Mon 24 Dec 00:16:22 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 2opk-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-3.6-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/2opk-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-3.6-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 ============================================================ Mon 24 Dec 00:16:27 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/2opk-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-3.6-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 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-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.6-parrot-mrncs.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 3980 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.2906 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2825 (Rfree = 0.000) for 3980 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 4040 seeds are put forward NCS extension: 0 residues added, 4040 seeds are put forward Round 1: 276 peptides, 42 chains. Longest chain 17 peptides. Score 0.490 Round 2: 329 peptides, 46 chains. Longest chain 26 peptides. Score 0.573 Round 3: 340 peptides, 40 chains. Longest chain 30 peptides. Score 0.650 Round 4: 351 peptides, 34 chains. Longest chain 37 peptides. Score 0.717 Round 5: 347 peptides, 37 chains. Longest chain 22 peptides. Score 0.687 Taking the results from Round 4 Chains 40, Residues 317, Estimated correctness of the model 54.7 % 5 chains (79 residues) have been docked in sequence Building loops using Loopy2018 40 chains (317 residues) following loop building 5 chains (79 residues) in sequence following loop building ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 5806 restraints for refining 3248 atoms. 4269 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2601 (Rfree = 0.000) for 3248 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 2: After refmac, R = 0.2401 (Rfree = 0.000) for 3188 atoms. Found 14 (20 requested) and removed 22 (10 requested) atoms. Cycle 3: After refmac, R = 0.2282 (Rfree = 0.000) for 3153 atoms. Found 14 (19 requested) and removed 20 (10 requested) atoms. Cycle 4: After refmac, R = 0.2238 (Rfree = 0.000) for 3131 atoms. Found 9 (19 requested) and removed 14 (10 requested) atoms. Cycle 5: After refmac, R = 0.2144 (Rfree = 0.000) for 3119 atoms. Found 10 (18 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 3188 seeds are put forward NCS extension: 25 residues added (18 deleted due to clashes), 3213 seeds are put forward Round 1: 300 peptides, 33 chains. Longest chain 20 peptides. Score 0.635 Round 2: 335 peptides, 33 chains. Longest chain 39 peptides. Score 0.699 Round 3: 345 peptides, 32 chains. Longest chain 29 peptides. Score 0.722 Round 4: 339 peptides, 37 chains. Longest chain 26 peptides. Score 0.673 Round 5: 351 peptides, 34 chains. Longest chain 26 peptides. Score 0.717 Taking the results from Round 3 Chains 33, Residues 313, Estimated correctness of the model 56.1 % 3 chains (61 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 48 A 31 chains (318 residues) following loop building 2 chains (71 residues) in sequence following loop building ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 5960 restraints for refining 3247 atoms. 4463 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2551 (Rfree = 0.000) for 3247 atoms. Found 18 (18 requested) and removed 21 (10 requested) atoms. Cycle 7: After refmac, R = 0.2397 (Rfree = 0.000) for 3221 atoms. Found 18 (18 requested) and removed 22 (10 requested) atoms. Cycle 8: After refmac, R = 0.2291 (Rfree = 0.000) for 3210 atoms. Found 7 (17 requested) and removed 21 (10 requested) atoms. Cycle 9: After refmac, R = 0.2200 (Rfree = 0.000) for 3195 atoms. Found 11 (17 requested) and removed 19 (10 requested) atoms. Cycle 10: After refmac, R = 0.2161 (Rfree = 0.000) for 3184 atoms. Found 5 (16 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.00 Search for helices and strands: 0 residues in 0 chains, 3253 seeds are put forward NCS extension: 37 residues added (19 deleted due to clashes), 3290 seeds are put forward Round 1: 297 peptides, 39 chains. Longest chain 22 peptides. Score 0.571 Round 2: 324 peptides, 27 chains. Longest chain 30 peptides. Score 0.727 Round 3: 328 peptides, 33 chains. Longest chain 27 peptides. Score 0.687 Round 4: 342 peptides, 33 chains. Longest chain 32 peptides. Score 0.710 Round 5: 340 peptides, 35 chains. Longest chain 25 peptides. Score 0.691 Taking the results from Round 2 Chains 29, Residues 297, Estimated correctness of the model 57.6 % 5 chains (93 residues) have been docked in sequence Building loops using Loopy2018 29 chains (297 residues) following loop building 5 chains (93 residues) in sequence following loop building ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6026 restraints for refining 3249 atoms. 