null Sun 23 Dec 22:23:01 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 2opk-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opk-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opk-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-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/2opk-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-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 22:23:11 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/2opk-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-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 400 and 0 Target number of residues in the AU: 400 Target solvent content: 0.6190 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.85 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: 28.177 3.801 Wilson plot Bfac: 60.71 6142 reflections ( 99.53 % complete ) and 0 restraints for refining 3973 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3044 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2921 (Rfree = 0.000) for 3973 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 4010 seeds are put forward NCS extension: 0 residues added, 4010 seeds are put forward Round 1: 243 peptides, 41 chains. Longest chain 12 peptides. Score 0.415 Round 2: 286 peptides, 38 chains. Longest chain 16 peptides. Score 0.557 Round 3: 330 peptides, 39 chains. Longest chain 23 peptides. Score 0.640 Round 4: 333 peptides, 35 chains. Longest chain 51 peptides. Score 0.679 Round 5: 332 peptides, 37 chains. Longest chain 29 peptides. Score 0.661 Taking the results from Round 4 Chains 39, Residues 298, Estimated correctness of the model 32.3 % 6 chains (105 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 5584 restraints for refining 3241 atoms. 4000 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2483 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 2: After refmac, R = 0.2323 (Rfree = 0.000) for 3181 atoms. Found 6 (17 requested) and removed 20 (8 requested) atoms. Cycle 3: After refmac, R = 0.2285 (Rfree = 0.000) for 3143 atoms. Found 10 (17 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2258 (Rfree = 0.000) for 3124 atoms. Found 11 (17 requested) and removed 13 (8 requested) atoms. Cycle 5: After refmac, R = 0.2246 (Rfree = 0.000) for 3109 atoms. Found 9 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 3191 seeds are put forward NCS extension: 50 residues added (19 deleted due to clashes), 3241 seeds are put forward Round 1: 277 peptides, 41 chains. Longest chain 22 peptides. Score 0.504 Round 2: 314 peptides, 45 chains. Longest chain 27 peptides. Score 0.550 Round 3: 324 peptides, 37 chains. Longest chain 29 peptides. Score 0.646 Round 4: 326 peptides, 37 chains. Longest chain 62 peptides. Score 0.650 Round 5: 324 peptides, 38 chains. Longest chain 22 peptides. Score 0.637 Taking the results from Round 4 Chains 39, Residues 289, Estimated correctness of the model 20.7 % 4 chains (88 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6004 restraints for refining 3240 atoms. 4540 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2590 (Rfree = 0.000) for 3240 atoms. Found 16 (17 requested) and removed 22 (8 requested) atoms. Cycle 7: After refmac, R = 0.2400 (Rfree = 0.000) for 3199 atoms. Found 11 (17 requested) and removed 16 (8 requested) atoms. Cycle 8: After refmac, R = 0.2372 (Rfree = 0.000) for 3177 atoms. Found 7 (17 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.2429 (Rfree = 0.000) for 3162 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 10: After refmac, R = 0.2292 (Rfree = 0.000) for 3151 atoms. Found 11 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 3208 seeds are put forward NCS extension: 59 residues added (39 deleted due to clashes), 3267 seeds are put forward Round 1: 267 peptides, 38 chains. Longest chain 25 peptides. Score 0.512 Round 2: 321 peptides, 39 chains. Longest chain 31 peptides. Score 0.622 Round 3: 323 peptides, 40 chains. Longest chain 24 peptides. Score 0.617 Round 4: 319 peptides, 43 chains. Longest chain 25 peptides. Score 0.581 Round 5: 316 peptides, 41 chains. Longest chain 28 peptides. Score 0.593 Taking the results from Round 2 Chains 42, Residues 282, Estimated correctness of the model 8.8 % 3 chains (48 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6470 restraints for refining 3241 atoms. 