32 requested) and removed 25 (16 requested) atoms. Cycle 30: After refmac, R = 0.1775 (Rfree = 0.000) for 5029 atoms. Found 13 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 5205 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5219 seeds are put forward Round 1: 288 peptides, 52 chains. Longest chain 12 peptides. Score 0.367 Round 2: 323 peptides, 51 chains. Longest chain 14 peptides. Score 0.452 Round 3: 326 peptides, 53 chains. Longest chain 14 peptides. Score 0.440 Round 4: 346 peptides, 50 chains. Longest chain 18 peptides. Score 0.506 Round 5: 339 peptides, 52 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 4 Chains 51, Residues 296, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11965 restraints for refining 5091 atoms. 10787 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2256 (Rfree = 0.000) for 5091 atoms. Found 31 (32 requested) and removed 25 (16 requested) atoms. Cycle 32: After refmac, R = 0.2055 (Rfree = 0.000) for 5078 atoms. Found 31 (32 requested) and removed 21 (16 requested) atoms. Cycle 33: After refmac, R = 0.2058 (Rfree = 0.000) for 5070 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. Cycle 34: After refmac, R = 0.1913 (Rfree = 0.000) for 5066 atoms. Found 30 (32 requested) and removed 16 (16 requested) atoms. Cycle 35: After refmac, R = 0.1904 (Rfree = 0.000) for 5068 atoms. Found 31 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 5227 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5250 seeds are put forward Round 1: 259 peptides, 49 chains. Longest chain 14 peptides. Score 0.329 Round 2: 305 peptides, 49 chains. Longest chain 19 peptides. Score 0.432 Round 3: 297 peptides, 50 chains. Longest chain 13 peptides. Score 0.406 Round 4: 299 peptides, 47 chains. Longest chain 17 peptides. Score 0.438 Round 5: 304 peptides, 47 chains. Longest chain 17 peptides. Score 0.449 Taking the results from Round 5 Chains 49, Residues 257, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 12106 restraints for refining 5091 atoms. 11062 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2136 (Rfree = 0.000) for 5091 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 37: After refmac, R = 0.1992 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 38: After refmac, R = 0.1931 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 39: After refmac, R = 0.1972 (Rfree = 0.000) for 5079 atoms. Found 32 (32 requested) and removed 21 (16 requested) atoms. Cycle 40: After refmac, R = 0.1966 (Rfree = 0.000) for 5083 atoms. Found 32 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 5280 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5297 seeds are put forward Round 1: 243 peptides, 51 chains. Longest chain 11 peptides. Score 0.269 Round 2: 270 peptides, 49 chains. Longest chain 10 peptides. Score 0.355 Round 3: 289 peptides, 52 chains. Longest chain 12 peptides. Score 0.369 Round 4: 289 peptides, 47 chains. Longest chain 12 peptides. Score 0.417 Round 5: 292 peptides, 46 chains. Longest chain 17 peptides. Score 0.433 Taking the results from Round 5 Chains 46, Residues 246, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 12087 restraints for refining 5091 atoms. 11130 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2164 (Rfree = 0.000) for 5091 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 42: After refmac, R = 0.2003 (Rfree = 0.000) for 5080 atoms. Found 27 (32 requested) and removed 17 (16 requested) atoms. Cycle 43: After refmac, R = 0.1855 (Rfree = 0.000) for 5086 atoms. Found 17 (32 requested) and removed 19 (16 requested) atoms. Cycle 44: After refmac, R = 0.1850 (Rfree = 0.000) for 5076 atoms. Found 24 (32 requested) and removed 18 (16 requested) atoms. Cycle 45: After refmac, R = 0.1888 (Rfree = 0.000) for 5080 atoms. Found 32 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 5265 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 5285 seeds are put forward Round 1: 205 peptides, 41 chains. Longest chain 12 peptides. Score 0.280 Round 2: 263 peptides, 47 chains. Longest chain 13 peptides. Score 0.359 Round 3: 260 peptides, 45 chains. Longest chain 15 peptides. Score 0.372 Round 4: 263 peptides, 44 chains. Longest chain 16 peptides. Score 0.388 Round 5: 257 peptides, 45 chains. Longest chain 14 peptides. Score 0.365 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 219, Estimated correctness of the model 0.0 % 4 chains (15 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 44 chains (219 residues) following loop building 4 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8743 reflections ( 99.44 % complete ) and 12375 restraints for refining 5091 atoms. 11509 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1968 (Rfree = 0.000) for 5091 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1893 (Rfree = 0.000) for 5056 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1911 (Rfree = 0.000) for 5032 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1862 (Rfree = 0.000) for 5013 atoms. TimeTaking 61.25