Starting phenix.real_space_refine on Wed Feb 21 10:16:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrb_32721/02_2024/7wrb_32721.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrb_32721/02_2024/7wrb_32721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrb_32721/02_2024/7wrb_32721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrb_32721/02_2024/7wrb_32721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrb_32721/02_2024/7wrb_32721.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrb_32721/02_2024/7wrb_32721.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 C 19756 2.51 5 N 5040 2.21 5 O 5436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 784": "NH1" <-> "NH2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 851": "NH1" <-> "NH2" Residue "A ARG 885": "NH1" <-> "NH2" Residue "A ARG 1008": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B ARG 784": "NH1" <-> "NH2" Residue "B ARG 816": "NH1" <-> "NH2" Residue "B ARG 842": "NH1" <-> "NH2" Residue "B ARG 851": "NH1" <-> "NH2" Residue "B ARG 885": "NH1" <-> "NH2" Residue "B ARG 1008": "NH1" <-> "NH2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C ARG 558": "NH1" <-> "NH2" Residue "C ARG 784": "NH1" <-> "NH2" Residue "C ARG 816": "NH1" <-> "NH2" Residue "C ARG 842": "NH1" <-> "NH2" Residue "C ARG 851": "NH1" <-> "NH2" Residue "C ARG 885": "NH1" <-> "NH2" Residue "C ARG 1008": "NH1" <-> "NH2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D ARG 558": "NH1" <-> "NH2" Residue "D ARG 784": "NH1" <-> "NH2" Residue "D ARG 816": "NH1" <-> "NH2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 851": "NH1" <-> "NH2" Residue "D ARG 885": "NH1" <-> "NH2" Residue "D ARG 1008": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30376 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "B" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "C" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "D" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.71, per 1000 atoms: 0.52 Number of scatterers: 30376 At special positions: 0 Unit cell: (153.114, 153.114, 157.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 140 16.00 O 5436 8.00 N 5040 7.00 C 19756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.02 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.02 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.02 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.25 Conformation dependent library (CDL) restraints added in 5.6 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 8 sheets defined 71.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 204 removed outlier: 3.692A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 removed outlier: 4.044A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.728A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.785A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 385 removed outlier: 4.512A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 removed outlier: 5.968A pdb=" N HIS A 389 " --> pdb=" O GLU A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.697A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.507A pdb=" N GLN A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.810A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.853A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 582 removed outlier: 3.719A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 607 through 636 removed outlier: 4.081A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 644 Processing helix chain 'A' and resid 655 through 663 removed outlier: 3.900A pdb=" N ALA A 660 " --> pdb=" O CYS A 656 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.767A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.754A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.992A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.755A pdb=" N VAL A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 821 through 847 removed outlier: 3.824A pdb=" N ARG A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 863 through 890 removed outlier: 3.918A pdb=" N ALA A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 904 removed outlier: 3.929A pdb=" N SER A 902 " --> pdb=" O TRP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 925 through 929 removed outlier: 4.115A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 929' Processing helix chain 'A' and resid 952 through 969 Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 969 through 1007 removed outlier: 3.887A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1015 through 1030 Processing helix chain 'A' and resid 1046 through 1070 removed outlier: 3.906A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A1070 " --> pdb=" O LYS A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1104 removed outlier: 3.607A pdb=" N MET A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 204 removed outlier: 3.692A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 309 through 322 removed outlier: 4.044A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.728A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.785A pdb=" N ARG B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 370 through 385 removed outlier: 4.513A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 removed outlier: 5.969A pdb=" N HIS B 389 " --> pdb=" O GLU B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.698A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.506A pdb=" N GLN B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.810A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.854A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.718A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 607 through 636 removed outlier: 4.081A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 644 Processing helix chain 'B' and resid 655 through 663 removed outlier: 3.901A pdb=" N ALA B 660 " --> pdb=" O CYS B 656 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.768A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.755A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.992A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 758 removed outlier: 3.755A pdb=" N VAL B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 817 Processing helix chain 'B' and resid 821 through 847 removed outlier: 3.823A pdb=" N ARG B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 838 " --> pdb=" O