5180 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2583 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 12: After refmac, R = 0.2422 (Rfree = 0.000) for 3204 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 13: After refmac, R = 0.2388 (Rfree = 0.000) for 3181 atoms. Found 16 (17 requested) and removed 21 (8 requested) atoms. Cycle 14: After refmac, R = 0.2318 (Rfree = 0.000) for 3164 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 15: After refmac, R = 0.2296 (Rfree = 0.000) for 3153 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 3217 seeds are put forward NCS extension: 34 residues added (4 deleted due to clashes), 3251 seeds are put forward Round 1: 253 peptides, 38 chains. Longest chain 18 peptides. Score 0.476 Round 2: 287 peptides, 34 chains. Longest chain 19 peptides. Score 0.599 Round 3: 278 peptides, 32 chains. Longest chain 34 peptides. Score 0.599 Round 4: 278 peptides, 30 chains. Longest chain 24 peptides. Score 0.619 Round 5: 284 peptides, 28 chains. Longest chain 41 peptides. Score 0.649 Taking the results from Round 5 Chains 30, Residues 256, Estimated correctness of the model 20.3 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6722 restraints for refining 3241 atoms. 5592 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2428 (Rfree = 0.000) for 3241 atoms. Found 11 (17 requested) and removed 30 (8 requested) atoms. Cycle 17: After refmac, R = 0.2346 (Rfree = 0.000) for 3200 atoms. Found 15 (17 requested) and removed 17 (8 requested) atoms. Cycle 18: After refmac, R = 0.2289 (Rfree = 0.000) for 3193 atoms. Found 6 (17 requested) and removed 19 (8 requested) atoms. Cycle 19: After refmac, R = 0.2217 (Rfree = 0.000) for 3177 atoms. Found 5 (17 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.2221 (Rfree = 0.000) for 3164 atoms. Found 10 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 3214 seeds are put forward NCS extension: 22 residues added (9 deleted due to clashes), 3236 seeds are put forward Round 1: 253 peptides, 40 chains. Longest chain 20 peptides. Score 0.454 Round 2: 261 peptides, 35 chains. Longest chain 28 peptides. Score 0.530 Round 3: 276 peptides, 36 chains. Longest chain 28 peptides. Score 0.554 Round 4: 275 peptides, 35 chains. Longest chain 17 peptides. Score 0.562 Round 5: 275 peptides, 36 chains. Longest chain 16 peptides. Score 0.552 Taking the results from Round 4 Chains 35, Residues 240, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 7250 restraints for refining 3241 atoms. 6325 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2427 (Rfree = 0.000) for 3241 atoms. Found 14 (17 requested) and removed 15 (8 requested) atoms. Cycle 22: After refmac, R = 0.2343 (Rfree = 0.000) for 3228 atoms. Found 14 (17 requested) and removed 13 (8 requested) atoms. Cycle 23: After refmac, R = 0.2299 (Rfree = 0.000) for 3223 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. Cycle 24: After refmac, R = 0.2056 (Rfree = 0.000) for 3214 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.1999 (Rfree = 0.000) for 3202 atoms. Found 4 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 3249 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3271 seeds are put forward Round 1: 271 peptides, 48 chains. Longest chain 16 peptides. Score 0.409 Round 2: 282 peptides, 37 chains. Longest chain 21 peptides. Score 0.558 Round 3: 294 peptides, 39 chains. Longest chain 26 peptides. Score 0.565 Round 4: 292 peptides, 37 chains. Longest chain 21 peptides. Score 0.580 Round 5: 272 peptides, 34 chains. Longest chain 21 peptides. Score 0.566 Taking the results from Round 4 Chains 37, Residues 255, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 7139 restraints for refining 3241 atoms. 6156 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2458 (Rfree = 0.000) for 3241 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 27: After refmac, R = 0.2346 (Rfree = 0.000) for 3225 atoms. Found 10 (17 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.2373 (Rfree = 0.000) for 3220 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 29: After refmac, R = 0.2365 (Rfree = 0.000) for 3219 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 30: After refmac, R = 0.2069 (Rfree = 0.000) for 3216 atoms. Found 4 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 3248 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 3273 seeds are put forward Round 1: 239 peptides, 38 chains. Longest chain 18 peptides. Score 0.439 Round 2: 259 peptides, 38 chains. Longest chain 18 peptides. Score 0.492 Round 3: 248 peptides, 30 chains. Longest chain 21 peptides. Score 0.553 Round 4: 258 peptides, 35 chains. Longest chain 18 peptides. Score 0.522 Round 5: 275 peptides, 35 chains. Longest chain 20 peptides. Score 0.562 Taking the results from Round 5 Chains 37, Residues 240, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6953 restraints for refining 3241 atoms. 