Tue 25 Dec 19:27:55 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 1vk3-2.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-2.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-2.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-2.8-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/1vk3-2.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-2.8-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 ============================================================ Tue 25 Dec 19:28:04 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/1vk3-2.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-2.8-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 509 and 0 Target number of residues in the AU: 509 Target solvent content: 0.5069 Checking the provided sequence file Detected sequence length: 615 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 615 Adjusted target solvent content: 0.40 Input MTZ file: 1vk3-2.8-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: 19 Cell parameters: 59.785 72.683 128.550 90.000 90.000 90.000 Input sequence file: 1vk3-2.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4920 target number of atoms Had to go as low as 0.50 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: 30.186 2.800 Wilson plot Bfac: 24.82 14219 reflections ( 99.00 % complete ) and 0 restraints for refining 5466 atoms. Observations/parameters ratio is 0.65 ------------------------------------------------------ Starting model: R = 0.3256 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2540 (Rfree = 0.000) for 5466 atoms. Found 30 (71 requested) and removed 52 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.43 2.78 Search for helices and strands: 0 residues in 0 chains, 5541 seeds are put forward Round 1: 248 peptides, 50 chains. Longest chain 11 peptides. Score 0.321 Round 2: 290 peptides, 47 chains. Longest chain 16 peptides. Score 0.474 Round 3: 320 peptides, 47 chains. Longest chain 17 peptides. Score 0.547 Round 4: 336 peptides, 47 chains. Longest chain 16 peptides. Score 0.583 Round 5: 371 peptides, 46 chains. Longest chain 26 peptides. Score 0.662 Taking the results from Round 5 Chains 48, Residues 325, Estimated correctness of the model 71.6 % 9 chains (76 residues) have been docked in sequence ------------------------------------------------------ 14219 reflections ( 99.00 % complete ) and 8848 restraints for refining 4547 atoms. 7328 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2952 (Rfree = 0.000) for 4547 atoms. Found 51 (59 requested) and removed 41 (29 requested) atoms. Cycle 2: After refmac, R = 0.2694 (Rfree = 0.000) for 4518 atoms. Found 28 (59 requested) and removed 31 (29 requested) atoms. Cycle 3: After refmac, R = 0.2517 (Rfree = 0.000) for 4493 atoms. Found 29 (59 requested) and removed 31 (29 requested) atoms. Cycle 4: After refmac, R = 0.2446 (Rfree = 0.000) for 4475 atoms. Found 18 (58 requested) and removed 29 (29 requested) atoms. Cycle 5: After refmac, R = 0.2371 (Rfree = 0.000) for 4455 atoms. Found 19 (58 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.47 2.83 Search for helices and strands: 0 residues in 0 chains, 4563 seeds are put forward Round 1: 332 peptides, 53 chains. Longest chain 21 peptides. Score 0.514 Round 2: 373 peptides, 47 chains. Longest chain 23 peptides. Score 0.657 Round 3: 385 peptides, 48 chains. Longest chain 23 peptides. Score 0.671 Round 4: 396 peptides, 48 chains. Longest chain 23 peptides. Score 0.689 Round 5: 393 peptides, 45 chains. Longest chain 21 peptides. Score 0.707 Taking the results from Round 5 Chains 45, Residues 348, Estimated correctness of the model 78.1 % 6 chains (51 residues) have been docked in sequence Building loops using Loopy2018 45 chains (348 residues) following loop building 6 chains (51 residues) in sequence following loop building ------------------------------------------------------ 14219 reflections ( 99.00 % complete ) and 9263 restraints for refining 4489 atoms. 