null Sun 23 Dec 22:22:49 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 2oh1-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oh1-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oh1-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-4.0-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/2oh1-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-4.0-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 22:22:59 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/2oh1-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-4.0-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 491 and 0 Target number of residues in the AU: 491 Target solvent content: 0.6702 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: 2oh1-4.0-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: 19 Cell parameters: 65.646 99.855 122.905 90.000 90.000 90.000 Input sequence file: 2oh1-4.0-parrot-hancs.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 4.000 Wilson plot Bfac: 92.22 7165 reflections ( 99.07 % complete ) and 0 restraints for refining 6312 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3445 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3299 (Rfree = 0.000) for 6312 atoms. Found 29 (29 requested) and removed 45 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 6431 seeds are put forward NCS extension: 0 residues added, 6431 seeds are put forward Round 1: 254 peptides, 48 chains. Longest chain 12 peptides. Score 0.317 Round 2: 334 peptides, 56 chains. Longest chain 16 peptides. Score 0.412 Round 3: 362 peptides, 54 chains. Longest chain 19 peptides. Score 0.481 Round 4: 369 peptides, 56 chains. Longest chain 15 peptides. Score 0.478 Round 5: 378 peptides, 52 chains. Longest chain 18 peptides. Score 0.525 Taking the results from Round 5 Chains 52, Residues 326, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12021 restraints for refining 5171 atoms. 10769 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2738 (Rfree = 0.000) for 5171 atoms. Found 20 (24 requested) and removed 34 (12 requested) atoms. Cycle 2: After refmac, R = 0.2736 (Rfree = 0.000) for 5081 atoms. Found 24 (24 requested) and removed 45 (12 requested) atoms. Cycle 3: After refmac, R = 0.2559 (Rfree = 0.000) for 5009 atoms. Found 19 (24 requested) and removed 31 (12 requested) atoms. Cycle 4: After refmac, R = 0.2349 (Rfree = 0.000) for 4961 atoms. Found 18 (23 requested) and removed 38 (11 requested) atoms. Cycle 5: After refmac, R = 0.2292 (Rfree = 0.000) for 4913 atoms. Found 11 (23 requested) and removed 31 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 5091 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5110 seeds are put forward Round 1: 325 peptides, 61 chains. Longest chain 12 peptides. Score 0.350 Round 2: 365 peptides, 54 chains. Longest chain 15 peptides. Score 0.487 Round 3: 373 peptides, 50 chains. Longest chain 17 peptides. Score 0.532 Round 4: 372 peptides, 48 chains. Longest chain 26 peptides. Score 0.545 Round 5: 370 peptides, 49 chains. Longest chain 28 peptides. Score 0.534 Taking the results from Round 4 Chains 51, Residues 324, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11453 restraints for refining 5173 atoms. 10109 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2460 (Rfree = 0.000) for 5173 atoms. Found 14 (24 requested) and removed 43 (12 requested) atoms. Cycle 7: After refmac, R = 0.2195 (Rfree = 0.000) for 5085 atoms. Found 11 (24 requested) and removed 48 (12 requested) atoms. Cycle 8: After refmac, R = 0.1802 (Rfree = 0.000) for 5027 atoms. Found 3 (23 requested) and removed 21 (11 requested) atoms. Cycle 9: After refmac, R = 0.1686 (Rfree = 0.000) for 4997 atoms. Found 4 (23 requested) and removed 20 (11 requested) atoms. Cycle 10: After refmac, R = 0.1648 (Rfree = 0.000) for 4977 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 44 residues added (3 deleted due to clashes), 5188 seeds are put forward Round 1: 334 peptides, 59 chains. Longest chain 14 peptides. Score 0.386 Round 2: 344 peptides, 50 chains. Longest chain 22 peptides. Score 0.481 Round 3: 360 peptides, 56 chains. Longest chain 14 peptides. Score 0.462 Round 4: 362 peptides, 49 chains. Longest chain 24 peptides. Score 0.521 Round 5: 349 peptides, 45 chains. Longest chain 16 peptides. Score 0.529 Taking the results from Round 5 Chains 46, Residues 304, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11797 restraints for refining 5171 atoms. 