Sun 23 Dec 22:23:09 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fna-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fna-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fna-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:18 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/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.8-parrot-hancs/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 510 and 0 Target number of residues in the AU: 510 Target solvent content: 0.6690 Checking the provided sequence file Detected sequence length: 357 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 714 Adjusted target solvent content: 0.54 Input MTZ file: 2fna-3.8-parrot-hancs.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: 4 Cell parameters: 55.380 108.390 70.600 90.000 100.307 90.000 Input sequence file: 2fna-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 5712 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: 69.461 3.800 Wilson plot Bfac: 91.32 8052 reflections ( 98.50 % complete ) and 0 restraints for refining 6339 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3356 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2902 (Rfree = 0.000) for 6339 atoms. Found 34 (34 requested) and removed 54 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 6455 seeds are put forward NCS extension: 0 residues added, 6455 seeds are put forward Round 1: 259 peptides, 51 chains. Longest chain 11 peptides. Score 0.296 Round 2: 323 peptides, 51 chains. Longest chain 13 peptides. Score 0.426 Round 3: 340 peptides, 50 chains. Longest chain 25 peptides. Score 0.466 Round 4: 355 peptides, 51 chains. Longest chain 17 peptides. Score 0.485 Round 5: 358 peptides, 48 chains. Longest chain 26 peptides. Score 0.513 Taking the results from Round 5 Chains 49, Residues 310, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8052 reflections ( 98.50 % complete ) and 12039 restraints for refining 5164 atoms. 10803 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2455 (Rfree = 0.000) for 5164 atoms. Found 20 (28 requested) and removed 27 (14 requested) atoms. Cycle 2: After refmac, R = 0.2214 (Rfree = 0.000) for 5085 atoms. Found 21 (28 requested) and removed 34 (14 requested) atoms. Cycle 3: After refmac, R = 0.1892 (Rfree = 0.000) for 5035 atoms. Found 5 (27 requested) and removed 17 (13 requested) atoms. Cycle 4: After refmac, R = 0.1888 (Rfree = 0.000) for 5003 atoms. Found 7 (27 requested) and removed 32 (13 requested) atoms. Cycle 5: After refmac, R = 0.1763 (Rfree = 0.000) for 4963 atoms. Found 4 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 5178 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 5212 seeds are put forward Round 1: 331 peptides, 60 chains. Longest chain 12 peptides. Score 0.366 Round 2: 360 peptides, 60 chains. Longest chain 15 peptides. Score 0.422 Round 3: 363 peptides, 56 chains. Longest chain 15 peptides. Score 0.460 Round 4: 360 peptides, 53 chains. Longest chain 20 peptides. Score 0.478 Round 5: 352 peptides, 51 chains. Longest chain 16 peptides. Score 0.479 Taking the results from Round 5 Chains 51, Residues 301, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12129 restraints for refining 5166 atoms. 10976 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2161 (Rfree = 0.000) for 5166 atoms. Found 10 (28 requested) and removed 23 (14 requested) atoms. Cycle 7: After refmac, R = 0.2124 (Rfree = 0.000) for 5124 atoms. Found 27 (28 requested) and removed 22 (14 requested) atoms. Cycle 8: After refmac, R = 0.2074 (Rfree = 0.000) for 5106 atoms. Found 15 (28 requested) and removed 18 (14 requested) atoms. Cycle 9: After refmac, R = 0.1730 (Rfree = 0.000) for 5079 atoms. Found 5 (28 requested) and removed 22 (14 requested) atoms. Cycle 10: After refmac, R = 0.1622 (Rfree = 0.000) for 5049 atoms. Found 4 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 5269 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5284 seeds are put forward Round 1: 304 peptides, 60 chains. Longest chain 10 peptides. Score 0.311 Round 2: 348 peptides, 58 chains. Longest chain 13 peptides. Score 0.416 Round 3: 358 peptides, 53 chains. Longest chain 19 peptides. Score 0.474 Round 4: 358 peptides, 54 chains. Longest chain 18 peptides. Score 0.466 Round 5: 347 peptides, 48 chains. Longest chain 22 peptides. Score 0.494 Taking the results from Round 5 Chains 48, Residues 299, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12062 restraints for refining 5163 atoms. 