7730 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2766 (Rfree = 0.000) for 4489 atoms. Found 50 (58 requested) and removed 38 (29 requested) atoms. Cycle 7: After refmac, R = 0.2629 (Rfree = 0.000) for 4489 atoms. Found 23 (58 requested) and removed 31 (29 requested) atoms. Cycle 8: After refmac, R = 0.2553 (Rfree = 0.000) for 4468 atoms. Found 15 (56 requested) and removed 30 (29 requested) atoms. Cycle 9: After refmac, R = 0.2491 (Rfree = 0.000) for 4439 atoms. Found 19 (55 requested) and removed 29 (29 requested) atoms. Cycle 10: After refmac, R = 0.2434 (Rfree = 0.000) for 4420 atoms. Found 13 (53 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.41 2.76 Search for helices and strands: 0 residues in 0 chains, 4508 seeds are put forward Round 1: 368 peptides, 48 chains. Longest chain 28 peptides. Score 0.639 Round 2: 374 peptides, 41 chains. Longest chain 28 peptides. Score 0.706 Round 3: 381 peptides, 42 chains. Longest chain 28 peptides. Score 0.710 Round 4: 374 peptides, 37 chains. Longest chain 28 peptides. Score 0.735 Round 5: 396 peptides, 44 chains. Longest chain 28 peptides. Score 0.719 Taking the results from Round 4 Chains 43, Residues 337, Estimated correctness of the model 81.8 % 8 chains (83 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 235 A and 244 A 40 chains (342 residues) following loop building 7 chains (91 residues) in sequence following loop building ------------------------------------------------------ 14219 reflections ( 99.00 % complete ) and 8768 restraints for refining 4469 atoms. 7175 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2693 (Rfree = 0.000) for 4469 atoms. Found 52 (52 requested) and removed 39 (29 requested) atoms. Cycle 12: After refmac, R = 0.2500 (Rfree = 0.000) for 4470 atoms. Found 22 (51 requested) and removed 30 (29 requested) atoms. Cycle 13: After refmac, R = 0.2457 (Rfree = 0.000) for 4454 atoms. Found 25 (50 requested) and removed 29 (29 requested) atoms. Cycle 14: After refmac, R = 0.2382 (Rfree = 0.000) for 4446 atoms. Found 18 (49 requested) and removed 29 (29 requested) atoms. Cycle 15: After refmac, R = 0.2349 (Rfree = 0.000) for 4427 atoms. Found 17 (48 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.41 2.76 Search for helices and strands: 0 residues in 0 chains, 4529 seeds are put forward Round 1: 346 peptides, 43 chains. Longest chain 28 peptides. Score 0.640 Round 2: 355 peptides, 39 chains. Longest chain 22 peptides. Score 0.690 Round 3: 381 peptides, 45 chains. Longest chain 30 peptides. Score 0.687 Round 4: 363 peptides, 41 chains. Longest chain 22 peptides. Score 0.688 Round 5: 354 peptides, 40 chains. Longest chain 26 peptides. Score 0.680 Taking the results from Round 2 Chains 42, Residues 316, Estimated correctness of the model 75.7 % 8 chains (79 residues) have been docked in sequence ------------------------------------------------------ 14219 reflections ( 99.00 % complete ) and 9222 restraints for refining 4515 atoms. 7742 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2451 (Rfree = 0.000) for 4515 atoms. Found 36 (47 requested) and removed 42 (29 requested) atoms. Cycle 17: After refmac, R = 0.2365 (Rfree = 0.000) for 4493 atoms. Found 18 (47 requested) and removed 33 (29 requested) atoms. Cycle 18: After refmac, R = 0.2301 (Rfree = 0.000) for 4465 atoms. Found 16 (46 requested) and removed 29 (29 requested) atoms. Cycle 19: After refmac, R = 0.2277 (Rfree = 0.000) for 4442 atoms. Found 20 (46 requested) and removed 29 (29 requested) atoms. Cycle 20: After refmac, R = 0.2191 (Rfree = 0.000) for 4430 atoms. Found 12 (46 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.43 2.78 Search for helices and strands: 0 residues in 0 chains, 4516 seeds are put forward Round 1: 330 peptides, 42 chains. Longest chain 28 peptides. Score 0.617 Round 2: 356 peptides, 40 chains. Longest chain 22 peptides. Score 0.683 Round 3: 345 peptides, 42 chains. Longest chain 22 peptides. Score 0.647 Round 4: 333 peptides, 36 chains. Longest chain 20 peptides. Score 0.675 Round 5: 339 peptides, 36 chains. Longest chain 28 peptides. Score 0.686 Taking the results from Round 5 Chains 41, Residues 303, Estimated correctness of the model 75.2 % 8 chains (92 residues) have been docked in sequence ------------------------------------------------------ 14219 reflections ( 99.00 % complete ) and 8982 restraints for refining 4546 atoms. 