LEU B 834 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 853 through 860 Processing helix chain 'B' and resid 863 through 890 removed outlier: 3.919A pdb=" N ALA B 884 " --> pdb=" O ALA B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 904 removed outlier: 3.930A pdb=" N SER B 902 " --> pdb=" O TRP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 925 through 929 removed outlier: 4.115A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 925 through 929' Processing helix chain 'B' and resid 952 through 969 Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 969 through 1007 removed outlier: 3.887A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1015 through 1030 Processing helix chain 'B' and resid 1046 through 1070 removed outlier: 3.907A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B1070 " --> pdb=" O LYS B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1104 removed outlier: 3.607A pdb=" N MET B1078 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS B1104 " --> pdb=" O ALA B1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 204 removed outlier: 3.693A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 removed outlier: 4.044A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 removed outlier: 3.728A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.785A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 370 through 385 removed outlier: 4.513A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 removed outlier: 5.969A pdb=" N HIS C 389 " --> pdb=" O GLU C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 402 through 418 removed outlier: 3.697A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.506A pdb=" N GLN C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.809A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 532 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.854A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.719A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 607 through 636 removed outlier: 4.081A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 644 Processing helix chain 'C' and resid 655 through 663 removed outlier: 3.901A pdb=" N ALA C 660 " --> pdb=" O CYS C 656 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 670 removed outlier: 3.768A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.754A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 3.992A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 758 removed outlier: 3.755A pdb=" N VAL C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 796 through 817 Processing helix chain 'C' and resid 821 through 847 removed outlier: 3.823A pdb=" N ARG C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 838 " --> pdb=" O LEU C 834 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 850 No H-bonds generated for 'chain 'C' and resid 848 through 850' Processing helix chain 'C' and resid 853 through 860 Processing helix chain 'C' and resid 863 through 890 removed outlier: 3.918A pdb=" N ALA C 884 " --> pdb=" O ALA C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 904 removed outlier: 3.929A pdb=" N SER C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 925 through 929 removed outlier: 4.114A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS C 929 " --> pdb=" O PHE C 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 925 through 929' Processing helix chain 'C' and resid 952 through 969 Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 969 through 1007 removed outlier: 3.887A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1014 No H-bonds generated for 'chain 'C' and resid 1012 through 1014' Processing helix chain 'C' and resid 1015 through 1030 Processing helix chain 'C' and resid 1046 through 1070 removed outlier: 3.906A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS C1070 " --> pdb=" O LYS C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1104 removed outlier: 3.608A pdb=" N MET C1078 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C1104 " --> pdb=" O ALA C1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 204 removed outlier: 3.693A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 309 through 322 removed outlier: 4.044A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 343 removed outlier: 3.729A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.786A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 370 through 385 removed outlier: 4.513A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 389 removed outlier: 5.970A pdb=" N HIS D 389 " --> pdb=" O GLU D 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 389' Processing helix chain 'D' and resid 402 through 418 removed outlier: 3.698A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 removed outlier: 3.506A pdb=" N GLN D 429 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.810A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 532 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.854A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 582 removed outlier: 3.718A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 607 through 636 removed outlier: 4.081A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 644 Processing helix chain 'D' and resid 655 through 663 removed outlier: 3.899A pdb=" N ALA D 660 " --> pdb=" O CYS D 656 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.768A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.754A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.992A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 733 through 758 removed outlier: 3.755A pdb=" N VAL D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 796 through 817 Processing helix chain 'D' and resid 821 through 847 removed outlier: 3.823A pdb=" N ARG D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 838 " --> pdb=" O LEU D 834 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 853 through 860 Processing helix chain 'D' and resid 863 through 890 removed outlier: 3.919A pdb=" N ALA D 884 " --> pdb=" O ALA D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 904 removed outlier: 3.929A pdb=" N SER D 902 " --> pdb=" O TRP D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 925 through 929 removed outlier: 4.115A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS D 929 " --> pdb=" O PHE D 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 925 through 