Starting phenix.real_space_refine on Wed Feb 21 10:12:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wra_32720/02_2024/7wra_32720.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wra_32720/02_2024/7wra_32720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wra_32720/02_2024/7wra_32720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wra_32720/02_2024/7wra_32720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wra_32720/02_2024/7wra_32720.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wra_32720/02_2024/7wra_32720.pdb" } resolution = 2.98 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 S 140 5.16 5 Na 1 4.78 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 ASP 450": "OD1" <-> "OD2" 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: 30373 Number of models: 1 Model: "" Number of chains: 5 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: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.13, per 1000 atoms: 0.50 Number of scatterers: 30373 At special positions: 0 Unit cell: (153.114, 153.114, 156.156, 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) S 140 16.00 Na 1 11.00 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=2.01 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.01 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.01 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.01 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: 10.87 Conformation dependent library (CDL) restraints added in 5.2 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: 184 helices and 8 sheets defined 70.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 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 186 through 204 removed outlier: 3.685A pdb=" N LYS A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.676A 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: 3.877A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.805A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.811A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 386 removed outlier: 4.446A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.843A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 439 through 446 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 removed outlier: 3.697A pdb=" N LEU A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.921A pdb=" N ARG A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 575 through 582 removed outlier: 3.586A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 603 Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.797A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 644 removed outlier: 3.633A pdb=" N ALA A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 663 removed outlier: 3.989A pdb=" N ALA A 660 " --> pdb=" O CYS A 656 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.783A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 removed outlier: 3.628A pdb=" N GLY A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.867A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.888A 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: 3.737A pdb=" N ARG A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.332A 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 852 through 861 removed outlier: 4.592A pdb=" N LYS A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 890 removed outlier: 3.879A pdb=" N ALA A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 904 removed outlier: 3.859A 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: 3.991A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.651A pdb=" N LEU A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 977 " --> pdb=" O ASN A 973 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.887A 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 1069 removed outlier: 3.831A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1104 removed outlier: 3.923A 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 186 through 204 removed outlier: 3.685A pdb=" N LYS B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 3.676A 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: 3.876A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.806A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.810A pdb=" N ARG B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 370 through 386 removed outlier: 4.446A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 418 removed outlier: 3.844A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 439 through 446 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 removed outlier: 3.697A pdb=" N LEU B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 533 removed outlier: 3.922A pdb=" N ARG B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.586A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.797A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 644 removed outlier: 3.633A pdb=" N ALA B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 663 removed outlier: 3.989A pdb=" N ALA B 660 " --> pdb=" O CYS B 656 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.784A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 removed outlier: 3.628A pdb=" N GLY B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.867A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 705 Processing helix chain 'B' and resid 723 through 732 Processing helix chain 'B' and resid 733 through 758 removed outlier: 3.889A 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: 3.737A pdb=" N ARG B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 838 " --> pdb=" O LEU B 834 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.332A 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 852 through 861 removed outlier: 4.592A pdb=" N LYS B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 890 removed outlier: 3.880A pdb=" N ALA B 884 " --> pdb=" O ALA B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 904 removed outlier: 3.859A 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: 3.991A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.651A pdb=" N LEU B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 977 " --> pdb=" O ASN B 973 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.887A 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 1069 removed outlier: 3.831A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1104 removed outlier: 3.923A 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 186 through 204 removed outlier: 3.685A pdb=" N LYS C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 3.676A 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: 3.877A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 removed outlier: 3.805A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.811A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 370 through 386 removed outlier: 4.446A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 418 removed outlier: 3.843A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 Processing helix chain 'C' and resid 439 through 446 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 removed outlier: 3.697A