Sun 23 Dec 22:22:56 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 2fg0-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fg0-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fg0-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-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/2fg0-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-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 22:23:06 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/2fg0-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-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 511 and 0 Target number of residues in the AU: 511 Target solvent content: 0.6364 Checking the provided sequence file Detected sequence length: 246 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 492 Adjusted target solvent content: 0.65 Input MTZ file: 2fg0-3.6-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: 92 Cell parameters: 124.890 124.890 97.540 90.000 90.000 90.000 Input sequence file: 2fg0-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3936 target number of atoms Had to go as low as 0.75 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: 88.311 3.600 Wilson plot Bfac: 69.79 9346 reflections ( 99.70 % complete ) and 0 restraints for refining 4343 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.2977 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2852 (Rfree = 0.000) for 4343 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 2.80 Search for helices and strands: 0 residues in 0 chains, 4426 seeds are put forward NCS extension: 0 residues added, 4426 seeds are put forward Round 1: 292 peptides, 42 chains. Longest chain 18 peptides. Score 0.462 Round 2: 331 peptides, 35 chains. Longest chain 26 peptides. Score 0.592 Round 3: 337 peptides, 29 chains. Longest chain 41 peptides. Score 0.646 Round 4: 331 peptides, 33 chains. Longest chain 21 peptides. Score 0.607 Round 5: 336 peptides, 28 chains. Longest chain 48 peptides. Score 0.651 Taking the results from Round 5 Chains 34, Residues 308, Estimated correctness of the model 33.5 % 5 chains (64 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6949 restraints for refining 3566 atoms. 5513 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2756 (Rfree = 0.000) for 3566 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 2: After refmac, R = 0.2647 (Rfree = 0.000) for 3497 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 3: After refmac, R = 0.2434 (Rfree = 0.000) for 3448 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 4: After refmac, R = 0.2382 (Rfree = 0.000) for 3412 atoms. Found 15 (22 requested) and removed 21 (11 requested) atoms. Cycle 5: After refmac, R = 0.2225 (Rfree = 0.000) for 3393 atoms. Found 4 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 2.78 Search for helices and strands: 0 residues in 0 chains, 3490 seeds are put forward NCS extension: 32 residues added (9 deleted due to clashes), 3522 seeds are put forward Round 1: 315 peptides, 33 chains. Longest chain 24 peptides. Score 0.581 Round 2: 324 peptides, 32 chains. Longest chain 32 peptides. Score 0.603 Round 3: 338 peptides, 31 chains. Longest chain 38 peptides. Score 0.633 Round 4: 339 peptides, 30 chains. Longest chain 39 peptides. Score 0.642 Round 5: 325 peptides, 29 chains. Longest chain 39 peptides. Score 0.628 Taking the results from Round 4 Chains 34, Residues 309, Estimated correctness of the model 30.3 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7075 restraints for refining 3567 atoms. 5691 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2626 (Rfree = 0.000) for 3567 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 7: After refmac, R = 0.2477 (Rfree = 0.000) for 3531 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 8: After refmac, R = 0.2427 (Rfree = 0.000) for 3520 atoms. Found 13 (22 requested) and removed 13 (11 requested) atoms. Cycle 9: After refmac, R = 0.2416 (Rfree = 0.000) for 3511 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. Cycle 10: After refmac, R = 0.2277 (Rfree = 0.000) for 3500 atoms. Found 1 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 2.81 Search for helices and strands: 0 residues in 0 chains, 3591 seeds are put forward NCS extension: 24 residues added (9 deleted due to clashes), 3615 seeds are put forward Round 1: 317 peptides, 35 chains. Longest chain 35 peptides. Score 0.568 Round 2: 328 peptides, 34 chains. Longest chain 28 peptides. Score 0.595 Round 3: 320 peptides, 32 chains. Longest chain 23 peptides. Score 0.597 Round 4: 324 peptides, 34 chains. Longest chain 21 peptides. Score 0.588 Round 5: 347 peptides, 30 chains. Longest chain 35 peptides. Score 0.653 Taking the results from Round 5 Chains 32, Residues 317, Estimated correctness of the model 34.2 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7268 restraints for refining 3567 atoms. 