Sun 23 Dec 22:22:43 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 2fg0-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fg0-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fg0-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-3.4-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/2fg0-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-3.4-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 22:22:52 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/2fg0-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-3.4-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 528 and 0 Target number of residues in the AU: 528 Target solvent content: 0.6243 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: 2fg0-3.4-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: 2fg0-3.4-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 3.400 Wilson plot Bfac: 63.58 11059 reflections ( 99.74 % complete ) and 0 restraints for refining 4389 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.2894 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3175 (Rfree = 0.000) for 4389 atoms. Found 33 (33 requested) and removed 36 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 4468 seeds are put forward NCS extension: 0 residues added, 4468 seeds are put forward Round 1: 269 peptides, 47 chains. Longest chain 12 peptides. Score 0.367 Round 2: 329 peptides, 40 chains. Longest chain 25 peptides. Score 0.549 Round 3: 332 peptides, 38 chains. Longest chain 25 peptides. Score 0.570 Round 4: 342 peptides, 28 chains. Longest chain 42 peptides. Score 0.660 Round 5: 336 peptides, 28 chains. Longest chain 39 peptides. Score 0.651 Taking the results from Round 4 Chains 29, Residues 314, Estimated correctness of the model 47.0 % 3 chains (62 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 7032 restraints for refining 3577 atoms. 5562 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2896 (Rfree = 0.000) for 3577 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 2: After refmac, R = 0.2826 (Rfree = 0.000) for 3469 atoms. Found 26 (26 requested) and removed 28 (13 requested) atoms. Cycle 3: After refmac, R = 0.2806 (Rfree = 0.000) for 3425 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2722 (Rfree = 0.000) for 3413 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 5: After refmac, R = 0.2542 (Rfree = 0.000) for 3392 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 2.74 Search for helices and strands: 0 residues in 0 chains, 3495 seeds are put forward NCS extension: 31 residues added (8 deleted due to clashes), 3526 seeds are put forward Round 1: 317 peptides, 41 chains. Longest chain 21 peptides. Score 0.519 Round 2: 333 peptides, 31 chains. Longest chain 29 peptides. Score 0.625 Round 3: 352 peptides, 33 chains. Longest chain 26 peptides. Score 0.639 Round 4: 354 peptides, 28 chains. Longest chain 45 peptides. Score 0.677 Round 5: 349 peptides, 28 chains. Longest chain 30 peptides. Score 0.670 Taking the results from Round 4 Chains 34, Residues 326, Estimated correctness of the model 51.8 % 8 chains (143 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6172 restraints for refining 3577 atoms. 4339 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2949 (Rfree = 0.000) for 3577 atoms. Found 27 (27 requested) and removed 41 (13 requested) atoms. Cycle 7: After refmac, R = 0.2789 (Rfree = 0.000) for 3509 atoms. Found 26 (26 requested) and removed 17 (13 requested) atoms. Cycle 8: After refmac, R = 0.2778 (Rfree = 0.000) for 3495 atoms. Found 25 (26 requested) and removed 29 (13 requested) atoms. Cycle 9: After refmac, R = 0.2744 (Rfree = 0.000) for 3476 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 10: After refmac, R = 0.2669 (Rfree = 0.000) for 3456 atoms. Found 26 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 2.71 Search for helices and strands: 0 residues in 0 chains, 3575 seeds are put forward NCS extension: 26 residues added (17 deleted due to clashes), 3601 seeds are put forward Round 1: 339 peptides, 37 chains. Longest chain 32 peptides. Score 0.589 Round 2: 347 peptides, 33 chains. Longest chain 27 peptides. Score 0.632 Round 3: 337 peptides, 29 chains. Longest chain 40 peptides. Score 0.646 Round 4: 344 peptides, 34 chains. Longest chain 30 peptides. Score 0.620 Round 5: 355 peptides, 29 chains. Longest chain 38 peptides. Score 0.672 Taking the results from Round 5 Chains 34, Residues 326, Estimated correctness of the model 50.4 % 6 chains (118 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6503 restraints for refining 3579 atoms. 