Mon 24 Dec 07:29:53 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 2opk-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2opk-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2opk-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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/2opk-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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 07:29:58 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/2opk-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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 409 and 0 Target number of residues in the AU: 409 Target solvent content: 0.6104 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-3.6-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.6-parrot-noncs.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 3.600 Wilson plot Bfac: 56.81 7177 reflections ( 99.58 % complete ) and 0 restraints for refining 3979 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3002 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2829 (Rfree = 0.000) for 3979 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 4014 seeds are put forward NCS extension: 0 residues added, 4014 seeds are put forward Round 1: 245 peptides, 39 chains. Longest chain 17 peptides. Score 0.444 Round 2: 310 peptides, 43 chains. Longest chain 16 peptides. Score 0.561 Round 3: 316 peptides, 39 chains. Longest chain 25 peptides. Score 0.612 Round 4: 327 peptides, 35 chains. Longest chain 29 peptides. Score 0.668 Round 5: 317 peptides, 36 chains. Longest chain 31 peptides. Score 0.641 Taking the results from Round 4 Chains 36, Residues 292, Estimated correctness of the model 39.3 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6648 restraints for refining 3248 atoms. 5484 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2445 (Rfree = 0.000) for 3248 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 2: After refmac, R = 0.2378 (Rfree = 0.000) for 3198 atoms. Found 17 (20 requested) and removed 20 (10 requested) atoms. Cycle 3: After refmac, R = 0.2296 (Rfree = 0.000) for 3180 atoms. Found 19 (20 requested) and removed 17 (10 requested) atoms. Cycle 4: After refmac, R = 0.2208 (Rfree = 0.000) for 3167 atoms. Found 18 (20 requested) and removed 18 (10 requested) atoms. Cycle 5: After refmac, R = 0.2211 (Rfree = 0.000) for 3160 atoms. Found 15 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 3225 seeds are put forward NCS extension: 19 residues added (9 deleted due to clashes), 3244 seeds are put forward Round 1: 285 peptides, 37 chains. Longest chain 18 peptides. Score 0.565 Round 2: 316 peptides, 33 chains. Longest chain 27 peptides. Score 0.665 Round 3: 329 peptides, 35 chains. Longest chain 33 peptides. Score 0.672 Round 4: 326 peptides, 31 chains. Longest chain 43 peptides. Score 0.699 Round 5: 329 peptides, 33 chains. Longest chain 28 peptides. Score 0.688 Taking the results from Round 4 Chains 33, Residues 295, Estimated correctness of the model 49.3 % 2 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6478 restraints for refining 3249 atoms. 5147 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2468 (Rfree = 0.000) for 3249 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 7: After refmac, R = 0.2347 (Rfree = 0.000) for 3221 atoms. Found 17 (20 requested) and removed 20 (10 requested) atoms. Cycle 8: After refmac, R = 0.2244 (Rfree = 0.000) for 3199 atoms. Found 19 (20 requested) and removed 13 (10 requested) atoms. Cycle 9: After refmac, R = 0.2158 (Rfree = 0.000) for 3195 atoms. Found 14 (20 requested) and removed 20 (10 requested) atoms. Cycle 10: After refmac, R = 0.2068 (Rfree = 0.000) for 3182 atoms. Found 9 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 3240 seeds are put forward NCS extension: 28 residues added (13 deleted due to clashes), 3268 seeds are put forward Round 1: 289 peptides, 37 chains. Longest chain 25 peptides. Score 0.574 Round 2: 324 peptides, 34 chains. Longest chain 36 peptides. Score 0.671 Round 3: 304 peptides, 30 chains. Longest chain 46 peptides. Score 0.669 Round 4: 335 peptides, 32 chains. Longest chain 34 peptides. Score 0.706 Round 5: 339 peptides, 31 chains. Longest chain 51 peptides. Score 0.720 Taking the results from Round 5 Chains 37, Residues 308, Estimated correctness of the model 55.6 % 4 chains (43 residues) have been docked in sequence Building loops using Loopy2018 37 chains (308 residues) following loop building 4 chains (43 residues) in sequence following loop building ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6462 restraints for refining 3247 atoms. 