929' Processing helix chain 'D' and resid 952 through 969 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 969 through 1007 removed outlier: 3.886A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1014 No H-bonds generated for 'chain 'D' and resid 1012 through 1014' Processing helix chain 'D' and resid 1015 through 1030 Processing helix chain 'D' and resid 1046 through 1070 removed outlier: 3.907A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS D1070 " --> pdb=" O LYS D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1104 removed outlier: 3.607A pdb=" N MET D1078 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS D1104 " --> pdb=" O ALA D1100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 121 removed outlier: 6.265A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU A 330 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA A 305 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'B' and resid 116 through 121 removed outlier: 6.264A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL B 328 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU B 330 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA B 305 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AA6, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.264A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU C 330 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA C 305 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AA8, first strand: chain 'D' and resid 116 through 121 removed outlier: 6.263A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL D 328 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU D 330 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA D 305 " --> pdb=" O GLU D 330 " (cutoff:3.500A) 1812 hydrogen bonds defined for protein. 5364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.11 Time building geometry restraints manager: 12.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9447 1.34 - 1.46: 7395 1.46 - 1.58: 14034 1.58 - 1.70: 0 1.70 - 1.82: 212 Bond restraints: 31088 Sorted by residual: bond pdb=" CA PRO D1014 " pdb=" C PRO D1014 " ideal model delta sigma weight residual 1.518 1.578 -0.060 1.75e-02 3.27e+03 1.17e+01 bond pdb=" CA PRO B1014 " pdb=" C PRO B1014 " ideal model delta sigma weight residual 1.518 1.573 -0.055 1.75e-02 3.27e+03 9.74e+00 bond pdb=" CA PRO C1014 " pdb=" C PRO C1014 " ideal model delta sigma weight residual 1.518 1.572 -0.054 1.75e-02 3.27e+03 9.61e+00 bond pdb=" CA PRO A1014 " pdb=" C PRO A1014 " ideal model delta sigma weight residual 1.518 1.569 -0.051 1.75e-02 3.27e+03 8.62e+00 bond pdb=" CA ILE A1011 " pdb=" C ILE A1011 " ideal model delta sigma weight residual 1.524 1.551 -0.027 1.05e-02 9.07e+03 6.54e+00 ... (remaining 31083 not shown) Histogram of bond angle deviations from ideal: 95.99 - 103.96: 259 103.96 - 111.92: 14376 111.92 - 119.89: 13015 119.89 - 127.86: 14107 127.86 - 135.82: 355 Bond angle restraints: 42112 Sorted by residual: angle pdb=" N SER C 917 " pdb=" CA SER C 917 " pdb=" C SER C 917 " ideal model delta sigma weight residual 111.28 118.73 -7.45 1.09e+00 8.42e-01 4.67e+01 angle pdb=" N SER D 917 " pdb=" CA SER D 917 " pdb=" C SER D 917 " ideal model delta sigma weight residual 111.28 118.68 -7.40 1.09e+00 8.42e-01 4.61e+01 angle pdb=" N SER B 917 " pdb=" CA SER B 917 " pdb=" C SER B 917 " ideal model delta sigma weight residual 111.28 118.64 -7.36 1.09e+00 8.42e-01 4.56e+01 angle pdb=" N SER A 917 " pdb=" CA SER A 917 " pdb=" C SER A 917 " ideal model delta sigma weight residual 111.28 118.62 -7.34 1.09e+00 8.42e-01 4.53e+01 angle pdb=" C PHE C1013 " pdb=" N PRO C1014 " pdb=" CA PRO C1014 " ideal model delta sigma weight residual 119.87 112.89 6.98 1.04e+00 9.25e-01 4.50e+01 ... (remaining 42107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 17049 14.89 - 29.79: 935 29.79 - 44.68: 256 44.68 - 59.58: 12 59.58 - 74.47: 28 Dihedral angle restraints: 18280 sinusoidal: 7368 harmonic: 10912 Sorted by residual: dihedral pdb=" CA ILE D 985 " pdb=" C ILE D 985 " pdb=" N VAL D 986 " pdb=" CA VAL D 986 " ideal model delta harmonic sigma weight residual 180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ILE A 985 " pdb=" C ILE A 985 " pdb=" N VAL A 986 " pdb=" CA VAL A 986 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ILE C 985 " pdb=" C ILE C 985 " pdb=" N VAL C 986 " pdb=" CA VAL C 986 " ideal model delta harmonic sigma weight residual 180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 18277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3839 0.066 - 0.132: 741 0.132 - 0.198: 107 0.198 - 0.264: 9 0.264 - 0.330: 12 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA ARG B 451 " pdb=" N ARG B 451 " pdb=" C ARG B 451 " pdb=" CB ARG B 451 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA PHE D1013 " pdb=" N PHE D1013 " pdb=" C PHE D1013 " pdb=" CB PHE D1013 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA PHE A1013 " pdb=" N PHE A1013 " pdb=" C PHE A1013 " pdb=" CB PHE A1013 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 4705 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1011 " 0.027 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C ILE A1011 " -0.096 2.00e-02 2.50e+03 pdb=" O ILE A1011 " 0.037 2.00e-02 2.50e+03 pdb=" N PRO A1012 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B1011 " 0.027 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C ILE B1011 " -0.096 2.00e-02 2.50e+03 pdb=" O ILE B1011 " 0.037 2.00e-02 2.50e+03 pdb=" N PRO B1012 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C1011 " 0.027 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C ILE C1011 " -0.096 2.00e-02 2.50e+03 pdb=" O ILE C1011 " 0.037 2.00e-02 2.50e+03 pdb=" N PRO C1012 " 0.032 2.00e-02 2.50e+03 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7939 2.80 - 3.33: 28158 3.33 - 3.85: 48301 3.85 - 4.38: 57078 4.38 - 4.90: 96163 Nonbonded interactions: 237639 Sorted by model distance: nonbonded pdb=" O VAL C1065 " pdb=" OG1 THR C1069 " model vdw 2.276 2.440 nonbonded pdb=" O VAL D1065 " pdb=" OG1 THR D1069 " model vdw 2.276 2.440 nonbonded pdb=" O VAL A1065 " pdb=" OG1 THR A1069 " model vdw 2.276 2.440 nonbonded pdb=" O VAL B1065 " pdb=" OG1 THR B1069 " model vdw 2.276 2.440 nonbonded pdb=" O VAL B 728 " pdb=" OG1 THR B 732 " model vdw 2.278 2.440 ... (remaining 237634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.210 