4762 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2821 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 12: After refmac, R = 0.2699 (Rfree = 0.000) for 3535 atoms. Found 24 (26 requested) and removed 20 (13 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2622 (Rfree = 0.000) for 3525 atoms. Found 22 (26 requested) and removed 22 (13 requested) atoms. Cycle 14: After refmac, R = 0.2444 (Rfree = 0.000) for 3508 atoms. Found 11 (26 requested) and removed 19 (13 requested) atoms. Cycle 15: After refmac, R = 0.2377 (Rfree = 0.000) for 3484 atoms. Found 9 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 2.72 Search for helices and strands: 0 residues in 0 chains, 3586 seeds are put forward NCS extension: 30 residues added (11 deleted due to clashes), 3616 seeds are put forward Round 1: 337 peptides, 37 chains. Longest chain 34 peptides. Score 0.586 Round 2: 352 peptides, 32 chains. Longest chain 38 peptides. Score 0.646 Round 3: 347 peptides, 32 chains. Longest chain 38 peptides. Score 0.639 Round 4: 342 peptides, 33 chains. Longest chain 33 peptides. Score 0.624 Round 5: 332 peptides, 31 chains. Longest chain 35 peptides. Score 0.624 Taking the results from Round 2 Chains 34, Residues 320, Estimated correctness of the model 43.0 % 5 chains (101 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6676 restraints for refining 3579 atoms. 5041 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2693 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 17: After refmac, R = 0.2626 (Rfree = 0.000) for 3556 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 18: After refmac, R = 0.2574 (Rfree = 0.000) for 3546 atoms. Found 26 (26 requested) and removed 17 (13 requested) atoms. Cycle 19: After refmac, R = 0.2513 (Rfree = 0.000) for 3537 atoms. Found 22 (26 requested) and removed 21 (13 requested) atoms. Cycle 20: After refmac, R = 0.2469 (Rfree = 0.000) for 3524 atoms. Found 24 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 3628 seeds are put forward NCS extension: 24 residues added (24 deleted due to clashes), 3652 seeds are put forward Round 1: 314 peptides, 38 chains. Longest chain 25 peptides. Score 0.538 Round 2: 347 peptides, 36 chains. Longest chain 20 peptides. Score 0.610 Round 3: 350 peptides, 36 chains. Longest chain 38 peptides. Score 0.615 Round 4: 359 peptides, 30 chains. Longest chain 40 peptides. Score 0.670 Round 5: 359 peptides, 30 chains. Longest chain 38 peptides. Score 0.670 Taking the results from Round 5 Chains 31, Residues 329, Estimated correctness of the model 49.8 % 4 chains (92 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6737 restraints for refining 3579 atoms. 5077 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2765 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 22: After refmac, R = 0.2631 (Rfree = 0.000) for 3540 atoms. Found 26 (26 requested) and removed 39 (13 requested) atoms. Cycle 23: After refmac, R = 0.2516 (Rfree = 0.000) for 3510 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 24: After refmac, R = 0.2317 (Rfree = 0.000) for 3500 atoms. Found 18 (26 requested) and removed 15 (13 requested) atoms. Cycle 25: After refmac, R = 0.2228 (Rfree = 0.000) for 3493 atoms. Found 9 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 3604 seeds are put forward NCS extension: 24 residues added (7 deleted due to clashes), 3628 seeds are put forward Round 1: 328 peptides, 40 chains. Longest chain 23 peptides. Score 0.547 Round 2: 339 peptides, 35 chains. Longest chain 25 peptides. Score 0.605 Round 3: 351 peptides, 35 chains. Longest chain 29 peptides. Score 0.623 Round 4: 353 peptides, 37 chains. Longest chain 26 peptides. Score 0.612 Round 5: 351 peptides, 30 chains. Longest chain 27 peptides. Score 0.659 Taking the results from Round 5 Chains 33, Residues 321, Estimated correctness of the model 46.7 % 5 chains (72 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6935 restraints for refining 3579 atoms. 5424 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2709 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 27: After refmac, R = 0.2684 (Rfree = 0.000) for 3555 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 28: After refmac, R = 0.2698 (Rfree = 0.000) for 3545 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 29: After refmac, R = 0.2617 (Rfree = 0.000) for 3531 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 30: After refmac, R = 0.2702 (Rfree = 0.000) for 3523 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 2.77 Search for helices and strands: 0 residues in 0 chains, 3615 seeds are put forward NCS extension: 24 residues added (11 deleted due to clashes), 3639 seeds are put forward Round 1: 320 peptides, 38 chains. Longest chain 28 peptides. Score 0.549 Round 2: 355 peptides, 30 chains. Longest chain 37 peptides. Score 0.665 Round 3: 339 peptides, 32 chains. Longest chain 30 peptides. Score 0.627 Round 4: 346 peptides, 35 chains. Longest chain 40 peptides. Score 0.616 Round 5: 345 peptides, 35 chains. Longest chain 29 peptides. Score 0.614 Taking the results from Round 2 Chains 32, Residues 325, Estimated correctness of the model 48.4 % 6 chains (80 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6716 restraints for refining 3578 atoms. 