7450 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2436 (Rfree = 0.000) for 4546 atoms. Found 43 (47 requested) and removed 45 (29 requested) atoms. Cycle 22: After refmac, R = 0.2294 (Rfree = 0.000) for 4525 atoms. Found 29 (47 requested) and removed 29 (29 requested) atoms. Cycle 23: After refmac, R = 0.2191 (Rfree = 0.000) for 4515 atoms. Found 19 (47 requested) and removed 29 (29 requested) atoms. Cycle 24: After refmac, R = 0.2142 (Rfree = 0.000) for 4502 atoms. Found 12 (47 requested) and removed 29 (29 requested) atoms. Cycle 25: After refmac, R = 0.2112 (Rfree = 0.000) for 4478 atoms. Found 15 (46 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.43 2.78 Search for helices and strands: 0 residues in 0 chains, 4591 seeds are put forward Round 1: 328 peptides, 43 chains. Longest chain 23 peptides. Score 0.604 Round 2: 333 peptides, 36 chains. Longest chain 29 peptides. Score 0.675 Round 3: 318 peptides, 38 chains. Longest chain 24 peptides. Score 0.630 Round 4: 322 peptides, 36 chains. Longest chain 21 peptides. Score 0.655 Round 5: 340 peptides, 39 chains. Longest chain 23 peptides. Score 0.663 Taking the results from Round 2 Chains 41, Residues 297, Estimated correctness of the model 73.6 % 7 chains (87 residues) have been docked in sequence ------------------------------------------------------ 14219 reflections ( 99.00 % complete ) and 8895 restraints for refining 4521 atoms. 7390 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2278 (Rfree = 0.000) for 4521 atoms. Found 43 (47 requested) and removed 47 (29 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2137 (Rfree = 0.000) for 4507 atoms. Found 14 (47 requested) and removed 31 (29 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2105 (Rfree = 0.000) for 4485 atoms. Found 17 (46 requested) and removed 29 (29 requested) atoms. Cycle 29: After refmac, R = 0.2068 (Rfree = 0.000) for 4469 atoms. Found 18 (46 requested) and removed 29 (29 requested) atoms. Cycle 30: After refmac, R = 0.2043 (Rfree = 0.000) for 4454 atoms. Found 15 (46 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.44 2.79 Search for helices and strands: 0 residues in 0 chains, 4534 seeds are put forward Round 1: 319 peptides, 36 chains. Longest chain 27 peptides. Score 0.649 Round 2: 339 peptides, 38 chains. Longest chain 28 peptides. Score 0.670 Round 3: 349 peptides, 38 chains. Longest chain 28 peptides. Score 0.687 Round 4: 352 peptides, 39 chains. Longest chain 29 peptides. Score 0.684 Round 5: 346 peptides, 35 chains. Longest chain 26 peptides. Score 0.706 Taking the results from Round 5 Chains 40, Residues 311, Estimated correctness of the model 78.0 % 7 chains (68 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 237 A and 244 A Built loop between residues 252 A and 263 A 38 chains (326 residues) following loop building 5 chains (84 residues) in sequence following loop building ------------------------------------------------------ 14219 reflections ( 99.00 % complete ) and 8937 restraints for refining 4546 atoms. 7413 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2379 (Rfree = 0.000) for 4546 atoms. Found 47 (47 requested) and removed 46 (29 requested) atoms. Cycle 32: After refmac, R = 0.2218 (Rfree = 0.000) for 4539 atoms. Found 34 (46 requested) and removed 32 (29 requested) atoms. Cycle 33: After refmac, R = 0.2190 (Rfree = 0.000) for 4534 atoms. Found 20 (45 requested) and removed 29 (29 requested) atoms. Cycle 34: After refmac, R = 0.2183 (Rfree = 0.000) for 4524 atoms. Found 12 (44 requested) and removed 29 (29 requested) atoms. Cycle 35: After refmac, R = 0.2188 (Rfree = 0.000) for 4502 atoms. Found 13 (42 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.41 2.76 Search for helices and strands: 0 residues in 0 chains, 4557 seeds are put forward Round 1: 298 peptides, 41 chains. Longest chain 27 peptides. Score 0.558 Round 2: 322 peptides, 32 chains. Longest chain 27 peptides. Score 0.689 Round 3: 324 peptides, 34 chains. Longest chain 29 peptides. Score 0.676 Round 4: 332 peptides, 35 chains. Longest chain 47 peptides. Score 0.682 Round 5: 311 peptides, 32 chains. Longest chain 26 peptides. Score 0.669 Taking the results from Round 2 Chains 35, Residues 290, Estimated correctness of the model 75.6 % 7 chains (72 residues) have been docked in sequence ------------------------------------------------------ 14219 reflections ( 99.00 % complete ) and 9240 restraints for refining 4547 atoms. 