Sun 23 Dec 23:53:37 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oh1-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-parrot-mrncs ############### 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 23:53:41 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/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-parrot-mrncs/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 501 and 0 Target number of residues in the AU: 501 Target solvent content: 0.6635 Checking the provided sequence file Detected sequence length: 179 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 716 Adjusted target solvent content: 0.52 Input MTZ file: 2oh1-3.8-parrot-mrncs.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: 65.646 99.855 122.905 90.000 90.000 90.000 Input sequence file: 2oh1-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5728 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: 77.501 3.800 Wilson plot Bfac: 87.48 8322 reflections ( 99.07 % complete ) and 0 restraints for refining 6334 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3338 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3159 (Rfree = 0.000) for 6334 atoms. Found 22 (34 requested) and removed 50 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 6449 seeds are put forward NCS extension: 0 residues added, 6449 seeds are put forward Round 1: 323 peptides, 57 chains. Longest chain 12 peptides. Score 0.381 Round 2: 391 peptides, 56 chains. Longest chain 16 peptides. Score 0.517 Round 3: 405 peptides, 55 chains. Longest chain 20 peptides. Score 0.548 Round 4: 422 peptides, 53 chains. Longest chain 22 peptides. Score 0.589 Round 5: 443 peptides, 56 chains. Longest chain 22 peptides. Score 0.600 Taking the results from Round 5 Chains 56, Residues 387, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11520 restraints for refining 5178 atoms. 10028 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2561 (Rfree = 0.000) for 5178 atoms. Found 7 (28 requested) and removed 32 (14 requested) atoms. Cycle 2: After refmac, R = 0.2418 (Rfree = 0.000) for 5086 atoms. Found 14 (28 requested) and removed 26 (14 requested) atoms. Cycle 3: After refmac, R = 0.2317 (Rfree = 0.000) for 5047 atoms. Found 11 (27 requested) and removed 23 (13 requested) atoms. Cycle 4: After refmac, R = 0.2246 (Rfree = 0.000) for 5020 atoms. Found 16 (27 requested) and removed 20 (13 requested) atoms. Cycle 5: After refmac, R = 0.2179 (Rfree = 0.000) for 4997 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 5190 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5209 seeds are put forward Round 1: 375 peptides, 62 chains. Longest chain 14 peptides. Score 0.441 Round 2: 413 peptides, 55 chains. Longest chain 21 peptides. Score 0.561 Round 3: 435 peptides, 57 chains. Longest chain 21 peptides. Score 0.581 Round 4: 408 peptides, 52 chains. Longest chain 21 peptides. Score 0.574 Round 5: 425 peptides, 48 chains. Longest chain 21 peptides. Score 0.626 Taking the results from Round 5 Chains 48, Residues 377, Estimated correctness of the model 10.6 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11423 restraints for refining 5181 atoms. 9877 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2408 (Rfree = 0.000) for 5181 atoms. Found 14 (28 requested) and removed 35 (14 requested) atoms. Cycle 7: After refmac, R = 0.2263 (Rfree = 0.000) for 5133 atoms. Found 12 (28 requested) and removed 28 (14 requested) atoms. Cycle 8: After refmac, R = 0.2164 (Rfree = 0.000) for 5110 atoms. Found 3 (28 requested) and removed 32 (14 requested) atoms. Cycle 9: After refmac, R = 0.2073 (Rfree = 0.000) for 5073 atoms. Found 7 (27 requested) and removed 22 (13 requested) atoms. Cycle 10: After refmac, R = 0.2015 (Rfree = 0.000) for 5052 atoms. Found 6 (27 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.55 Search for helices and strands: 0 residues in 0 chains, 5183 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 5217 seeds are put forward Round 1: 345 peptides, 58 chains. Longest chain 18 peptides. Score 0.417 Round 2: 389 peptides, 53 chains. Longest chain 27 peptides. Score 0.536 Round 3: 399 peptides, 53 chains. Longest chain 35 peptides. Score 0.552 Round 4: 403 peptides, 58 chains. Longest chain 19 peptides. Score 0.522 Round 5: 426 peptides, 57 chains. Longest chain 16 peptides. Score 0.567 Taking the results from Round 5 Chains 57, Residues 369, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11623 restraints for refining 5180 atoms. 