Sun 23 Dec 22:22:40 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 2o5r-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-3.6-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/2o5r-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-3.6-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 22:22:49 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/2o5r-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-3.6-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 473 and 0 Target number of residues in the AU: 473 Target solvent content: 0.6809 Checking the provided sequence file Detected sequence length: 481 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 481 Adjusted target solvent content: 0.68 Input MTZ file: 2o5r-3.6-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: 152 Cell parameters: 69.953 69.953 283.945 90.000 90.000 120.000 Input sequence file: 2o5r-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3848 target number of atoms Had to go as low as 1.05 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 Loops will be built when appropriate and at the last cycle Resolution range: 19.992 3.600 Wilson plot Bfac: 101.95 9941 reflections ( 99.15 % complete ) and 0 restraints for refining 4246 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3529 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3354 (Rfree = 0.000) for 4246 atoms. Found 27 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 2.98 Search for helices and strands: 0 residues in 0 chains, 4343 seeds are put forward Round 1: 219 peptides, 36 chains. Longest chain 18 peptides. Score 0.356 Round 2: 278 peptides, 33 chains. Longest chain 20 peptides. Score 0.503 Round 3: 270 peptides, 33 chains. Longest chain 33 peptides. Score 0.488 Round 4: 281 peptides, 33 chains. Longest chain 20 peptides. Score 0.508 Round 5: 288 peptides, 29 chains. Longest chain 34 peptides. Score 0.554 Taking the results from Round 5 Chains 32, Residues 259, Estimated correctness of the model 0.0 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9941 reflections ( 99.15 % complete ) and 7362 restraints for refining 3487 atoms. 6174 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2905 (Rfree = 0.000) for 3487 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. Cycle 2: After refmac, R = 0.2766 (Rfree = 0.000) for 3418 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 3: After refmac, R = 0.2641 (Rfree = 0.000) for 3389 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 4: After refmac, R = 0.2583 (Rfree = 0.000) for 3360 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 5: After refmac, R = 0.2523 (Rfree = 0.000) for 3336 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.84 2.99 Search for helices and strands: 0 residues in 0 chains, 3506 seeds are put forward Round 1: 291 peptides, 37 chains. Longest chain 25 peptides. Score 0.492 Round 2: 302 peptides, 30 chains. Longest chain 33 peptides. Score 0.569 Round 3: 298 peptides, 30 chains. Longest chain 49 peptides. Score 0.562 Round 4: 308 peptides, 31 chains. Longest chain 30 peptides. Score 0.571 Round 5: 322 peptides, 30 chains. Longest chain 45 peptides. Score 0.601 Taking the results from Round 5 Chains 32, Residues 292, Estimated correctness of the model 15.0 % 3 chains (89 residues) have been docked in sequence ------------------------------------------------------ 9941 reflections ( 99.15 % complete ) and 6419 restraints for refining 3488 atoms. 4851 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2998 (Rfree = 0.000) for 3488 atoms. Found 22 (22 requested) and removed 98 (11 requested) atoms. Cycle 7: After refmac, R = 0.2888 (Rfree = 0.000) for 3372 atoms. Found 21 (21 requested) and removed 46 (10 requested) atoms. Cycle 8: After refmac, R = 0.2669 (Rfree = 0.000) for 3327 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 9: After refmac, R = 0.2552 (Rfree = 0.000) for 3314 atoms. Found 18 (21 requested) and removed 21 (10 requested) atoms. Cycle 10: After refmac, R = 0.2475 (Rfree = 0.000) for 3298 atoms. Found 16 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.81 2.96 Search for helices and strands: 0 residues in 0 chains, 3460 seeds are put forward Round 1: 276 peptides, 37 chains. Longest chain 14 peptides. Score 0.464 Round 2: 294 peptides, 35 chains. Longest chain 19 peptides. Score 0.515 Round 3: 293 peptides, 30 chains. Longest chain 24 peptides. Score 0.554 Round 4: 304 peptides, 29 chains. Longest chain 27 peptides. Score 0.580 Round 5: 296 peptides, 28 chains. Longest chain 28 peptides. Score 0.575 Taking the results from Round 4 Chains 33, Residues 275, Estimated correctness of the model 6.7 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 9941 reflections ( 99.15 % complete ) and 6925 restraints for refining 3488 atoms. 