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 78.510 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 31088 Z= 0.366 Angle : 1.009 11.056 42112 Z= 0.573 Chirality : 0.055 0.330 4708 Planarity : 0.007 0.072 5264 Dihedral : 10.444 73.991 11188 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.02 % Favored : 93.87 % Rotamer: Outliers : 0.12 % Allowed : 1.92 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.11), residues: 3656 helix: -2.08 (0.08), residues: 2436 sheet: -1.83 (0.34), residues: 200 loop : -3.26 (0.15), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 651 HIS 0.009 0.002 HIS D 257 PHE 0.041 0.003 PHE C 108 TYR 0.029 0.003 TYR D 808 ARG 0.005 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 912 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8809 (tttt) cc_final: 0.8555 (tptt) REVERT: A 164 ILE cc_start: 0.8621 (mt) cc_final: 0.8329 (mt) REVERT: A 441 LEU cc_start: 0.8574 (tp) cc_final: 0.8135 (mp) REVERT: A 468 LYS cc_start: 0.8182 (mttp) cc_final: 0.7832 (mtpp) REVERT: A 1023 MET cc_start: 0.7117 (mmt) cc_final: 0.6895 (tpt) REVERT: A 1097 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7596 (ttmt) REVERT: B 163 LYS cc_start: 0.8810 (tttt) cc_final: 0.8541 (tptt) REVERT: B 164 ILE cc_start: 0.8584 (mt) cc_final: 0.8270 (mt) REVERT: B 441 LEU cc_start: 0.8551 (tp) cc_final: 0.8063 (mp) REVERT: B 468 LYS cc_start: 0.8184 (mttp) cc_final: 0.7832 (mtpp) REVERT: B 665 ASP cc_start: 0.7647 (t0) cc_final: 0.6691 (t0) REVERT: B 1023 MET cc_start: 0.7135 (mmt) cc_final: 0.6916 (tpt) REVERT: B 1097 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7627 (ttmt) REVERT: C 163 LYS cc_start: 0.8835 (tttt) cc_final: 0.8576 (tptt) REVERT: C 164 ILE cc_start: 0.8588 (mt) cc_final: 0.8255 (mt) REVERT: C 441 LEU cc_start: 0.8580 (tp) cc_final: 0.8083 (mp) REVERT: C 468 LYS cc_start: 0.8195 (mttp) cc_final: 0.7832 (mtpp) REVERT: C 665 ASP cc_start: 0.7645 (t0) cc_final: 0.6636 (t0) REVERT: C 1023 MET cc_start: 0.7110 (mmt) cc_final: 0.6891 (tpt) REVERT: C 1097 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7620 (ttmt) REVERT: D 163 LYS cc_start: 0.8827 (tttt) cc_final: 0.8579 (tptt) REVERT: D 164 ILE cc_start: 0.8591 (mt) cc_final: 0.8258 (mt) REVERT: D 441 LEU cc_start: 0.8587 (tp) cc_final: 0.8129 (mp) REVERT: D 468 LYS cc_start: 0.8193 (mttp) cc_final: 0.7831 (mtpp) REVERT: D 1023 MET cc_start: 0.7099 (mmt) cc_final: 0.6884 (tpt) REVERT: D 1097 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7557 (ttmt) outliers start: 4 outliers final: 4 residues processed: 912 average time/residue: 1.5097 time to fit residues: 1598.1178 Evaluate side-chains 455 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 451 time to evaluate : 3.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain D residue 807 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 7.9990 chunk 281 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 291 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 337 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 173 GLN A 185 HIS A 199 ASN A 235 HIS ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 987 GLN A1074 ASN A1102 ASN B 136 HIS B 173 GLN B 185 HIS B 199 ASN B 235 HIS ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 987 GLN B1074 ASN B1102 ASN C 136 HIS C 173 GLN C 185 HIS C 199 ASN C 235 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 987 GLN C1074 ASN C1102 ASN D 136 HIS D 173 GLN D 185 HIS D 199 ASN D 235 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN D 987 GLN D1074 ASN D1102 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 31088 Z= 0.292 Angle : 0.695 8.088 42112 Z= 0.364 Chirality : 0.043 0.137 4708 Planarity : 0.005 0.052 5264 Dihedral : 5.554 28.813 4008 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.45 % Allowed : 14.33 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3656 helix: -0.24 (0.10), residues: 2452 sheet: -1.63 (0.33), residues: 200 loop : -2.89 (0.16), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 693 HIS 0.005 0.001 HIS C 138 PHE 0.027 0.002 PHE C 779 TYR 0.025 0.002 TYR D 117 ARG 0.008 0.001 ARG C 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 461 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8304 (pp) cc_final: 0.7896 (tm) REVERT: A 163 LYS cc_start: 0.8875 (tttt) cc_final: 0.8642 (tptt) REVERT: A 164 ILE cc_start: 0.8551 (mt) cc_final: 0.8248 (mt) REVERT: A 277 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8525 (tm) REVERT: A 431 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8416 (mppt) REVERT: A 441 LEU cc_start: 0.8585 (tp) cc_final: 0.8340 (tt) REVERT: A 815 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7742 (t80) REVERT: A 1061 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: B 139 LEU cc_start: 0.8338 (pp) cc_final: 0.7942 (tm) REVERT: B 163 LYS cc_start: 0.8873 (tttt) cc_final: 0.8640 (tptt) REVERT: B 164 ILE cc_start: 0.8583 (mt) cc_final: 0.8297 (mt) REVERT: B 431 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8389 (mppt) REVERT: B 441 LEU cc_start: 0.8504 (tp) cc_final: 0.8293 (tt) REVERT: B 622 GLU cc_start: 0.7657 (tt0) cc_final: 0.7436 (tt0) REVERT: B 815 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7754 (t80) REVERT: B 1061 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: B 1097 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7631 (ttmt) REVERT: C 139 LEU cc_start: 0.8324 (pp) cc_final: 0.7949 (tm) REVERT: C 163 LYS cc_start: 0.8883 (tttt) cc_final: 0.8657 (tptt) REVERT: C 164 ILE cc_start: 0.8619 (mt) cc_final: 0.8307 (mt) REVERT: C 277 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8547 (tm) REVERT: C 431 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8413 (mppt) REVERT: C 441 LEU cc_start: 0.8509 (tp) cc_final: 0.8300 (tt) REVERT: C 815 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7700 (t80) REVERT: C 1061 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: D 139 LEU cc_start: 0.8324 (pp) cc_final: 0.7917 (tm) REVERT: D 163 LYS cc_start: 0.8876 (tttt) cc_final: 0.8653 (tptt) REVERT: D 164 ILE cc_start: 0.8602 (mt) cc_final: 0.8287 (mt) REVERT: D 277 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8525 (tm) REVERT: D 431 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8392 (mppt) REVERT: D 441 LEU cc_start: 0.8583 (tp) cc_final: 0.8337 (tt) REVERT: D 815 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7755 (t80) REVERT: D 1061 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7631 (mt-10) outliers start: 148 outliers final: 52 residues processed: 571 average time/residue: 1.3495 time to fit residues: 911.8089 Evaluate side-chains 443 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 376 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 815 PHE Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain D residue 1087 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 281 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 338 optimal weight: 2.9990 chunk 365 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 chunk 335 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 271 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 235 HIS ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 HIS A 510 GLN A 671 GLN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 HIS B 510 GLN B 635 ASN B 671 GLN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 HIS C 510 GLN C 635 ASN C 671 GLN D 199 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 HIS D 510 GLN D 635 ASN D 671 GLN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31088 Z= 0.284 Angle : 0.668 12.315 42112 Z= 0.344 Chirality : 0.044 0.245 4708 Planarity : 0.004 0.043 5264 Dihedral : 5.132 20.487 4000 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.74 % Allowed : 14.63 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 3656 helix: 0.42 (0.10), residues: 2476 sheet: -1.49 (0.33), residues: 200 loop : -2.77 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 786 HIS 0.009 0.001 HIS B1080 PHE 0.032 0.002 PHE B 752 TYR 0.025 0.002 TYR A 117 ARG 0.006 0.001 ARG D 451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 431 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8645 (mt) cc_final: 0.8344 (mt) REVERT: A 431 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8276 (mppt) REVERT: A 1061 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: B 164 ILE cc_start: 0.8643 (mt) cc_final: 0.8339 (mt) REVERT: B 194 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8084 (mt-10) REVERT: B 431 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8177 (mppt) REVERT: B 802 ASP cc_start: 0.7802 (m-30) cc_final: 0.7276 (m-30) REVERT: B 815 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7623 (t80) REVERT: B 1061 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: C 164 ILE cc_start: 0.8644 (mt) cc_final: 0.8339 (mt) REVERT: C 194 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8110 (mt-10) REVERT: C 431 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8184 (mppt) REVERT: C 802 ASP cc_start: 0.7810 (m-30) cc_final: 0.7278 (m-30) REVERT: C 815 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7644 (t80) REVERT: C 1061 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: D 164 ILE cc_start: 0.8667 (mt) cc_final: 0.8365 (mt) REVERT: D 431 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8324 (mppt) REVERT: D 1061 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7633 (mt-10) outliers start: 191 outliers final: 79 residues processed: 568 average time/residue: 1.2601 time to fit residues: 856.1171 Evaluate side-chains 476 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 387 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 807 PHE Chi-restraints excluded: chain D residue 815 PHE Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 10.0000 chunk 254 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 339 optimal weight: 0.6980 chunk 359 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 635 ASN ** A 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** B 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN ** C 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** D 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31088 Z= 0.171 Angle : 0.629 13.848 42112 Z= 0.317 Chirality : 0.040 0.214 4708 Planarity : 0.004 0.037 5264 Dihedral : 4.798 20.356 4000 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.33 % Allowed : 17.22 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3656 helix: 0.94 (0.10), residues: 2480 sheet: -1.52 (0.30), residues: 228 loop : -2.44 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 453 HIS 0.012 0.001 HIS B1080 PHE 0.025 0.001 PHE D 779 TYR 0.024 0.001 TYR B 117 ARG 0.003 0.000 ARG C1083 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 451 time to evaluate : 3.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8634 (mt) cc_final: 0.8382 (mt) REVERT: A 194 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8218 (mt-10) REVERT: A 283 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8777 (mmmm) REVERT: A 337 ASP cc_start: 0.7331 (m-30) cc_final: 0.6723 (t70) REVERT: A 431 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8230 (mppt) REVERT: A 863 MET cc_start: 0.8551 (mmt) cc_final: 0.7905 (mmt) REVERT: A 1061 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: A 1097 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7247 (ttmt) REVERT: B 164 ILE cc_start: 0.8631 (mt) cc_final: 0.8377 (mt) REVERT: B 194 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8187 (mt-10) REVERT: B 337 ASP cc_start: 0.7330 (m-30) cc_final: 0.6726 (t70) REVERT: B 431 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8214 (mppt) REVERT: B 815 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7601 (t80) REVERT: B 1004 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6582 (tm-30) REVERT: B 1061 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: B 1097 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7277 (tmtm) REVERT: C 164 ILE cc_start: 0.8630 (mt) cc_final: 0.8375 (mt) REVERT: C 194 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8187 (mt-10) REVERT: C 283 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8786 (mmmm) REVERT: C 337 ASP cc_start: 0.7321 (m-30) cc_final: 0.6726 (t70) REVERT: C 431 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8163 (mppt) REVERT: C 1004 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6681 (tm-30) REVERT: C 1061 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: C 1097 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7246 (ttmt) REVERT: D 164 ILE cc_start: 0.8652 (mt) cc_final: 0.8400 (mt) REVERT: D 194 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8139 (mt-10) REVERT: D 283 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8776 (mmmm) REVERT: D 337 ASP cc_start: 0.7325 (m-30) cc_final: 0.6604 (t70) REVERT: D 431 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8253 (mppt) REVERT: D 815 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7584 (t80) REVERT: D 863 MET cc_start: 0.8548 (mmt) cc_final: 0.7900 (mmt) REVERT: D 1061 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: D 1097 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7225 (ttmt) outliers start: 144 outliers final: 70 residues processed: 552 average time/residue: 1.2799 time to fit residues: 840.9688 Evaluate side-chains 475 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 392 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 815 PHE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1061 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 322 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN B 199 ASN B 204 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 199 ASN D 204 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 31088 Z= 0.451 Angle : 0.758 10.446 42112 Z= 0.388 Chirality : 0.047 0.199 4708 Planarity : 0.005 0.052 5264 Dihedral : 5.096 23.394 4000 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.65 % Allowed : 17.58 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3656 helix: 0.78 (0.10), residues: 2472 sheet: -1.33 (0.32), residues: 196 loop : -2.52 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 453 HIS 0.011 0.002 HIS B1080 PHE 0.042 0.003 PHE D 752 TYR 0.028 0.002 TYR A 117 ARG 0.005 0.001 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 390 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1027 LYS cc_start: 0.5262 (mttp) cc_final: 0.4912 (pptt) REVERT: B 158 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7446 (mppt) REVERT: B 431 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8280 (mppt) REVERT: B 1027 LYS cc_start: 0.5292 (mttp) cc_final: 0.4930 (pptt) REVERT: C 194 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8235 (mt-10) REVERT: C 431 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8301 (mppt) REVERT: C 1027 LYS cc_start: 0.5245 (mttp) cc_final: 0.4907 (pptt) REVERT: C 1059 MET cc_start: 0.6364 (mpt) cc_final: 0.5925 (pmm) REVERT: D 158 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7484 (tmmm) REVERT: D 194 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8150 (mt-10) REVERT: D 283 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8790 (mmmm) REVERT: D 431 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8283 (mppt) REVERT: D 441 LEU cc_start: 0.8648 (tp) cc_final: 0.8301 (tt) REVERT: D 622 GLU cc_start: 0.7663 (tt0) cc_final: 0.7344 (tp30) REVERT: D 1027 LYS cc_start: 0.5288 (mttp) cc_final: 0.4927 (pptt) outliers start: 188 outliers final: 91 residues processed: 517 average time/residue: 1.2847 time to fit residues: 792.7235 Evaluate side-chains 459 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 362 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 526 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 526 LYS Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain D residue 1087 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 9.9990 chunk 323 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 359 optimal weight: 0.8980 chunk 298 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN A 667 HIS A 671 GLN A 785 GLN B 107 GLN B 199 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 HIS B 671 GLN C 107 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 667 HIS C 671 GLN D 107 GLN D 199 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 HIS D 671 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31088 Z= 0.188 Angle : 0.669 16.575 42112 Z= 0.330 Chirality : 0.042 0.167 4708 Planarity : 0.004 0.046 5264 Dihedral : 4.775 22.944 4000 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.12 % Allowed : 20.22 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3656 helix: 1.17 (0.10), residues: 2476 sheet: -1.23 (0.31), residues: 228 loop : -2.34 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 453 HIS 0.011 0.001 HIS C1080 PHE 0.029 0.001 PHE B 779 TYR 0.025 0.001 TYR D 117 ARG 0.007 0.000 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 411 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8137 (mt-10) REVERT: A 431 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8279 (mppt) REVERT: A 435 GLU cc_start: 0.8759 (tp30) cc_final: 0.8513 (tp30) REVERT: A 441 LEU cc_start: 0.8685 (tp) cc_final: 0.8172 (tt) REVERT: A 570 LEU cc_start: 0.7711 (mp) cc_final: 0.7407 (mm) REVERT: A 815 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7644 (t80) REVERT: A 863 MET cc_start: 0.8562 (mmt) cc_final: 0.7882 (mmt) REVERT: A 1027 LYS cc_start: 0.5211 (mttp) cc_final: 0.4890 (pptt) REVERT: B 194 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8139 (mt-10) REVERT: B 431 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8228 (mppt) REVERT: B 453 TRP cc_start: 0.6267 (m-10) cc_final: 0.6067 (m-10) REVERT: B 641 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: B 863 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7895 (mmt) REVERT: B 1027 LYS cc_start: 0.5169 (mttp) cc_final: 0.4854 (pptt) REVERT: C 431 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8342 (mppt) REVERT: C 641 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: C 666 GLN cc_start: 0.8230 (pt0) cc_final: 0.8015 (pt0) REVERT: C 863 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7892 (mmt) REVERT: C 1027 LYS cc_start: 0.5156 (mttp) cc_final: 0.4841 (pptt) REVERT: D 283 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8852 (mmmm) REVERT: D 431 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8227 (mppt) REVERT: D 441 LEU cc_start: 0.8680 (tp) cc_final: 0.8160 (tt) REVERT: D 641 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: D 863 MET cc_start: 0.8565 (mmt) cc_final: 0.7876 (mmt) REVERT: D 1027 LYS cc_start: 0.5215 (mttp) cc_final: 0.4893 (pptt) outliers start: 137 outliers final: 51 residues processed: 501 average time/residue: 1.2664 time to fit residues: 759.7627 Evaluate side-chains 428 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 366 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 262 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 302 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 358 optimal weight: 0.8980 chunk 224 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN ** D1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 31088 Z= 0.253 Angle : 0.685 13.777 42112 Z= 0.341 Chirality : 0.043 0.323 4708 Planarity : 0.004 0.043 5264 Dihedral : 4.741 22.441 4000 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.06 % Allowed : 21.78 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3656 helix: 1.20 (0.10), residues: 2488 sheet: -1.04 (0.32), residues: 228 loop : -2.35 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 786 HIS 0.011 0.001 HIS D1080 PHE 0.034 0.002 PHE B 779 TYR 0.034 0.001 TYR D 646 ARG 0.006 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 375 time to evaluate : 3.