10185 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2199 (Rfree = 0.000) for 5180 atoms. Found 18 (28 requested) and removed 24 (14 requested) atoms. Cycle 12: After refmac, R = 0.2030 (Rfree = 0.000) for 5146 atoms. Found 8 (28 requested) and removed 22 (14 requested) atoms. Cycle 13: After refmac, R = 0.2004 (Rfree = 0.000) for 5121 atoms. Found 10 (28 requested) and removed 19 (14 requested) atoms. Cycle 14: After refmac, R = 0.1974 (Rfree = 0.000) for 5101 atoms. Found 5 (28 requested) and removed 25 (14 requested) atoms. Cycle 15: After refmac, R = 0.1990 (Rfree = 0.000) for 5076 atoms. Found 9 (27 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 5253 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5272 seeds are put forward Round 1: 336 peptides, 62 chains. Longest chain 11 peptides. Score 0.364 Round 2: 388 peptides, 52 chains. Longest chain 17 peptides. Score 0.542 Round 3: 372 peptides, 52 chains. Longest chain 15 peptides. Score 0.515 Round 4: 386 peptides, 54 chains. Longest chain 16 peptides. Score 0.523 Round 5: 381 peptides, 53 chains. Longest chain 17 peptides. Score 0.523 Taking the results from Round 2 Chains 52, Residues 336, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11852 restraints for refining 5181 atoms. 10560 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2180 (Rfree = 0.000) for 5181 atoms. Found 19 (28 requested) and removed 25 (14 requested) atoms. Cycle 17: After refmac, R = 0.2082 (Rfree = 0.000) for 5162 atoms. Found 4 (28 requested) and removed 17 (14 requested) atoms. Cycle 18: After refmac, R = 0.2042 (Rfree = 0.000) for 5138 atoms. Found 7 (28 requested) and removed 20 (14 requested) atoms. Cycle 19: After refmac, R = 0.2006 (Rfree = 0.000) for 5117 atoms. Found 7 (28 requested) and removed 18 (14 requested) atoms. Cycle 20: After refmac, R = 0.1909 (Rfree = 0.000) for 5096 atoms. Found 5 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 5229 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 5255 seeds are put forward Round 1: 325 peptides, 60 chains. Longest chain 14 peptides. Score 0.359 Round 2: 387 peptides, 58 chains. Longest chain 14 peptides. Score 0.495 Round 3: 393 peptides, 57 chains. Longest chain 15 peptides. Score 0.513 Round 4: 378 peptides, 53 chains. Longest chain 22 peptides. Score 0.517 Round 5: 380 peptides, 52 chains. Longest chain 21 peptides. Score 0.528 Taking the results from Round 5 Chains 52, Residues 328, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11890 restraints for refining 5181 atoms. 10630 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2357 (Rfree = 0.000) for 5181 atoms. Found 16 (28 requested) and removed 21 (14 requested) atoms. Cycle 22: After refmac, R = 0.2235 (Rfree = 0.000) for 5146 atoms. Found 12 (28 requested) and removed 31 (14 requested) atoms. Cycle 23: After refmac, R = 0.2055 (Rfree = 0.000) for 5115 atoms. Found 10 (28 requested) and removed 22 (14 requested) atoms. Cycle 24: After refmac, R = 0.2020 (Rfree = 0.000) for 5088 atoms. Found 13 (28 requested) and removed 17 (14 requested) atoms. Cycle 25: After refmac, R = 0.1898 (Rfree = 0.000) for 5081 atoms. Found 8 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 5234 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5248 seeds are put forward Round 1: 303 peptides, 59 chains. Longest chain 12 peptides. Score 0.322 Round 2: 340 peptides, 57 chains. Longest chain 16 peptides. Score 0.415 Round 3: 339 peptides, 54 chains. Longest chain 14 peptides. Score 0.439 Round 4: 355 peptides, 56 chains. Longest chain 16 peptides. Score 0.452 Round 5: 349 peptides, 53 chains. Longest chain 15 peptides. Score 0.466 Taking the results from Round 5 Chains 54, Residues 296, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 12052 restraints for refining 5181 atoms. 10881 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2183 (Rfree = 0.000) for 5181 atoms. Found 10 (28 requested) and removed 28 (14 requested) atoms. Cycle 27: After refmac, R = 0.2016 (Rfree = 0.000) for 5141 atoms. Found 3 (28 requested) and removed 18 (14 requested) atoms. Cycle 28: After refmac, R = 0.1949 (Rfree = 0.000) for 5118 atoms. Found 2 (28 requested) and removed 17 (14 requested) atoms. Cycle 29: After refmac, R = 0.1905 (Rfree = 0.000) for 5097 atoms. Found 3 (28 requested) and removed 23 (14 requested) atoms. Cycle 30: After refmac, R = 0.1859 (Rfree = 0.000) for 5074 atoms. Found 3 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 5231 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5245 seeds are put forward Round 1: 313 peptides, 64 chains. Longest chain 11 peptides. Score 0.298 Round 2: 360 peptides, 59 chains. Longest chain 17 peptides. Score 0.437 Round 3: 378 peptides, 62 chains. Longest chain 14 peptides. Score 0.447 Round 4: 359 peptides, 60 chains. Longest chain 12 peptides. Score 0.427 Round 5: 356 peptides, 52 chains. Longest chain 20 peptides. Score 0.486 Taking the results from Round 5 Chains 52, Residues 304, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11755 restraints for refining 5180 atoms. 