5635 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2932 (Rfree = 0.000) for 3488 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 12: After refmac, R = 0.2726 (Rfree = 0.000) for 3428 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 13: After refmac, R = 0.2612 (Rfree = 0.000) for 3410 atoms. Found 17 (22 requested) and removed 20 (11 requested) atoms. Cycle 14: After refmac, R = 0.2598 (Rfree = 0.000) for 3383 atoms. Found 16 (21 requested) and removed 17 (10 requested) atoms. Cycle 15: After refmac, R = 0.2548 (Rfree = 0.000) for 3369 atoms. Found 20 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 2.97 Search for helices and strands: 0 residues in 0 chains, 3518 seeds are put forward Round 1: 276 peptides, 36 chains. Longest chain 18 peptides. Score 0.473 Round 2: 290 peptides, 30 chains. Longest chain 24 peptides. Score 0.549 Round 3: 288 peptides, 28 chains. Longest chain 30 peptides. Score 0.562 Round 4: 296 peptides, 30 chains. Longest chain 33 peptides. Score 0.559 Round 5: 298 peptides, 30 chains. Longest chain 29 peptides. Score 0.562 Taking the results from Round 5 Chains 32, Residues 268, Estimated correctness of the model 0.0 % 2 chains (43 residues) have been docked in sequence ------------------------------------------------------ 9941 reflections ( 99.15 % complete ) and 7271 restraints for refining 3488 atoms. 6037 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3037 (Rfree = 0.000) for 3488 atoms. Found 22 (22 requested) and removed 76 (11 requested) atoms. Cycle 17: After refmac, R = 0.2728 (Rfree = 0.000) for 3398 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 18: After refmac, R = 0.2560 (Rfree = 0.000) for 3377 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 19: After refmac, R = 0.2469 (Rfree = 0.000) for 3361 atoms. Found 18 (21 requested) and removed 12 (10 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2390 (Rfree = 0.000) for 3359 atoms. Found 9 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 2.97 Search for helices and strands: 0 residues in 0 chains, 3496 seeds are put forward Round 1: 262 peptides, 37 chains. Longest chain 14 peptides. Score 0.437 Round 2: 264 peptides, 28 chains. Longest chain 25 peptides. Score 0.520 Round 3: 291 peptides, 34 chains. Longest chain 25 peptides. Score 0.518 Round 4: 284 peptides, 27 chains. Longest chain 24 peptides. Score 0.563 Round 5: 280 peptides, 27 chains. Longest chain 31 peptides. Score 0.556 Taking the results from Round 4 Chains 31, Residues 257, Estimated correctness of the model 0.0 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 9941 reflections ( 99.15 % complete ) and 7066 restraints for refining 3487 atoms. 5869 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2776 (Rfree = 0.000) for 3487 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 22: After refmac, R = 0.2537 (Rfree = 0.000) for 3448 atoms. Found 22 (22 requested) and removed 13 (11 requested) atoms. Cycle 23: After refmac, R = 0.2481 (Rfree = 0.000) for 3438 atoms. Found 18 (22 requested) and removed 17 (11 requested) atoms. Cycle 24: After refmac, R = 0.2404 (Rfree = 0.000) for 3420 atoms. Found 14 (22 requested) and removed 21 (11 requested) atoms. Cycle 25: After refmac, R = 0.2357 (Rfree = 0.000) for 3401 atoms. Found 9 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 2.96 Search for helices and strands: 0 residues in 0 chains, 3586 seeds are put forward Round 1: 260 peptides, 38 chains. Longest chain 14 peptides. Score 0.424 Round 2: 283 peptides, 36 chains. Longest chain 25 peptides. Score 0.486 Round 3: 300 peptides, 36 chains. Longest chain 25 peptides. Score 0.517 Round 4: 305 peptides, 34 chains. Longest chain 22 peptides. Score 0.542 Round 5: 287 peptides, 30 chains. Longest chain 31 peptides. Score 0.544 Taking the results from Round 5 Chains 31, Residues 257, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9941 reflections ( 99.15 % complete ) and 7538 restraints for refining 3486 atoms. 6506 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2912 (Rfree = 0.000) for 3486 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. Cycle 27: After refmac, R = 0.2620 (Rfree = 0.000) for 3446 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.2576 (Rfree = 0.000) for 3438 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 29: After refmac, R = 0.2470 (Rfree = 0.000) for 3416 atoms. Found 18 (22 requested) and removed 15 (11 requested) atoms. Cycle 30: After refmac, R = 0.2449 (Rfree = 0.000) for 3403 atoms. Found 14 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 2.96 Search for helices and strands: 0 residues in 0 chains, 3604 seeds are put forward Round 1: 258 peptides, 42 chains. Longest chain 14 peptides. Score 0.383 Round 2: 297 peptides, 40 chains. Longest chain 19 peptides. Score 0.478 Round 3: 294 peptides, 38 chains. Longest chain 16 peptides. Score 0.489 Round 4: 302 peptides, 35 chains. Longest chain 25 peptides. Score 0.529 Round 5: 303 peptides, 37 chains. Longest chain 19 peptides. Score 0.514 Taking the results from Round 4 Chains 38, Residues 267, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 9941 reflections ( 99.15 % complete ) and 7240 restraints for refining 3487 atoms. 