5989 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2473 (Rfree = 0.000) for 3241 atoms. Found 14 (17 requested) and removed 17 (8 requested) atoms. Cycle 32: After refmac, R = 0.2467 (Rfree = 0.000) for 3220 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 33: After refmac, R = 0.2313 (Rfree = 0.000) for 3206 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 34: After refmac, R = 0.2228 (Rfree = 0.000) for 3198 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 35: After refmac, R = 0.1956 (Rfree = 0.000) for 3200 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 3219 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3243 seeds are put forward Round 1: 223 peptides, 43 chains. Longest chain 18 peptides. Score 0.332 Round 2: 252 peptides, 38 chains. Longest chain 18 peptides. Score 0.474 Round 3: 271 peptides, 35 chains. Longest chain 32 peptides. Score 0.553 Round 4: 256 peptides, 39 chains. Longest chain 19 peptides. Score 0.473 Round 5: 256 peptides, 37 chains. Longest chain 23 peptides. Score 0.495 Taking the results from Round 3 Chains 37, Residues 236, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6933 restraints for refining 3241 atoms. 5968 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2270 (Rfree = 0.000) for 3241 atoms. Found 13 (17 requested) and removed 15 (8 requested) atoms. Cycle 37: After refmac, R = 0.2109 (Rfree = 0.000) for 3227 atoms. Found 8 (17 requested) and removed 11 (8 requested) atoms. Cycle 38: After refmac, R = 0.2196 (Rfree = 0.000) for 3217 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 39: After refmac, R = 0.2258 (Rfree = 0.000) for 3213 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. Cycle 40: After refmac, R = 0.2207 (Rfree = 0.000) for 3205 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 3251 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3269 seeds are put forward Round 1: 227 peptides, 41 chains. Longest chain 15 peptides. Score 0.369 Round 2: 250 peptides, 40 chains. Longest chain 12 peptides. Score 0.446 Round 3: 255 peptides, 42 chains. Longest chain 12 peptides. Score 0.436 Round 4: 254 peptides, 36 chains. Longest chain 14 peptides. Score 0.502 Round 5: 264 peptides, 39 chains. Longest chain 14 peptides. Score 0.493 Taking the results from Round 4 Chains 36, Residues 218, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 7103 restraints for refining 3241 atoms. 6228 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2348 (Rfree = 0.000) for 3241 atoms. Found 16 (17 requested) and removed 11 (8 requested) atoms. Cycle 42: After refmac, R = 0.2334 (Rfree = 0.000) for 3237 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.2216 (Rfree = 0.000) for 3234 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 44: After refmac, R = 0.2193 (Rfree = 0.000) for 3230 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 45: After refmac, R = 0.2089 (Rfree = 0.000) for 3227 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 3280 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3291 seeds are put forward Round 1: 208 peptides, 41 chains. Longest chain 12 peptides. Score 0.312 Round 2: 225 peptides, 37 chains. Longest chain 20 peptides. Score 0.413 Round 3: 239 peptides, 39 chains. Longest chain 18 peptides. Score 0.427 Round 4: 249 peptides, 34 chains. Longest chain 25 peptides. Score 0.511 Round 5: 259 peptides, 36 chains. Longest chain 25 peptides. Score 0.514 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, 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 2opk-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6142 reflections ( 99.53 % complete ) and 7211 restraints for refining 3241 atoms. 6355 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2303 (Rfree = 0.000) for 3241 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2230 (Rfree = 0.000) for 3221 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2309 (Rfree = 0.000) for 3203 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2187 (Rfree = 0.000) for 3188 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:18:59 GMT 2018 Job finished. TimeTaking 55.96 Used memory is bytes: 9582664