10914 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2190 (Rfree = 0.000) for 5163 atoms. Found 18 (28 requested) and removed 19 (14 requested) atoms. Cycle 12: After refmac, R = 0.2212 (Rfree = 0.000) for 5119 atoms. Found 19 (28 requested) and removed 22 (14 requested) atoms. Cycle 13: After refmac, R = 0.1840 (Rfree = 0.000) for 5092 atoms. Found 12 (28 requested) and removed 22 (14 requested) atoms. Cycle 14: After refmac, R = 0.1876 (Rfree = 0.000) for 5061 atoms. Found 3 (27 requested) and removed 15 (13 requested) atoms. Cycle 15: After refmac, R = 0.1691 (Rfree = 0.000) for 5034 atoms. Found 5 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 5222 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5241 seeds are put forward Round 1: 290 peptides, 59 chains. Longest chain 9 peptides. Score 0.290 Round 2: 321 peptides, 52 chains. Longest chain 16 peptides. Score 0.414 Round 3: 332 peptides, 50 chains. Longest chain 17 peptides. Score 0.451 Round 4: 338 peptides, 51 chains. Longest chain 12 peptides. Score 0.454 Round 5: 358 peptides, 56 chains. Longest chain 15 peptides. Score 0.451 Taking the results from Round 4 Chains 51, Residues 287, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12128 restraints for refining 5166 atoms. 11031 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2053 (Rfree = 0.000) for 5166 atoms. Found 12 (28 requested) and removed 29 (14 requested) atoms. Cycle 17: After refmac, R = 0.1821 (Rfree = 0.000) for 5112 atoms. Found 8 (28 requested) and removed 19 (14 requested) atoms. Cycle 18: After refmac, R = 0.1835 (Rfree = 0.000) for 5090 atoms. Found 8 (28 requested) and removed 20 (14 requested) atoms. Cycle 19: After refmac, R = 0.1582 (Rfree = 0.000) for 5067 atoms. Found 1 (27 requested) and removed 15 (13 requested) atoms. Cycle 20: After refmac, R = 0.1553 (Rfree = 0.000) for 5048 atoms. Found 6 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 5242 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5256 seeds are put forward Round 1: 277 peptides, 57 chains. Longest chain 8 peptides. Score 0.280 Round 2: 316 peptides, 50 chains. Longest chain 13 peptides. Score 0.421 Round 3: 314 peptides, 52 chains. Longest chain 12 peptides. Score 0.401 Round 4: 323 peptides, 50 chains. Longest chain 18 peptides. Score 0.435 Round 5: 329 peptides, 47 chains. Longest chain 13 peptides. Score 0.470 Taking the results from Round 5 Chains 47, Residues 282, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 11980 restraints for refining 5165 atoms. 10899 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2038 (Rfree = 0.000) for 5165 atoms. Found 14 (28 requested) and removed 22 (14 requested) atoms. Cycle 22: After refmac, R = 0.1843 (Rfree = 0.000) for 5127 atoms. Found 9 (28 requested) and removed 23 (14 requested) atoms. Cycle 23: After refmac, R = 0.1699 (Rfree = 0.000) for 5096 atoms. Found 5 (28 requested) and removed 19 (14 requested) atoms. Cycle 24: After refmac, R = 0.1661 (Rfree = 0.000) for 5073 atoms. Found 3 (27 requested) and removed 15 (13 requested) atoms. Cycle 25: After refmac, R = 0.1621 (Rfree = 0.000) for 5055 atoms. Found 2 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 5209 seeds are put forward NCS extension: 0 residues added, 5209 seeds are put forward Round 1: 263 peptides, 52 chains. Longest chain 11 peptides. Score 0.295 Round 2: 319 peptides, 55 chains. Longest chain 17 peptides. Score 0.385 Round 3: 319 peptides, 50 chains. Longest chain 14 peptides. Score 0.427 Round 4: 324 peptides, 47 chains. Longest chain 24 peptides. Score 0.461 Round 5: 323 peptides, 47 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 4 Chains 47, Residues 277, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 11673 restraints for refining 5166 atoms. 10480 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2046 (Rfree = 0.000) for 5166 atoms. Found 15 (28 requested) and removed 23 (14 requested) atoms. Cycle 27: After refmac, R = 0.1932 (Rfree = 0.000) for 5134 atoms. Found 17 (28 requested) and removed 21 (14 requested) atoms. Cycle 28: After refmac, R = 0.1797 (Rfree = 0.000) for 5116 atoms. Found 12 (28 requested) and removed 15 (14 requested) atoms. Cycle 29: After refmac, R = 0.1855 (Rfree = 0.000) for 5107 atoms. Found 15 (28 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.1535 (Rfree = 0.000) for 5096 atoms. Found 3 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 5279 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 5308 seeds are put forward Round 1: 267 peptides, 53 chains. Longest chain 14 peptides. Score 0.295 Round 2: 314 peptides, 54 chains. Longest chain 18 peptides. Score 0.384 Round 3: 306 peptides, 57 chains. Longest chain 11 peptides. Score 0.341 Round 4: 326 peptides, 56 chains. Longest chain 13 peptides. Score 0.390 Round 5: 325 peptides, 53 chains. Longest chain 14 peptides. Score 0.413 Taking the results from Round 5 Chains 53, Residues 272, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12214 restraints for refining 5166 atoms. 