pdb=" N LEU C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 533 removed outlier: 3.921A pdb=" N ARG C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.586A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 603 Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.797A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 644 removed outlier: 3.633A pdb=" N ALA C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 removed outlier: 3.989A pdb=" N ALA C 660 " --> pdb=" O CYS C 656 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 670 removed outlier: 3.783A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 removed outlier: 3.628A pdb=" N GLY C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.867A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 705 Processing helix chain 'C' and resid 723 through 732 Processing helix chain 'C' and resid 733 through 758 removed outlier: 3.889A 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: 3.737A pdb=" N ARG C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE C 838 " --> pdb=" O LEU C 834 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.332A 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 852 through 861 removed outlier: 4.592A pdb=" N LYS C 856 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 890 removed outlier: 3.880A pdb=" N ALA C 884 " --> pdb=" O ALA C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 904 removed outlier: 3.859A 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: 3.992A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.651A pdb=" N LEU C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 977 " --> pdb=" O ASN C 973 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.887A 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 1069 removed outlier: 3.831A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1104 removed outlier: 3.923A 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 186 through 204 removed outlier: 3.684A pdb=" N LYS D 190 " --> pdb=" O TYR D 186 " (cutoff:3.500A) removed outlier: 3.676A 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: 3.876A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 343 removed outlier: 3.805A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.810A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 370 through 386 removed outlier: 4.446A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 418 removed outlier: 3.843A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 439 through 446 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 removed outlier: 3.697A pdb=" N LEU D 493 " --> pdb=" O THR D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 533 removed outlier: 3.922A pdb=" N ARG D 533 " --> pdb=" O ALA D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 Processing helix chain 'D' and resid 575 through 582 removed outlier: 3.586A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 603 Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.797A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 644 removed outlier: 3.633A pdb=" N ALA D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 663 removed outlier: 3.989A pdb=" N ALA D 660 " --> pdb=" O CYS D 656 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.784A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 removed outlier: 3.628A pdb=" N GLY D 684 " --> pdb=" O LYS D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.867A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 705 Processing helix chain 'D' and resid 723 through 732 Processing helix chain 'D' and resid 733 through 758 removed outlier: 3.889A 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: 3.737A pdb=" N ARG D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE D 838 " --> pdb=" O LEU D 834 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.332A 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 852 through 861 removed outlier: 4.592A pdb=" N LYS D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 890 removed outlier: 3.880A pdb=" N ALA D 884 " --> pdb=" O ALA D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 904 removed outlier: 3.859A 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: 3.991A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.651A pdb=" N LEU D 975 " --> pdb=" O LEU D 971 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 977 " --> pdb=" O ASN D 973 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.887A 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 1069 removed outlier: 3.831A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1104 removed outlier: 3.923A pdb=" N LYS D1104 " --> pdb=" O ALA D1100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.981A pdb=" N GLY A 104 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 234 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 removed outlier: 5.874A pdb=" N ALA A 211 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU A 261 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A 213 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL A 263 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA A 215 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLU A 330 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA A 305 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.981A pdb=" N GLY B 104 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 234 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121 removed outlier: 5.873A pdb=" N ALA B 211 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU B 261 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY B 213 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 263 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA B 215 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 145 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL B 328 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLU B 330 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA B 305 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 117 removed outlier: 3.981A pdb=" N GLY C 104 " --> pdb=" O TYR C 117 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 234 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 removed outlier: 5.874A pdb=" N ALA C 211 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU C 261 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY C 213 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL C 263 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA C 215 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLU C 330 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA C 305 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 117 removed outlier: 3.981A pdb=" N GLY D 104 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY D 234 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121 removed outlier: 5.873A pdb=" N ALA D 211 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU D 261 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY D 213 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL D 263 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA D 215 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL D 145 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL D 328 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLU D 330 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA D 305 " --> pdb=" O GLU D 330 " (cutoff:3.500A) 1774 hydrogen bonds defined for protein. 