5851 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2696 (Rfree = 0.000) for 3567 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 12: After refmac, R = 0.2501 (Rfree = 0.000) for 3537 atoms. Found 19 (22 requested) and removed 16 (11 requested) atoms. Cycle 13: After refmac, R = 0.2390 (Rfree = 0.000) for 3519 atoms. Found 14 (22 requested) and removed 14 (11 requested) atoms. Cycle 14: After refmac, R = 0.2344 (Rfree = 0.000) for 3501 atoms. Found 17 (22 requested) and removed 19 (11 requested) atoms. Cycle 15: After refmac, R = 0.2328 (Rfree = 0.000) for 3485 atoms. Found 15 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 2.79 Search for helices and strands: 0 residues in 0 chains, 3613 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 3638 seeds are put forward Round 1: 322 peptides, 36 chains. Longest chain 24 peptides. Score 0.569 Round 2: 321 peptides, 34 chains. Longest chain 22 peptides. Score 0.583 Round 3: 340 peptides, 30 chains. Longest chain 31 peptides. Score 0.643 Round 4: 335 peptides, 31 chains. Longest chain 48 peptides. Score 0.628 Round 5: 341 peptides, 26 chains. Longest chain 45 peptides. Score 0.673 Taking the results from Round 5 Chains 30, Residues 315, Estimated correctness of the model 41.0 % 4 chains (114 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6522 restraints for refining 3568 atoms. 4843 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2638 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 40 (11 requested) atoms. Cycle 17: After refmac, R = 0.2458 (Rfree = 0.000) for 3515 atoms. Found 14 (22 requested) and removed 15 (11 requested) atoms. Cycle 18: After refmac, R = 0.2382 (Rfree = 0.000) for 3502 atoms. Found 8 (22 requested) and removed 14 (11 requested) atoms. Cycle 19: After refmac, R = 0.2351 (Rfree = 0.000) for 3476 atoms. Found 4 (22 requested) and removed 15 (11 requested) atoms. Cycle 20: After refmac, R = 0.2341 (Rfree = 0.000) for 3456 atoms. Found 7 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 2.78 Search for helices and strands: 0 residues in 0 chains, 3558 seeds are put forward NCS extension: 43 residues added (9 deleted due to clashes), 3601 seeds are put forward Round 1: 298 peptides, 34 chains. Longest chain 26 peptides. Score 0.543 Round 2: 325 peptides, 31 chains. Longest chain 32 peptides. Score 0.613 Round 3: 333 peptides, 32 chains. Longest chain 30 peptides. Score 0.618 Round 4: 325 peptides, 35 chains. Longest chain 37 peptides. Score 0.582 Round 5: 333 peptides, 36 chains. Longest chain 27 peptides. Score 0.587 Taking the results from Round 3 Chains 33, Residues 301, Estimated correctness of the model 21.6 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7382 restraints for refining 3568 atoms. 6056 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2600 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 22: After refmac, R = 0.2679 (Rfree = 0.000) for 3543 atoms. Found 19 (22 requested) and removed 23 (11 requested) atoms. Cycle 23: After refmac, R = 0.2735 (Rfree = 0.000) for 3533 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 24: After refmac, R = 0.2468 (Rfree = 0.000) for 3519 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.2403 (Rfree = 0.000) for 3516 atoms. Found 20 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 2.80 Search for helices and strands: 0 residues in 0 chains, 3622 seeds are put forward NCS extension: 36 residues added (11 deleted due to clashes), 3658 seeds are put forward Round 1: 306 peptides, 40 chains. Longest chain 20 peptides. Score 0.507 Round 2: 325 peptides, 34 chains. Longest chain 29 peptides. Score 0.590 Round 3: 320 peptides, 32 chains. Longest chain 24 peptides. Score 0.597 Round 4: 325 peptides, 32 chains. Longest chain 31 peptides. Score 0.605 Round 5: 334 peptides, 29 chains. Longest chain 27 peptides. Score 0.641 Taking the results from Round 5 Chains 31, Residues 305, Estimated correctness of the model 30.0 % 3 chains (53 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7180 restraints for refining 3568 atoms. 5770 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2578 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 27: After refmac, R = 0.2512 (Rfree = 0.000) for 3531 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 28: After refmac, R = 0.2433 (Rfree = 0.000) for 3508 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 29: After refmac, R = 0.2342 (Rfree = 0.000) for 3499 atoms. Found 20 (22 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.2369 (Rfree = 0.000) for 3488 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 2.75 Search for helices and strands: 0 residues in 0 chains, 3593 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 3615 seeds are put forward Round 1: 306 peptides, 37 chains. Longest chain 28 peptides. Score 0.532 Round 2: 329 peptides, 34 chains. Longest chain 40 peptides. Score 0.596 Round 3: 335 peptides, 31 chains. Longest chain 39 peptides. Score 0.628 Round 4: 318 peptides, 33 chains. Longest chain 28 peptides. Score 0.586 Round 5: 319 peptides, 31 chains. Longest chain 34 peptides. Score 0.603 Taking the results from Round 3 Chains 35, Residues 304, Estimated correctness of the model 25.3 % 4 chains (66 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6998 restraints for refining 3568 atoms. 