4493 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2546 (Rfree = 0.000) for 3249 atoms. Found 14 (16 requested) and removed 26 (10 requested) atoms. Cycle 12: After refmac, R = 0.2435 (Rfree = 0.000) for 3213 atoms. Found 16 (16 requested) and removed 18 (10 requested) atoms. Cycle 13: After refmac, R = 0.2327 (Rfree = 0.000) for 3196 atoms. Found 6 (15 requested) and removed 17 (10 requested) atoms. Cycle 14: After refmac, R = 0.2291 (Rfree = 0.000) for 3183 atoms. Found 8 (15 requested) and removed 16 (10 requested) atoms. Cycle 15: After refmac, R = 0.2234 (Rfree = 0.000) for 3166 atoms. Found 12 (14 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 17 residues added (11 deleted due to clashes), 3207 seeds are put forward Round 1: 303 peptides, 40 chains. Longest chain 21 peptides. Score 0.575 Round 2: 333 peptides, 30 chains. Longest chain 38 peptides. Score 0.718 Round 3: 329 peptides, 35 chains. Longest chain 32 peptides. Score 0.672 Round 4: 340 peptides, 28 chains. Longest chain 30 peptides. Score 0.744 Round 5: 332 peptides, 29 chains. Longest chain 35 peptides. Score 0.725 Taking the results from Round 4 Chains 35, Residues 312, Estimated correctness of the model 62.3 % 6 chains (103 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 72 A 32 chains (310 residues) following loop building 5 chains (111 residues) in sequence following loop building ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 5739 restraints for refining 3249 atoms. 4161 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2760 (Rfree = 0.000) for 3249 atoms. Found 14 (14 requested) and removed 37 (10 requested) atoms. Cycle 17: After refmac, R = 0.2496 (Rfree = 0.000) for 3209 atoms. Found 14 (14 requested) and removed 26 (10 requested) atoms. Cycle 18: After refmac, R = 0.2425 (Rfree = 0.000) for 3187 atoms. Found 13 (13 requested) and removed 20 (10 requested) atoms. Cycle 19: After refmac, R = 0.2312 (Rfree = 0.000) for 3175 atoms. Found 13 (13 requested) and removed 17 (10 requested) atoms. Cycle 20: After refmac, R = 0.2294 (Rfree = 0.000) for 3165 atoms. Found 10 (12 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 3225 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 3249 seeds are put forward Round 1: 286 peptides, 39 chains. Longest chain 25 peptides. Score 0.546 Round 2: 309 peptides, 36 chains. Longest chain 28 peptides. Score 0.625 Round 3: 323 peptides, 36 chains. Longest chain 29 peptides. Score 0.652 Round 4: 318 peptides, 36 chains. Longest chain 30 peptides. Score 0.643 Round 5: 330 peptides, 34 chains. Longest chain 30 peptides. Score 0.682 Taking the results from Round 5 Chains 35, Residues 296, Estimated correctness of the model 43.9 % 2 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6351 restraints for refining 3248 atoms. 5030 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2559 (Rfree = 0.000) for 3248 atoms. Found 12 (12 requested) and removed 26 (10 requested) atoms. Cycle 22: After refmac, R = 0.2432 (Rfree = 0.000) for 3221 atoms. Found 11 (12 requested) and removed 15 (10 requested) atoms. Cycle 23: After refmac, R = 0.2338 (Rfree = 0.000) for 3211 atoms. Found 9 (12 requested) and removed 15 (10 requested) atoms. Cycle 24: After refmac, R = 0.2368 (Rfree = 0.000) for 3200 atoms. Found 12 (12 requested) and removed 18 (10 requested) atoms. Cycle 25: After refmac, R = 0.2245 (Rfree = 0.000) for 3189 atoms. Found 12 (12 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 3246 seeds are put forward NCS extension: 27 residues added (14 deleted due to clashes), 3273 seeds are put forward Round 1: 273 peptides, 42 chains. Longest chain 20 peptides. Score 0.483 Round 2: 309 peptides, 41 chains. Longest chain 23 peptides. Score 0.578 Round 3: 318 peptides, 40 chains. Longest chain 23 peptides. Score 0.607 Round 4: 321 peptides, 38 chains. Longest chain 30 peptides. Score 0.631 Round 5: 310 peptides, 37 chains. Longest chain 21 peptides. Score 0.618 Taking the results from Round 4 Chains 40, Residues 283, Estimated correctness of the model 26.4 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6795 restraints for refining 3249 atoms. 5610 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2514 (Rfree = 0.000) for 3249 atoms. Found 12 (12 requested) and removed 21 (10 requested) atoms. Cycle 27: After refmac, R = 0.2355 (Rfree = 0.000) for 3228 atoms. Found 12 (12 requested) and removed 18 (10 requested) atoms. Cycle 28: After refmac, R = 0.2228 (Rfree = 0.000) for 3214 atoms. Found 7 (12 requested) and removed 14 (10 requested) atoms. Cycle 29: After refmac, R = 0.2163 (Rfree = 0.000) for 3203 atoms. Found 4 (12 requested) and removed 15 (10 requested) atoms. Cycle 30: After refmac, R = 0.2101 (Rfree = 0.000) for 3190 atoms. Found 9 (12 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 3248 seeds are put forward NCS extension: 17 residues added (10 deleted due to clashes), 3265 seeds are put forward Round 1: 247 peptides, 39 chains. Longest chain 20 peptides. Score 0.449 Round 2: 278 peptides, 38 chains. Longest chain 21 peptides. Score 0.538 Round 3: 289 peptides, 34 chains. Longest chain 30 peptides. Score 0.603 Round 4: 286 peptides, 37 chains. Longest chain 22 peptides. Score 0.567 Round 5: 290 peptides, 35 chains. Longest chain 22 peptides. Score 0.596 Taking the results from Round 3 Chains 36, Residues 255, Estimated correctness of the model 15.8 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6866 restraints for refining 3249 atoms. 