7882 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2344 (Rfree = 0.000) for 4547 atoms. Found 41 (41 requested) and removed 54 (29 requested) atoms. Cycle 37: After refmac, R = 0.2221 (Rfree = 0.000) for 4529 atoms. Found 23 (41 requested) and removed 30 (29 requested) atoms. Cycle 38: After refmac, R = 0.2173 (Rfree = 0.000) for 4517 atoms. Found 21 (41 requested) and removed 30 (29 requested) atoms. Cycle 39: After refmac, R = 0.2124 (Rfree = 0.000) for 4507 atoms. Found 26 (41 requested) and removed 30 (29 requested) atoms. Cycle 40: After refmac, R = 0.2075 (Rfree = 0.000) for 4500 atoms. Found 20 (41 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.43 2.78 Search for helices and strands: 0 residues in 0 chains, 4580 seeds are put forward Round 1: 289 peptides, 36 chains. Longest chain 26 peptides. Score 0.588 Round 2: 309 peptides, 33 chains. Longest chain 28 peptides. Score 0.657 Round 3: 319 peptides, 37 chains. Longest chain 28 peptides. Score 0.641 Round 4: 322 peptides, 37 chains. Longest chain 28 peptides. Score 0.646 Round 5: 303 peptides, 38 chains. Longest chain 20 peptides. Score 0.599 Taking the results from Round 2 Chains 36, Residues 276, Estimated correctness of the model 70.8 % 7 chains (77 residues) have been docked in sequence ------------------------------------------------------ 14219 reflections ( 99.00 % complete ) and 8985 restraints for refining 4547 atoms. 7629 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2218 (Rfree = 0.000) for 4547 atoms. Found 37 (41 requested) and removed 36 (29 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2108 (Rfree = 0.000) for 4543 atoms. Found 22 (41 requested) and removed 31 (29 requested) atoms. Cycle 43: After refmac, R = 0.2100 (Rfree = 0.000) for 4529 atoms. Found 13 (41 requested) and removed 29 (29 requested) atoms. Cycle 44: After refmac, R = 0.2105 (Rfree = 0.000) for 4509 atoms. Found 15 (41 requested) and removed 29 (29 requested) atoms. Cycle 45: After refmac, R = 0.2101 (Rfree = 0.000) for 4492 atoms. Found 19 (41 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.44 2.79 Search for helices and strands: 0 residues in 0 chains, 4571 seeds are put forward Round 1: 255 peptides, 37 chains. Longest chain 18 peptides. Score 0.496 Round 2: 284 peptides, 34 chains. Longest chain 23 peptides. Score 0.597 Round 3: 289 peptides, 37 chains. Longest chain 26 peptides. Score 0.578 Round 4: 300 peptides, 37 chains. Longest chain 22 peptides. Score 0.602 Round 5: 291 peptides, 39 chains. Longest chain 27 peptides. Score 0.562 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 263, Estimated correctness of the model 61.7 % 5 chains (57 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 1vk3-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 237 A and 251 A 37 chains (274 residues) following loop building 4 chains (70 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14219 reflections ( 99.00 % complete ) and 9226 restraints for refining 4547 atoms. 7954 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2326 (Rfree = 0.000) for 4547 atoms. Found 0 (41 requested) and removed 8 (29 requested) atoms. Cycle 47: After refmac, R = 0.2244 (Rfree = 0.000) for 4531 atoms. Found 0 (41 requested) and removed 3 (29 requested) atoms. Cycle 48: After refmac, R = 0.2216 (Rfree = 0.000) for 4526 atoms. Found 0 (41 requested) and removed 3 (29 requested) atoms. Cycle 49: After refmac, R = 0.2237 (Rfree = 0.000) for 4520 atoms. Found 0 (41 requested) and removed 2 (29 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB TimeTaking 65.29