10584 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2381 (Rfree = 0.000) for 5171 atoms. Found 16 (24 requested) and removed 41 (12 requested) atoms. Cycle 12: After refmac, R = 0.2225 (Rfree = 0.000) for 5117 atoms. Found 24 (24 requested) and removed 36 (12 requested) atoms. Cycle 13: After refmac, R = 0.2174 (Rfree = 0.000) for 5092 atoms. Found 23 (24 requested) and removed 37 (12 requested) atoms. Cycle 14: After refmac, R = 0.2271 (Rfree = 0.000) for 5063 atoms. Found 24 (24 requested) and removed 32 (12 requested) atoms. Cycle 15: After refmac, R = 0.2092 (Rfree = 0.000) for 5035 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 5236 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5257 seeds are put forward Round 1: 292 peptides, 50 chains. Longest chain 13 peptides. Score 0.380 Round 2: 326 peptides, 51 chains. Longest chain 13 peptides. Score 0.439 Round 3: 340 peptides, 51 chains. Longest chain 15 peptides. Score 0.465 Round 4: 364 peptides, 49 chains. Longest chain 14 peptides. Score 0.524 Round 5: 352 peptides, 52 chains. Longest chain 15 peptides. Score 0.479 Taking the results from Round 4 Chains 49, Residues 315, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11651 restraints for refining 5173 atoms. 10433 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2291 (Rfree = 0.000) for 5173 atoms. Found 16 (24 requested) and removed 26 (12 requested) atoms. Cycle 17: After refmac, R = 0.2024 (Rfree = 0.000) for 5112 atoms. Found 11 (24 requested) and removed 31 (12 requested) atoms. Cycle 18: After refmac, R = 0.2150 (Rfree = 0.000) for 5073 atoms. Found 20 (24 requested) and removed 32 (12 requested) atoms. Cycle 19: After refmac, R = 0.2148 (Rfree = 0.000) for 5049 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 20: After refmac, R = 0.2106 (Rfree = 0.000) for 5031 atoms. Found 17 (23 requested) and removed 29 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 5179 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5194 seeds are put forward Round 1: 286 peptides, 55 chains. Longest chain 10 peptides. Score 0.321 Round 2: 327 peptides, 51 chains. Longest chain 16 peptides. Score 0.441 Round 3: 311 peptides, 49 chains. Longest chain 13 peptides. Score 0.427 Round 4: 306 peptides, 47 chains. Longest chain 14 peptides. Score 0.434 Round 5: 319 peptides, 49 chains. Longest chain 15 peptides. Score 0.442 Taking the results from Round 5 Chains 49, Residues 270, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12207 restraints for refining 5172 atoms. 11176 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2322 (Rfree = 0.000) for 5172 atoms. Found 23 (24 requested) and removed 36 (12 requested) atoms. Cycle 22: After refmac, R = 0.2155 (Rfree = 0.000) for 5136 atoms. Found 12 (24 requested) and removed 22 (12 requested) atoms. Cycle 23: After refmac, R = 0.1799 (Rfree = 0.000) for 5111 atoms. Found 7 (24 requested) and removed 19 (12 requested) atoms. Cycle 24: After refmac, R = 0.1789 (Rfree = 0.000) for 5083 atoms. Found 5 (24 requested) and removed 18 (12 requested) atoms. Cycle 25: After refmac, R = 0.1719 (Rfree = 0.000) for 5066 atoms. Found 1 (24 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 5175 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5189 seeds are put forward Round 1: 269 peptides, 51 chains. Longest chain 11 peptides. Score 0.321 Round 2: 267 peptides, 45 chains. Longest chain 12 peptides. Score 0.373 Round 3: 301 peptides, 51 chains. Longest chain 11 peptides. Score 0.389 Round 4: 287 peptides, 49 chains. Longest chain 15 peptides. Score 0.378 Round 5: 293 peptides, 47 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 5 Chains 47, Residues 246, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12415 restraints for refining 5173 atoms. 11478 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2421 (Rfree = 0.000) for 5173 atoms. Found 22 (24 requested) and removed 34 (12 requested) atoms. Cycle 27: After refmac, R = 0.2391 (Rfree = 0.000) for 5132 atoms. Found 24 (24 requested) and removed 37 (12 requested) atoms. Cycle 28: After refmac, R = 0.2193 (Rfree = 0.000) for 5089 atoms. Found 23 (24 requested) and removed 27 (12 requested) atoms. Cycle 29: After refmac, R = 0.1763 (Rfree = 0.000) for 5062 atoms. Found 4 (24 requested) and removed 16 (12 requested) atoms. Cycle 30: After refmac, R = 0.1658 (Rfree = 0.000) for 5037 atoms. Found 4 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 5155 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5171 seeds are put forward Round 1: 261 peptides, 54 chains. Longest chain 9 peptides. Score 0.275 Round 2: 296 peptides, 49 chains. Longest chain 13 peptides. Score 0.397 Round 3: 299 peptides, 49 chains. Longest chain 17 peptides. Score 0.403 Round 4: 298 peptides, 47 chains. Longest chain 14 peptides. Score 0.419 Round 5: 300 peptides, 44 chains. Longest chain 13 peptides. Score 0.449 Taking the results from Round 5 Chains 44, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12186 restraints for refining 5172 atoms. 