5116 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2490 (Rfree = 0.000) for 3247 atoms. Found 18 (20 requested) and removed 21 (10 requested) atoms. Cycle 12: After refmac, R = 0.2319 (Rfree = 0.000) for 3220 atoms. Found 10 (20 requested) and removed 19 (10 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2382 (Rfree = 0.000) for 3195 atoms. Found 19 (19 requested) and removed 14 (10 requested) atoms. Cycle 14: After refmac, R = 0.2310 (Rfree = 0.000) for 3193 atoms. Found 17 (19 requested) and removed 15 (10 requested) atoms. Cycle 15: After refmac, R = 0.2238 (Rfree = 0.000) for 3184 atoms. Found 8 (18 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 3264 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 3284 seeds are put forward Round 1: 284 peptides, 37 chains. Longest chain 21 peptides. Score 0.562 Round 2: 328 peptides, 37 chains. Longest chain 42 peptides. Score 0.653 Round 3: 307 peptides, 32 chains. Longest chain 29 peptides. Score 0.657 Round 4: 297 peptides, 30 chains. Longest chain 25 peptides. Score 0.656 Round 5: 302 peptides, 34 chains. Longest chain 28 peptides. Score 0.630 Taking the results from Round 3 Chains 35, Residues 275, Estimated correctness of the model 35.6 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6676 restraints for refining 3249 atoms. 5446 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2455 (Rfree = 0.000) for 3249 atoms. Found 18 (18 requested) and removed 19 (10 requested) atoms. Cycle 17: After refmac, R = 0.2263 (Rfree = 0.000) for 3233 atoms. Found 10 (18 requested) and removed 15 (10 requested) atoms. Cycle 18: After refmac, R = 0.2220 (Rfree = 0.000) for 3223 atoms. Found 12 (18 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.2170 (Rfree = 0.000) for 3219 atoms. Found 11 (18 requested) and removed 13 (10 requested) atoms. Cycle 20: After refmac, R = 0.2124 (Rfree = 0.000) for 3214 atoms. Found 8 (18 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 3254 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 3276 seeds are put forward Round 1: 261 peptides, 35 chains. Longest chain 21 peptides. Score 0.530 Round 2: 278 peptides, 30 chains. Longest chain 26 peptides. Score 0.619 Round 3: 298 peptides, 32 chains. Longest chain 30 peptides. Score 0.640 Round 4: 300 peptides, 29 chains. Longest chain 25 peptides. Score 0.670 Round 5: 314 peptides, 27 chains. Longest chain 33 peptides. Score 0.711 Taking the results from Round 5 Chains 35, Residues 287, Estimated correctness of the model 52.9 % 6 chains (92 residues) have been docked in sequence Building loops using Loopy2018 35 chains (287 residues) following loop building 6 chains (92 residues) in sequence following loop building ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6013 restraints for refining 3248 atoms. 4552 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2595 (Rfree = 0.000) for 3248 atoms. Found 18 (18 requested) and removed 26 (10 requested) atoms. Cycle 22: After refmac, R = 0.2400 (Rfree = 0.000) for 3226 atoms. Found 13 (18 requested) and removed 14 (10 requested) atoms. Cycle 23: After refmac, R = 0.2328 (Rfree = 0.000) for 3218 atoms. Found 11 (17 requested) and removed 15 (10 requested) atoms. Cycle 24: After refmac, R = 0.2311 (Rfree = 0.000) for 3204 atoms. Found 15 (17 requested) and removed 15 (10 requested) atoms. Cycle 25: After refmac, R = 0.2244 (Rfree = 0.000) for 3198 atoms. Found 12 (16 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 3254 seeds are put forward NCS extension: 35 residues added (15 deleted due to clashes), 3289 seeds are put forward Round 1: 266 peptides, 35 chains. Longest chain 22 peptides. Score 0.542 Round 2: 304 peptides, 30 chains. Longest chain 42 peptides. Score 0.669 Round 3: 290 peptides, 30 chains. Longest chain 22 peptides. Score 0.643 Round 4: 302 peptides, 31 chains. Longest chain 22 peptides. Score 0.657 Round 5: 298 peptides, 28 chains. Longest chain 30 peptides. Score 0.675 Taking the results from Round 5 Chains 28, Residues 270, Estimated correctness of the model 41.6 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6607 restraints for refining 3249 atoms. 5395 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2518 (Rfree = 0.000) for 3249 atoms. Found 16 (16 requested) and removed 22 (10 requested) atoms. Cycle 27: After refmac, R = 0.2304 (Rfree = 0.000) for 3236 atoms. Found 15 (16 requested) and removed 18 (10 requested) atoms. Cycle 28: After refmac, R = 0.2277 (Rfree = 0.000) for 3228 atoms. Found 12 (16 requested) and removed 13 (10 requested) atoms. Cycle 29: After refmac, R = 0.2214 (Rfree = 0.000) for 3225 atoms. Found 11 (16 requested) and removed 22 (10 requested) atoms. Cycle 30: After refmac, R = 0.2179 (Rfree = 0.000) for 3212 atoms. Found 11 (16 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 3258 seeds are put forward NCS extension: 20 residues added (12 deleted due to clashes), 3278 seeds are put forward Round 1: 260 peptides, 37 chains. Longest chain 20 peptides. Score 0.505 Round 2: 282 peptides, 32 chains. Longest chain 19 peptides. Score 0.608 Round 3: 296 peptides, 33 chains. Longest chain 25 peptides. Score 0.627 Round 4: 280 peptides, 34 chains. Longest chain 17 peptides. Score 0.584 Round 5: 285 peptides, 33 chains. Longest chain 23 peptides. Score 0.604 Taking the results from Round 3 Chains 40, Residues 263, Estimated correctness of the model 24.9 % 6 chains (70 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6375 restraints for refining 3249 atoms. 