5805 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2462 (Rfree = 0.000) for 3249 atoms. Found 9 (12 requested) and removed 13 (10 requested) atoms. Cycle 32: After refmac, R = 0.2320 (Rfree = 0.000) for 3238 atoms. Found 12 (12 requested) and removed 18 (10 requested) atoms. Cycle 33: After refmac, R = 0.2186 (Rfree = 0.000) for 3227 atoms. Found 7 (12 requested) and removed 14 (10 requested) atoms. Cycle 34: After refmac, R = 0.2164 (Rfree = 0.000) for 3214 atoms. Found 8 (12 requested) and removed 13 (10 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2112 (Rfree = 0.000) for 3209 atoms. Found 7 (12 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 3242 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3269 seeds are put forward Round 1: 248 peptides, 45 chains. Longest chain 14 peptides. Score 0.380 Round 2: 290 peptides, 39 chains. Longest chain 22 peptides. Score 0.556 Round 3: 285 peptides, 39 chains. Longest chain 19 peptides. Score 0.544 Round 4: 273 peptides, 35 chains. Longest chain 18 peptides. Score 0.558 Round 5: 283 peptides, 39 chains. Longest chain 23 peptides. Score 0.540 Taking the results from Round 4 Chains 36, Residues 238, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6976 restraints for refining 3248 atoms. 5981 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2531 (Rfree = 0.000) for 3248 atoms. Found 12 (12 requested) and removed 21 (10 requested) atoms. Cycle 37: After refmac, R = 0.2386 (Rfree = 0.000) for 3223 atoms. Found 12 (12 requested) and removed 12 (10 requested) atoms. Cycle 38: After refmac, R = 0.2250 (Rfree = 0.000) for 3210 atoms. Found 12 (12 requested) and removed 15 (10 requested) atoms. Cycle 39: After refmac, R = 0.2169 (Rfree = 0.000) for 3203 atoms. Found 12 (12 requested) and removed 14 (10 requested) atoms. Cycle 40: After refmac, R = 0.2218 (Rfree = 0.000) for 3199 atoms. Found 12 (12 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 3245 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3258 seeds are put forward Round 1: 234 peptides, 42 chains. Longest chain 16 peptides. Score 0.377 Round 2: 262 peptides, 37 chains. Longest chain 17 peptides. Score 0.510 Round 3: 260 peptides, 38 chains. Longest chain 18 peptides. Score 0.494 Round 4: 260 peptides, 39 chains. Longest chain 18 peptides. Score 0.483 Round 5: 276 peptides, 39 chains. Longest chain 26 peptides. Score 0.523 Taking the results from Round 5 Chains 40, Residues 237, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 7138 restraints for refining 3248 atoms. 6167 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2432 (Rfree = 0.000) for 3248 atoms. Found 12 (12 requested) and removed 22 (10 requested) atoms. Cycle 42: After refmac, R = 0.2399 (Rfree = 0.000) for 3228 atoms. Found 12 (12 requested) and removed 13 (10 requested) atoms. Cycle 43: After refmac, R = 0.2306 (Rfree = 0.000) for 3217 atoms. Found 12 (12 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.2328 (Rfree = 0.000) for 3211 atoms. Found 12 (12 requested) and removed 20 (10 requested) atoms. Cycle 45: After refmac, R = 0.2238 (Rfree = 0.000) for 3200 atoms. Found 12 (12 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 3252 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3272 seeds are put forward Round 1: 211 peptides, 40 chains. Longest chain 14 peptides. Score 0.334 Round 2: 240 peptides, 39 chains. Longest chain 14 peptides. Score 0.430 Round 3: 235 peptides, 39 chains. Longest chain 15 peptides. Score 0.416 Round 4: 236 peptides, 37 chains. Longest chain 24 peptides. Score 0.443 Round 5: 239 peptides, 36 chains. Longest chain 13 peptides. Score 0.463 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 203, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2opk-3_warpNtrace.pdb as input Building loops using Loopy2018 36 chains (203 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7177 reflections ( 99.58 % complete ) and 7395 restraints for refining 3249 atoms. 6612 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2529 (Rfree = 0.000) for 3249 atoms. Found 0 (12 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2382 (Rfree = 0.000) for 3231 atoms. Found 0 (12 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2237 (Rfree = 0.000) for 3212 atoms. Found 0 (12 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2175 (Rfree = 0.000) for 3192 atoms. Found 0 (12 requested) and removed 10 (10 requested) atoms. Writing output files ... TimeTaking 40.6