5563 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2599 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 32: After refmac, R = 0.2429 (Rfree = 0.000) for 3524 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 33: After refmac, R = 0.2385 (Rfree = 0.000) for 3518 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 34: After refmac, R = 0.2387 (Rfree = 0.000) for 3509 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 35: After refmac, R = 0.2287 (Rfree = 0.000) for 3505 atoms. Found 15 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 2.79 Search for helices and strands: 0 residues in 0 chains, 3606 seeds are put forward NCS extension: 9 residues added (9 deleted due to clashes), 3615 seeds are put forward Round 1: 318 peptides, 42 chains. Longest chain 28 peptides. Score 0.512 Round 2: 339 peptides, 31 chains. Longest chain 43 peptides. Score 0.634 Round 3: 315 peptides, 35 chains. Longest chain 30 peptides. Score 0.565 Round 4: 319 peptides, 30 chains. Longest chain 38 peptides. Score 0.611 Round 5: 324 peptides, 30 chains. Longest chain 39 peptides. Score 0.619 Taking the results from Round 2 Chains 33, Residues 308, Estimated correctness of the model 27.5 % 5 chains (102 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6725 restraints for refining 3568 atoms. 5109 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2454 (Rfree = 0.000) for 3568 atoms. Found 20 (22 requested) and removed 17 (11 requested) atoms. Cycle 37: After refmac, R = 0.2354 (Rfree = 0.000) for 3543 atoms. Found 17 (22 requested) and removed 16 (11 requested) atoms. Cycle 38: After refmac, R = 0.2322 (Rfree = 0.000) for 3528 atoms. Found 21 (22 requested) and removed 15 (11 requested) atoms. Cycle 39: After refmac, R = 0.2253 (Rfree = 0.000) for 3521 atoms. Found 17 (22 requested) and removed 13 (11 requested) atoms. Cycle 40: After refmac, R = 0.2253 (Rfree = 0.000) for 3517 atoms. Found 18 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 2.77 Search for helices and strands: 0 residues in 0 chains, 3627 seeds are put forward NCS extension: 36 residues added (9 deleted due to clashes), 3663 seeds are put forward Round 1: 305 peptides, 36 chains. Longest chain 29 peptides. Score 0.539 Round 2: 356 peptides, 33 chains. Longest chain 45 peptides. Score 0.645 Round 3: 345 peptides, 37 chains. Longest chain 34 peptides. Score 0.599 Round 4: 320 peptides, 31 chains. Longest chain 47 peptides. Score 0.605 Round 5: 318 peptides, 33 chains. Longest chain 31 peptides. Score 0.586 Taking the results from Round 2 Chains 35, Residues 323, Estimated correctness of the model 31.4 % 6 chains (105 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6530 restraints for refining 3568 atoms. 4871 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2540 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 42: After refmac, R = 0.2296 (Rfree = 0.000) for 3540 atoms. Found 10 (22 requested) and removed 20 (11 requested) atoms. Cycle 43: After refmac, R = 0.2282 (Rfree = 0.000) for 3522 atoms. Found 12 (22 requested) and removed 20 (11 requested) atoms. Cycle 44: After refmac, R = 0.2269 (Rfree = 0.000) for 3505 atoms. Found 13 (22 requested) and removed 14 (11 requested) atoms. Cycle 45: After refmac, R = 0.2224 (Rfree = 0.000) for 3499 atoms. Found 12 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 2.77 Search for helices and strands: 0 residues in 0 chains, 3622 seeds are put forward NCS extension: 26 residues added (11 deleted due to clashes), 3648 seeds are put forward Round 1: 278 peptides, 41 chains. Longest chain 23 peptides. Score 0.443 Round 2: 305 peptides, 32 chains. Longest chain 30 peptides. Score 0.572 Round 3: 307 peptides, 28 chains. Longest chain 45 peptides. Score 0.607 Round 4: 318 peptides, 33 chains. Longest chain 30 peptides. Score 0.586 Round 5: 330 peptides, 33 chains. Longest chain 28 peptides. Score 0.605 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 279, Estimated correctness of the model 17.4 % 5 chains (105 residues) have been docked in sequence Sequence coverage is 37 % Consider running further cycles of model building using 2fg0-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (279 residues) following loop building 5 chains (105 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9346 reflections ( 99.70 % complete ) and 6943 restraints for refining 3568 atoms. 5461 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2716 (Rfree = 0.000) for 3568 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2553 (Rfree = 0.000) for 3539 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2495 (Rfree = 0.000) for 3524 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2410 (Rfree = 0.000) for 3507 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... TimeTaking 63.73