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8194 (mt-10) REVERT: A 431 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8211 (mppt) REVERT: A 445 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: A 453 TRP cc_start: 0.6241 (m-10) cc_final: 0.5963 (m-10) REVERT: A 641 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: A 863 MET cc_start: 0.8638 (mmt) cc_final: 0.7966 (mmt) REVERT: A 1027 LYS cc_start: 0.5090 (mttp) cc_final: 0.4825 (pptt) REVERT: B 194 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8178 (mt-10) REVERT: B 435 GLU cc_start: 0.8766 (tp30) cc_final: 0.8519 (tp30) REVERT: B 1027 LYS cc_start: 0.5099 (mttp) cc_final: 0.4857 (pptt) REVERT: B 1061 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: C 396 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5615 (mpm) REVERT: C 431 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8363 (mppt) REVERT: C 435 GLU cc_start: 0.8790 (tp30) cc_final: 0.8538 (tp30) REVERT: C 863 MET cc_start: 0.8623 (mmt) cc_final: 0.7913 (mmt) REVERT: C 1027 LYS cc_start: 0.5081 (mttp) cc_final: 0.4848 (pptt) REVERT: C 1061 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: D 283 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8848 (mmmm) REVERT: D 435 GLU cc_start: 0.8770 (tp30) cc_final: 0.8526 (tp30) REVERT: D 665 ASP cc_start: 0.7209 (t0) cc_final: 0.6980 (t0) REVERT: D 863 MET cc_start: 0.8634 (mmt) cc_final: 0.7961 (mmt) REVERT: D 1027 LYS cc_start: 0.5058 (mttp) cc_final: 0.4830 (pptt) REVERT: D 1061 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7501 (mt-10) outliers start: 135 outliers final: 61 residues processed: 477 average time/residue: 1.3018 time to fit residues: 739.4258 Evaluate side-chains 421 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 351 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1061 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 227 optimal weight: 0.1980 chunk 244 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 ASN ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 517 ASN ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31088 Z= 0.186 Angle : 0.662 13.057 42112 Z= 0.328 Chirality : 0.042 0.327 4708 Planarity : 0.004 0.041 5264 Dihedral : 4.581 21.289 4000 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.37 % Allowed : 22.99 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3656 helix: 1.30 (0.10), residues: 2492 sheet: -0.98 (0.32), residues: 228 loop : -2.20 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 525 HIS 0.008 0.001 HIS A1080 PHE 0.033 0.001 PHE B 779 TYR 0.026 0.001 TYR D 117 ARG 0.007 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 374 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8298 (mppt) REVERT: A 435 GLU cc_start: 0.8790 (tp30) cc_final: 0.8522 (tp30) REVERT: A 445 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: A 526 LYS cc_start: 0.6213 (pptt) cc_final: 0.5475 (mtmt) REVERT: A 815 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7598 (t80) REVERT: A 863 MET cc_start: 0.8602 (mmt) cc_final: 0.7942 (mmt) REVERT: A 1027 LYS cc_start: 0.5078 (mttp) cc_final: 0.4849 (pptt) REVERT: B 526 LYS cc_start: 0.6145 (pptt) cc_final: 0.5429 (mtmt) REVERT: B 863 MET cc_start: 0.8608 (mmt) cc_final: 0.7927 (mmt) REVERT: C 453 TRP cc_start: 0.5993 (m-10) cc_final: 0.5727 (m-10) REVERT: C 526 LYS cc_start: 0.6209 (pptt) cc_final: 0.5467 (mtmt) REVERT: C 863 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7874 (mmt) REVERT: C 1027 LYS cc_start: 0.4868 (mttp) cc_final: 0.4662 (pptt) REVERT: D 283 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8855 (mmmm) REVERT: D 431 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8220 (mppt) REVERT: D 453 TRP cc_start: 0.6187 (m-10) cc_final: 0.5936 (m-10) REVERT: D 526 LYS cc_start: 0.6216 (pptt) cc_final: 0.5478 (mtmt) REVERT: D 665 ASP cc_start: 0.7298 (t0) cc_final: 0.6965 (t0) REVERT: D 863 MET cc_start: 0.8589 (mmt) cc_final: 0.7902 (mmt) outliers start: 112 outliers final: 52 residues processed: 448 average time/residue: 1.2974 time to fit residues: 695.8793 Evaluate side-chains 400 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 342 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 585 LYS Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 585 LYS Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 585 LYS Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 4.9990 chunk 343 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 chunk 334 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 301 optimal weight: 20.0000 chunk 316 optimal weight: 9.9990 chunk 332 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A 559 HIS ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 ASN B 559 HIS ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 HIS ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 HIS ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31088 Z= 0.319 Angle : 0.727 12.487 42112 Z= 0.364 Chirality : 0.046 0.311 4708 Planarity : 0.004 0.048 5264 Dihedral : 4.721 22.144 4000 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.22 % Allowed : 23.26 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3656 helix: 1.25 (0.10), residues: 2464 sheet: -0.92 (0.32), residues: 228 loop : -2.23 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 525 HIS 0.009 0.001 HIS B1080 PHE 0.035 0.002 PHE D 779 TYR 0.027 0.002 TYR A 117 ARG 0.010 0.001 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 368 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8229 (mppt) REVERT: A 435 GLU cc_start: 0.8771 (tp30) cc_final: 0.8516 (tp30) REVERT: A 804 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8811 (mt) REVERT: B 