11206 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2304 (Rfree = 0.000) for 5172 atoms. Found 17 (24 requested) and removed 48 (12 requested) atoms. Cycle 32: After refmac, R = 0.2192 (Rfree = 0.000) for 5113 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 33: After refmac, R = 0.2248 (Rfree = 0.000) for 5091 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 34: After refmac, R = 0.2172 (Rfree = 0.000) for 5072 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 35: After refmac, R = 0.2137 (Rfree = 0.000) for 5059 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 5196 seeds are put forward NCS extension: 0 residues added, 5196 seeds are put forward Round 1: 252 peptides, 54 chains. Longest chain 8 peptides. Score 0.254 Round 2: 280 peptides, 45 chains. Longest chain 14 peptides. Score 0.400 Round 3: 286 peptides, 47 chains. Longest chain 17 peptides. Score 0.394 Round 4: 283 peptides, 47 chains. Longest chain 11 peptides. Score 0.388 Round 5: 287 peptides, 44 chains. Longest chain 13 peptides. Score 0.423 Taking the results from Round 5 Chains 44, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12192 restraints for refining 5172 atoms. 11264 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2502 (Rfree = 0.000) for 5172 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. Cycle 37: After refmac, R = 0.2207 (Rfree = 0.000) for 5126 atoms. Found 21 (24 requested) and removed 29 (12 requested) atoms. Cycle 38: After refmac, R = 0.2189 (Rfree = 0.000) for 5089 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 39: After refmac, R = 0.1696 (Rfree = 0.000) for 5068 atoms. Found 5 (24 requested) and removed 20 (12 requested) atoms. Cycle 40: After refmac, R = 0.1560 (Rfree = 0.000) for 5043 atoms. Found 4 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 5153 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5168 seeds are put forward Round 1: 200 peptides, 43 chains. Longest chain 7 peptides. Score 0.240 Round 2: 255 peptides, 46 chains. Longest chain 11 peptides. Score 0.338 Round 3: 261 peptides, 43 chains. Longest chain 18 peptides. Score 0.379 Round 4: 257 peptides, 47 chains. Longest chain 12 peptides. Score 0.333 Round 5: 263 peptides, 44 chains. Longest chain 14 peptides. Score 0.374 Taking the results from Round 3 Chains 45, Residues 218, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11916 restraints for refining 5055 atoms. 11045 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2140 (Rfree = 0.000) for 5055 atoms. Found 18 (24 requested) and removed 35 (12 requested) atoms. Cycle 42: After refmac, R = 0.2179 (Rfree = 0.000) for 5012 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 43: After refmac, R = 0.1907 (Rfree = 0.000) for 4984 atoms. Found 22 (23 requested) and removed 25 (11 requested) atoms. Cycle 44: After refmac, R = 0.2031 (Rfree = 0.000) for 4967 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 45: After refmac, R = 0.1860 (Rfree = 0.000) for 4948 atoms. Found 23 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 5072 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5090 seeds are put forward Round 1: 220 peptides, 49 chains. Longest chain 7 peptides. Score 0.228 Round 2: 250 peptides, 48 chains. Longest chain 10 peptides. Score 0.308 Round 3: 241 peptides, 44 chains. Longest chain 9 peptides. Score 0.326 Round 4: 239 peptides, 42 chains. Longest chain 10 peptides. Score 0.341 Round 5: 239 peptides, 44 chains. Longest chain 14 peptides. Score 0.322 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 197, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2oh1-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7165 reflections ( 99.07 % complete ) and 11893 restraints for refining 5097 atoms. 11135 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2078 (Rfree = 0.000) for 5097 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2075 (Rfree = 0.000) for 5065 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2154 (Rfree = 0.000) for 5037 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2065 (Rfree = 0.000) for 5014 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:34:06 GMT 2018 Job finished. TimeTaking 71.28 Used memory is bytes: 6581288