5112 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2733 (Rfree = 0.000) for 3578 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 32: After refmac, R = 0.2708 (Rfree = 0.000) for 3562 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 33: After refmac, R = 0.2702 (Rfree = 0.000) for 3557 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 34: After refmac, R = 0.2590 (Rfree = 0.000) for 3552 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 35: After refmac, R = 0.2493 (Rfree = 0.000) for 3546 atoms. Found 23 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.74 Search for helices and strands: 0 residues in 0 chains, 3650 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 3683 seeds are put forward Round 1: 303 peptides, 36 chains. Longest chain 22 peptides. Score 0.535 Round 2: 315 peptides, 36 chains. Longest chain 31 peptides. Score 0.557 Round 3: 349 peptides, 33 chains. Longest chain 39 peptides. Score 0.635 Round 4: 341 peptides, 32 chains. Longest chain 32 peptides. Score 0.630 Round 5: 346 peptides, 34 chains. Longest chain 29 peptides. Score 0.623 Taking the results from Round 3 Chains 40, Residues 316, Estimated correctness of the model 39.7 % 5 chains (72 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6857 restraints for refining 3579 atoms. 5354 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2634 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 37: After refmac, R = 0.2538 (Rfree = 0.000) for 3556 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 38: After refmac, R = 0.2490 (Rfree = 0.000) for 3543 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 39: After refmac, R = 0.2496 (Rfree = 0.000) for 3536 atoms. Found 26 (26 requested) and removed 19 (13 requested) atoms. Cycle 40: After refmac, R = 0.2438 (Rfree = 0.000) for 3533 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 3662 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3693 seeds are put forward Round 1: 296 peptides, 41 chains. Longest chain 16 peptides. Score 0.479 Round 2: 319 peptides, 37 chains. Longest chain 25 peptides. Score 0.555 Round 3: 335 peptides, 31 chains. Longest chain 31 peptides. Score 0.628 Round 4: 314 peptides, 37 chains. Longest chain 23 peptides. Score 0.547 Round 5: 337 peptides, 33 chains. Longest chain 29 peptides. Score 0.616 Taking the results from Round 3 Chains 32, Residues 304, Estimated correctness of the model 37.5 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 7217 restraints for refining 3579 atoms. 5869 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2564 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 42: After refmac, R = 0.2558 (Rfree = 0.000) for 3557 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 43: After refmac, R = 0.2420 (Rfree = 0.000) for 3542 atoms. Found 18 (26 requested) and removed 15 (13 requested) atoms. Cycle 44: After refmac, R = 0.2412 (Rfree = 0.000) for 3533 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 45: After refmac, R = 0.2380 (Rfree = 0.000) for 3538 atoms. Found 25 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 2.74 Search for helices and strands: 0 residues in 0 chains, 3673 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 3703 seeds are put forward Round 1: 287 peptides, 40 chains. Longest chain 17 peptides. Score 0.470 Round 2: 342 peptides, 42 chains. Longest chain 26 peptides. Score 0.555 Round 3: 344 peptides, 42 chains. Longest chain 22 peptides. Score 0.559 Round 4: 351 peptides, 37 chains. Longest chain 40 peptides. Score 0.609 Round 5: 354 peptides, 32 chains. Longest chain 39 peptides. Score 0.649 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 322, Estimated correctness of the model 43.8 % 5 chains (67 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 2fg0-3_warpNtrace.pdb as input Building loops using Loopy2018 40 chains (322 residues) following loop building 5 chains (67 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11059 reflections ( 99.74 % complete ) and 6908 restraints for refining 3579 atoms. 5395 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2540 (Rfree = 0.000) for 3579 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2529 (Rfree = 0.000) for 3539 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2511 (Rfree = 0.000) for 3520 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2444 (Rfree = 0.000) for 3504 atoms. TimeTaking 64.9