5101 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2498 (Rfree = 0.000) for 3249 atoms. Found 13 (16 requested) and removed 19 (10 requested) atoms. Cycle 32: After refmac, R = 0.2269 (Rfree = 0.000) for 3236 atoms. Found 5 (16 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.2208 (Rfree = 0.000) for 3219 atoms. Found 5 (16 requested) and removed 14 (10 requested) atoms. Cycle 34: After refmac, R = 0.2168 (Rfree = 0.000) for 3207 atoms. Found 6 (16 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.2212 (Rfree = 0.000) for 3201 atoms. Found 10 (16 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 3251 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3269 seeds are put forward Round 1: 254 peptides, 37 chains. Longest chain 24 peptides. Score 0.490 Round 2: 274 peptides, 37 chains. Longest chain 21 peptides. Score 0.539 Round 3: 298 peptides, 36 chains. Longest chain 20 peptides. Score 0.603 Round 4: 295 peptides, 37 chains. Longest chain 22 peptides. Score 0.587 Round 5: 292 peptides, 36 chains. Longest chain 20 peptides. Score 0.590 Taking the results from Round 3 Chains 38, Residues 262, Estimated correctness of the model 15.8 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6815 restraints for refining 3249 atoms. 5706 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2437 (Rfree = 0.000) for 3249 atoms. Found 15 (16 requested) and removed 16 (10 requested) atoms. Cycle 37: After refmac, R = 0.2326 (Rfree = 0.000) for 3243 atoms. Found 6 (16 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.2285 (Rfree = 0.000) for 3234 atoms. Found 12 (16 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.2261 (Rfree = 0.000) for 3232 atoms. Found 11 (16 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.2213 (Rfree = 0.000) for 3227 atoms. Found 8 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 3251 seeds are put forward NCS extension: 11 residues added (7 deleted due to clashes), 3262 seeds are put forward Round 1: 265 peptides, 41 chains. Longest chain 14 peptides. Score 0.473 Round 2: 300 peptides, 34 chains. Longest chain 28 peptides. Score 0.626 Round 3: 289 peptides, 38 chains. Longest chain 16 peptides. Score 0.564 Round 4: 296 peptides, 37 chains. Longest chain 26 peptides. Score 0.589 Round 5: 286 peptides, 39 chains. Longest chain 19 peptides. Score 0.546 Taking the results from Round 2 Chains 38, Residues 266, Estimated correctness of the model 24.5 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6854 restraints for refining 3247 atoms. 5751 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2368 (Rfree = 0.000) for 3247 atoms. Found 16 (16 requested) and removed 16 (10 requested) atoms. Cycle 42: After refmac, R = 0.2280 (Rfree = 0.000) for 3236 atoms. Found 13 (16 requested) and removed 15 (10 requested) atoms. Cycle 43: After refmac, R = 0.2233 (Rfree = 0.000) for 3227 atoms. Found 13 (16 requested) and removed 15 (10 requested) atoms. Cycle 44: After refmac, R = 0.2179 (Rfree = 0.000) for 3222 atoms. Found 11 (16 requested) and removed 13 (10 requested) atoms. Cycle 45: After refmac, R = 0.2155 (Rfree = 0.000) for 3218 atoms. Found 15 (16 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 3259 seeds are put forward NCS extension: 27 residues added (7 deleted due to clashes), 3286 seeds are put forward Round 1: 236 peptides, 36 chains. Longest chain 15 peptides. Score 0.455 Round 2: 262 peptides, 34 chains. Longest chain 17 peptides. Score 0.543 Round 3: 266 peptides, 33 chains. Longest chain 21 peptides. Score 0.563 Round 4: 254 peptides, 32 chains. Longest chain 17 peptides. Score 0.545 Round 5: 270 peptides, 34 chains. Longest chain 19 peptides. Score 0.561 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 233, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2opk-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (233 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7177 reflections ( 99.58 % complete ) and 7246 restraints for refining 3248 atoms. 6328 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2454 (Rfree = 0.000) for 3248 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2329 (Rfree = 0.000) for 3228 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2226 (Rfree = 0.000) for 3215 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2122 (Rfree = 0.000) for 3203 atoms. TimeTaking 46.87