10568 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2262 (Rfree = 0.000) for 5180 atoms. Found 13 (28 requested) and removed 28 (14 requested) atoms. Cycle 32: After refmac, R = 0.2100 (Rfree = 0.000) for 5136 atoms. Found 14 (28 requested) and removed 21 (14 requested) atoms. Cycle 33: After refmac, R = 0.2096 (Rfree = 0.000) for 5109 atoms. Found 16 (28 requested) and removed 21 (14 requested) atoms. Cycle 34: After refmac, R = 0.1808 (Rfree = 0.000) for 5091 atoms. Found 4 (28 requested) and removed 18 (14 requested) atoms. Cycle 35: After refmac, R = 0.1727 (Rfree = 0.000) for 5070 atoms. Found 1 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 5192 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 5220 seeds are put forward Round 1: 273 peptides, 58 chains. Longest chain 9 peptides. Score 0.264 Round 2: 309 peptides, 54 chains. Longest chain 14 peptides. Score 0.379 Round 3: 310 peptides, 51 chains. Longest chain 14 peptides. Score 0.407 Round 4: 329 peptides, 52 chains. Longest chain 16 peptides. Score 0.436 Round 5: 336 peptides, 54 chains. Longest chain 15 peptides. Score 0.433 Taking the results from Round 4 Chains 52, Residues 277, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11972 restraints for refining 5180 atoms. 10893 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2169 (Rfree = 0.000) for 5180 atoms. Found 17 (28 requested) and removed 27 (14 requested) atoms. Cycle 37: After refmac, R = 0.2189 (Rfree = 0.000) for 5150 atoms. Found 20 (28 requested) and removed 25 (14 requested) atoms. Cycle 38: After refmac, R = 0.2081 (Rfree = 0.000) for 5136 atoms. Found 7 (28 requested) and removed 33 (14 requested) atoms. Cycle 39: After refmac, R = 0.1925 (Rfree = 0.000) for 5099 atoms. Found 5 (28 requested) and removed 22 (14 requested) atoms. Cycle 40: After refmac, R = 0.1917 (Rfree = 0.000) for 5080 atoms. Found 2 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.55 Search for helices and strands: 0 residues in 0 chains, 5212 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5228 seeds are put forward Round 1: 258 peptides, 53 chains. Longest chain 14 peptides. Score 0.278 Round 2: 294 peptides, 52 chains. Longest chain 15 peptides. Score 0.366 Round 3: 278 peptides, 46 chains. Longest chain 15 peptides. Score 0.387 Round 4: 281 peptides, 47 chains. Longest chain 19 peptides. Score 0.384 Round 5: 279 peptides, 45 chains. Longest chain 22 peptides. Score 0.398 Taking the results from Round 5 Chains 45, Residues 234, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 12458 restraints for refining 5181 atoms. 11567 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2141 (Rfree = 0.000) for 5181 atoms. Found 17 (28 requested) and removed 26 (14 requested) atoms. Cycle 42: After refmac, R = 0.2062 (Rfree = 0.000) for 5160 atoms. Found 19 (28 requested) and removed 21 (14 requested) atoms. Cycle 43: After refmac, R = 0.1955 (Rfree = 0.000) for 5150 atoms. Found 7 (28 requested) and removed 22 (14 requested) atoms. Cycle 44: After refmac, R = 0.1901 (Rfree = 0.000) for 5130 atoms. Found 13 (28 requested) and removed 19 (14 requested) atoms. Cycle 45: After refmac, R = 0.1552 (Rfree = 0.000) for 5117 atoms. Found 3 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 5251 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 5279 seeds are put forward Round 1: 234 peptides, 52 chains. Longest chain 9 peptides. Score 0.231 Round 2: 247 peptides, 46 chains. Longest chain 10 peptides. Score 0.320 Round 3: 256 peptides, 47 chains. Longest chain 14 peptides. Score 0.331 Round 4: 267 peptides, 45 chains. Longest chain 13 peptides. Score 0.373 Round 5: 266 peptides, 43 chains. Longest chain 14 peptides. Score 0.389 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 223, 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 2oh1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8322 reflections ( 99.07 % complete ) and 12258 restraints for refining 5181 atoms. 11409 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1957 (Rfree = 0.000) for 5181 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1960 (Rfree = 0.000) for 5155 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1904 (Rfree = 0.000) for 5132 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1857 (Rfree = 0.000) for 5111 atoms. TimeTaking 51.1