6104 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2799 (Rfree = 0.000) for 3487 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 32: After refmac, R = 0.2528 (Rfree = 0.000) for 3450 atoms. Found 19 (22 requested) and removed 18 (11 requested) atoms. Cycle 33: After refmac, R = 0.2442 (Rfree = 0.000) for 3438 atoms. Found 11 (22 requested) and removed 17 (11 requested) atoms. Cycle 34: After refmac, R = 0.2334 (Rfree = 0.000) for 3419 atoms. Found 16 (22 requested) and removed 17 (11 requested) atoms. Cycle 35: After refmac, R = 0.2168 (Rfree = 0.000) for 3410 atoms. Found 12 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 2.96 Search for helices and strands: 0 residues in 0 chains, 3566 seeds are put forward Round 1: 272 peptides, 40 chains. Longest chain 19 peptides. Score 0.430 Round 2: 295 peptides, 36 chains. Longest chain 19 peptides. Score 0.508 Round 3: 287 peptides, 35 chains. Longest chain 21 peptides. Score 0.502 Round 4: 292 peptides, 36 chains. Longest chain 17 peptides. Score 0.503 Round 5: 298 peptides, 35 chains. Longest chain 25 peptides. Score 0.522 Taking the results from Round 5 Chains 36, Residues 263, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9941 reflections ( 99.15 % complete ) and 7247 restraints for refining 3487 atoms. 6158 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2866 (Rfree = 0.000) for 3487 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 37: After refmac, R = 0.2532 (Rfree = 0.000) for 3452 atoms. Found 16 (22 requested) and removed 21 (11 requested) atoms. Cycle 38: After refmac, R = 0.2475 (Rfree = 0.000) for 3430 atoms. Found 14 (22 requested) and removed 15 (11 requested) atoms. Cycle 39: After refmac, R = 0.2402 (Rfree = 0.000) for 3413 atoms. Found 14 (21 requested) and removed 15 (10 requested) atoms. Cycle 40: After refmac, R = 0.2376 (Rfree = 0.000) for 3403 atoms. Found 18 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 2.97 Search for helices and strands: 0 residues in 0 chains, 3561 seeds are put forward Round 1: 258 peptides, 41 chains. Longest chain 14 peptides. Score 0.392 Round 2: 274 peptides, 36 chains. Longest chain 18 peptides. Score 0.469 Round 3: 286 peptides, 35 chains. Longest chain 21 peptides. Score 0.500 Round 4: 290 peptides, 35 chains. Longest chain 22 peptides. Score 0.507 Round 5: 289 peptides, 31 chains. Longest chain 22 peptides. Score 0.539 Taking the results from Round 5 Chains 32, Residues 258, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9941 reflections ( 99.15 % complete ) and 7520 restraints for refining 3487 atoms. 6487 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2975 (Rfree = 0.000) for 3487 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. Cycle 42: After refmac, R = 0.2571 (Rfree = 0.000) for 3454 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 43: After refmac, R = 0.2485 (Rfree = 0.000) for 3448 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 44: After refmac, R = 0.2428 (Rfree = 0.000) for 3446 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 45: After refmac, R = 0.2383 (Rfree = 0.000) for 3438 atoms. Found 15 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 2.96 Search for helices and strands: 0 residues in 0 chains, 3579 seeds are put forward Round 1: 237 peptides, 36 chains. Longest chain 17 peptides. Score 0.395 Round 2: 290 peptides, 33 chains. Longest chain 18 peptides. Score 0.524 Round 3: 284 peptides, 36 chains. Longest chain 22 peptides. Score 0.488 Round 4: 278 peptides, 35 chains. Longest chain 19 peptides. Score 0.485 Round 5: 288 peptides, 33 chains. Longest chain 20 peptides. Score 0.521 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 257, Estimated correctness of the model 0.0 % 5 chains (46 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 2o5r-3_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (257 residues) following loop building 5 chains (46 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9941 reflections ( 99.15 % complete ) and 6961 restraints for refining 3487 atoms. 5773 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2739 (Rfree = 0.000) for 3487 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2504 (Rfree = 0.000) for 3457 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2450 (Rfree = 0.000) for 3435 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2356 (Rfree = 0.000) for 3417 atoms. TimeTaking 62.48