11179 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2113 (Rfree = 0.000) for 5166 atoms. Found 19 (28 requested) and removed 17 (14 requested) atoms. Cycle 32: After refmac, R = 0.1985 (Rfree = 0.000) for 5149 atoms. Found 15 (28 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.2058 (Rfree = 0.000) for 5138 atoms. Found 16 (28 requested) and removed 23 (14 requested) atoms. Cycle 34: After refmac, R = 0.1629 (Rfree = 0.000) for 5120 atoms. Found 7 (28 requested) and removed 27 (14 requested) atoms. Cycle 35: After refmac, R = 0.1524 (Rfree = 0.000) for 5093 atoms. Found 4 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 5223 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5245 seeds are put forward Round 1: 245 peptides, 49 chains. Longest chain 9 peptides. Score 0.284 Round 2: 284 peptides, 49 chains. Longest chain 14 peptides. Score 0.367 Round 3: 269 peptides, 46 chains. Longest chain 12 peptides. Score 0.363 Round 4: 289 peptides, 50 chains. Longest chain 11 peptides. Score 0.368 Round 5: 293 peptides, 46 chains. Longest chain 16 peptides. Score 0.411 Taking the results from Round 5 Chains 46, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12285 restraints for refining 5163 atoms. 11343 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2140 (Rfree = 0.000) for 5163 atoms. Found 16 (28 requested) and removed 89 (14 requested) atoms. Cycle 37: After refmac, R = 0.2003 (Rfree = 0.000) for 5073 atoms. Found 9 (27 requested) and removed 51 (13 requested) atoms. Cycle 38: After refmac, R = 0.2010 (Rfree = 0.000) for 5022 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. Cycle 39: After refmac, R = 0.1930 (Rfree = 0.000) for 5023 atoms. Found 16 (27 requested) and removed 19 (13 requested) atoms. Cycle 40: After refmac, R = 0.1912 (Rfree = 0.000) for 5016 atoms. Found 21 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 5208 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 5241 seeds are put forward Round 1: 232 peptides, 51 chains. Longest chain 8 peptides. Score 0.235 Round 2: 269 peptides, 49 chains. Longest chain 13 peptides. Score 0.336 Round 3: 269 peptides, 48 chains. Longest chain 14 peptides. Score 0.345 Round 4: 262 peptides, 44 chains. Longest chain 17 peptides. Score 0.367 Round 5: 278 peptides, 49 chains. Longest chain 15 peptides. Score 0.355 Taking the results from Round 4 Chains 44, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12398 restraints for refining 5166 atoms. 11570 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2185 (Rfree = 0.000) for 5166 atoms. Found 26 (28 requested) and removed 18 (14 requested) atoms. Cycle 42: After refmac, R = 0.1908 (Rfree = 0.000) for 5146 atoms. Found 17 (28 requested) and removed 18 (14 requested) atoms. Cycle 43: After refmac, R = 0.1932 (Rfree = 0.000) for 5131 atoms. Found 13 (28 requested) and removed 20 (14 requested) atoms. Cycle 44: After refmac, R = 0.1800 (Rfree = 0.000) for 5117 atoms. Found 17 (28 requested) and removed 16 (14 requested) atoms. Cycle 45: After refmac, R = 0.1944 (Rfree = 0.000) for 5106 atoms. Found 24 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 5243 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 5265 seeds are put forward Round 1: 191 peptides, 43 chains. Longest chain 9 peptides. Score 0.216 Round 2: 231 peptides, 44 chains. Longest chain 12 peptides. Score 0.300 Round 3: 242 peptides, 45 chains. Longest chain 12 peptides. Score 0.315 Round 4: 255 peptides, 43 chains. Longest chain 15 peptides. Score 0.361 Round 5: 226 peptides, 39 chains. Longest chain 15 peptides. Score 0.337 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 212, 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 2fna-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8052 reflections ( 98.50 % complete ) and 12376 restraints for refining 5166 atoms. 11571 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2152 (Rfree = 0.000) for 5166 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2037 (Rfree = 0.000) for 5131 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1936 (Rfree = 0.000) for 5103 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1881 (Rfree = 0.000) for 5083 atoms. TimeTaking 68.85