396 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5598 (mpm) REVERT: B 431 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8341 (mppt) REVERT: B 453 TRP cc_start: 0.6235 (m-10) cc_final: 0.5988 (m-10) REVERT: B 607 ASP cc_start: 0.8241 (t0) cc_final: 0.7876 (t0) REVERT: B 638 ASP cc_start: 0.7575 (t0) cc_final: 0.7309 (t0) REVERT: B 1023 MET cc_start: 0.7480 (mmt) cc_final: 0.6244 (tmt) REVERT: B 1027 LYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5113 (mmmm) REVERT: C 163 LYS cc_start: 0.8498 (tptt) cc_final: 0.8286 (tptt) REVERT: C 194 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8180 (mt-10) REVERT: C 396 MET cc_start: 0.5931 (OUTLIER) cc_final: 0.5699 (mpm) REVERT: C 431 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8211 (mppt) REVERT: C 435 GLU cc_start: 0.8786 (tp30) cc_final: 0.8554 (tp30) REVERT: C 453 TRP cc_start: 0.6004 (m-10) cc_final: 0.5731 (m-10) REVERT: C 607 ASP cc_start: 0.8246 (t0) cc_final: 0.7907 (t0) REVERT: D 283 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8841 (mmmm) REVERT: D 453 TRP cc_start: 0.6239 (m-10) cc_final: 0.5954 (m-10) REVERT: D 804 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8733 (mt) REVERT: D 1023 MET cc_start: 0.7420 (mmt) cc_final: 0.6186 (tmt) REVERT: D 1027 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5047 (mmmm) outliers start: 107 outliers final: 63 residues processed: 442 average time/residue: 1.3599 time to fit residues: 716.1206 Evaluate side-chains 411 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 338 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 585 LYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1027 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 585 LYS Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 585 LYS Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 1027 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.9990 chunk 353 optimal weight: 0.9980 chunk 215 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 370 optimal weight: 5.9990 chunk 341 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 227 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31088 Z= 0.231 Angle : 0.713 12.853 42112 Z= 0.357 Chirality : 0.044 0.302 4708 Planarity : 0.004 0.044 5264 Dihedral : 4.663 22.131 4000 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.49 % Allowed : 24.22 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3656 helix: 1.28 (0.10), residues: 2468 sheet: -0.63 (0.32), residues: 220 loop : -2.19 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 525 HIS 0.009 0.001 HIS B1080 PHE 0.035 0.002 PHE C 776 TYR 0.036 0.001 TYR D 191 ARG 0.010 0.000 ARG B 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 364 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8287 (mppt) REVERT: A 435 GLU cc_start: 0.8735 (tp30) cc_final: 0.8494 (tp30) REVERT: A 804 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8711 (mt) REVERT: A 863 MET cc_start: 0.8613 (mmt) cc_final: 0.7882 (mmt) REVERT: A 1023 MET cc_start: 0.7488 (mmt) cc_final: 0.6311 (tmt) REVERT: A 1059 MET cc_start: 0.6091 (mpt) cc_final: 0.5772 (pmm) REVERT: B 453 TRP cc_start: 0.6011 (m-10) cc_final: 0.5748 (m-10) REVERT: B 607 ASP cc_start: 0.8207 (t0) cc_final: 0.7859 (t0) REVERT: B 863 MET cc_start: 0.8610 (mmt) cc_final: 0.7894 (mmt) REVERT: B 1023 MET cc_start: 0.7487 (mmt) cc_final: 0.6261 (tmt) REVERT: B 1027 LYS cc_start: 0.6200 (OUTLIER) cc_final: 0.5331 (mmmm) REVERT: B 1059 MET cc_start: 0.5939 (mpt) cc_final: 0.5663 (pmm) REVERT: C 431 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8278 (mppt) REVERT: C 435 GLU cc_start: 0.8767 (tp30) cc_final: 0.8540 (tp30) REVERT: C 453 TRP cc_start: 0.5953 (m-10) cc_final: 0.5716 (m-10) REVERT: C 607 ASP cc_start: 0.8214 (t0) cc_final: 0.7870 (t0) REVERT: C 622 GLU cc_start: 0.7767 (tt0) cc_final: 0.7566 (tp30) REVERT: C 863 MET cc_start: 0.8582 (mmt) cc_final: 0.7858 (mmt) REVERT: C 1023 MET cc_start: 0.7433 (mmt) cc_final: 0.6318 (tmt) REVERT: C 1027 LYS cc_start: 0.5283 (mmmm) cc_final: 0.4428 (tmmt) REVERT: C 1059 MET cc_start: 0.6113 (mpt) cc_final: 0.5887 (pmm) REVERT: D 283 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8838 (mmmm) REVERT: D 431 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8339 (mppt) REVERT: D 453 TRP cc_start: 0.6135 (m-10) cc_final: 0.5877 (m-10) REVERT: D 804 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8709 (mt) REVERT: D 863 MET cc_start: 0.8609 (mmt) cc_final: 0.7961 (mmt) REVERT: D 1023 MET cc_start: 0.7444 (mmt) cc_final: 0.6208 (tmt) REVERT: D 1027 LYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5301 (mmmm) REVERT: D 1059 MET cc_start: 0.6008 (mpt) cc_final: 0.5759 (pmm) outliers start: 83 outliers final: 58 residues processed: 431 average time/residue: 1.2530 time to fit residues: 647.6582 Evaluate side-chains 414 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 348 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 585 LYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1027 LYS Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 585 LYS Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 585 LYS Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 1027 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 4.9990 chunk 314 optimal weight: 7.9990 chunk 90 optimal weight: 30.0000 chunk 272 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 295 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 303 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.159212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.106338 restraints weight = 54323.895| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.46 r_work: 0.3314 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31088 Z= 0.337 Angle : 0.752 12.701 42112 Z= 0.379 Chirality : 0.046 0.296 4708 Planarity : 0.004 0.057 5264 Dihedral : 4.795 23.142 4000 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.64 % Allowed : 23.98 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3656 helix: 1.19 (0.10), residues: 2468 sheet: -0.67 (0.32), residues: 220 loop : -2.23 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 525 HIS 0.008 0.002 HIS D1080 PHE 0.036 0.002 PHE A 779 TYR 0.029 0.002 TYR B 117 ARG 0.019 0.001 ARG B 784 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13170.11 seconds wall clock time: 233 minutes 58.24 seconds (14038.24 seconds total)