5262 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: 10.18 Time building geometry restraints manager: 11.74 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: 8676 1.34 - 1.46: 6675 1.46 - 1.58: 15519 1.58 - 1.70: 6 1.70 - 1.82: 212 Bond restraints: 31088 Sorted by residual: bond pdb=" CA ILE D1011 " pdb=" C ILE D1011 " ideal model delta sigma weight residual 1.524 1.591 -0.067 1.05e-02 9.07e+03 4.07e+01 bond pdb=" CA ILE A1011 " pdb=" C ILE A1011 " ideal model delta sigma weight residual 1.524 1.588 -0.064 1.05e-02 9.07e+03 3.71e+01 bond pdb=" C PRO D1012 " pdb=" O PRO D1012 " ideal model delta sigma weight residual 1.233 1.290 -0.057 1.21e-02 6.83e+03 2.24e+01 bond pdb=" C PRO A1012 " pdb=" O PRO A1012 " ideal model delta sigma weight residual 1.233 1.288 -0.055 1.21e-02 6.83e+03 2.06e+01 bond pdb=" CA PHE B1013 " pdb=" C PHE B1013 " ideal model delta sigma weight residual 1.522 1.579 -0.058 1.29e-02 6.01e+03 1.99e+01 ... (remaining 31083 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.33: 286 104.33 - 111.79: 13999 111.79 - 119.25: 11434 119.25 - 126.71: 15871 126.71 - 134.17: 522 Bond angle restraints: 42112 Sorted by residual: angle pdb=" N PHE B1013 " pdb=" CA PHE B1013 " pdb=" C PHE B1013 " ideal model delta sigma weight residual 113.45 124.02 -10.57 1.39e+00 5.18e-01 5.78e+01 angle pdb=" N PHE D1013 " pdb=" CA PHE D1013 " pdb=" C PHE D1013 " ideal model delta sigma weight residual 113.45 123.93 -10.48 1.39e+00 5.18e-01 5.68e+01 angle pdb=" N PHE A1013 " pdb=" CA PHE A1013 " pdb=" C PHE A1013 " ideal model delta sigma weight residual 113.45 123.65 -10.20 1.39e+00 5.18e-01 5.38e+01 angle pdb=" N PHE C1013 " pdb=" CA PHE C1013 " pdb=" C PHE C1013 " ideal model delta sigma weight residual 113.45 123.10 -9.65 1.39e+00 5.18e-01 4.82e+01 angle pdb=" N ARG D 452 " pdb=" CA ARG D 452 " pdb=" C ARG D 452 " ideal model delta sigma weight residual 108.26 119.11 -10.85 1.66e+00 3.63e-01 4.27e+01 ... (remaining 42107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.95: 17020 14.95 - 29.91: 976 29.91 - 44.86: 243 44.86 - 59.82: 13 59.82 - 74.77: 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 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+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 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+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 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 18277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4287 0.089 - 0.178: 405 0.178 - 0.268: 12 0.268 - 0.357: 1 0.357 - 0.446: 3 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA ILE D1011 " pdb=" N ILE D1011 " pdb=" C ILE D1011 " pdb=" CB ILE D1011 " both_signs ideal model delta sigma weight residual False 2.43 2.88 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA ILE A1011 " pdb=" N ILE A1011 " pdb=" C ILE A1011 " pdb=" CB ILE A1011 " both_signs ideal model delta sigma weight residual False 2.43 2.86 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA ILE B1011 " pdb=" N ILE B1011 " pdb=" C ILE B1011 " pdb=" CB ILE B1011 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 4705 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D1011 " -0.076 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO D1012 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO D1012 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D1012 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1011 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A1012 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A1012 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A1012 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B1011 " -0.074 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO B1012 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO B1012 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B1012 " -0.060 5.00e-02 4.00e+02 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5307 2.76 - 3.30: 28769 3.30 - 3.83: 48828 3.83 - 4.37: 57261 4.37 - 4.90: 97374 Nonbonded interactions: 237539 Sorted by model distance: nonbonded pdb=" O VAL C1065 " pdb=" OG1 THR C1069 " model vdw 2.231 2.440 nonbonded pdb=" O VAL A1065 " pdb=" OG1 THR A1069 " model vdw 2.231 2.440 nonbonded pdb=" O VAL B1065 " pdb=" OG1 THR B1069 " model vdw 2.232 2.440 nonbonded pdb=" O VAL D1065 " pdb=" OG1 THR D1069 " model vdw 2.232 2.440 nonbonded pdb=" O VAL A 196 " pdb=" OG1 THR A 200 " model vdw 2.292 2.440 ... (remaining 237534 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' and resid 102 through 1104) 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: 0.860 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: 5.400 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 72.990 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.130 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:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 0.078 31088 Z= 0.393 Angle : 0.993 10.847 42112 Z= 0.567 Chirality : 0.055 0.446 4708 Planarity : 0.007 0.117 5264 Dihedral : 10.557 74.772 11188 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.60 % Allowed : 2.28 % Favored : 97.12 % 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: -3.96 (0.10), residues: 3656 helix: -2.20 (0.08), residues: 2472 sheet: -1.38 (0.36), residues: 184 loop : -3.51 (0.15), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 651 HIS 0.006 0.002 HIS D 257 PHE 0.030 0.003 PHE C 832 TYR 0.030 0.003 TYR B 808 ARG 0.006 0.001 ARG C 816 *********************** 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 796 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 776 time to evaluate : 3.663 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 302 VAL cc_start: 0.8855 (t) cc_final: 0.8636 (p) REVERT: A 518 ASP cc_start: 0.7655 (m-30) cc_final: 0.7271 (m-30) REVERT: A 615 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7515 (tp30) REVERT: A 619 ASN cc_start: 0.7769 (m110) cc_final: 0.7569 (m-40) REVERT: A 779 PHE cc_start: 0.8445 (t80) cc_final: 0.8206 (t80) REVERT: B 302 VAL cc_start: 0.8856 (t) cc_final: 0.8638 (p) REVERT: B 518 ASP cc_start: 0.7666 (m-30) cc_final: 0.7279 (m-30) REVERT: B 615 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7519 (tp30) REVERT: B 779 PHE cc_start: 0.8447 (t80) cc_final: 0.8208 (t80) REVERT: C 302 VAL cc_start: 0.8859 (t) cc_final: 0.8639 (p) REVERT: C 426 TRP cc_start: 0.6606 (p-90) cc_final: 0.6016 (p-90) REVERT: C 518 ASP cc_start: 0.7669 (m-30) cc_final: 0.7280 (m-30) REVERT: C 615 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7513 (tp30) REVERT: C 619 ASN cc_start: 0.7775 (m110) cc_final: 0.7575 (m-40) REVERT: C 779 PHE cc_start: 0.8452 (t80) cc_final: 0.8211 (t80) REVERT: D 302 VAL cc_start: 0.8856 (t) cc_final: 0.8636 (p) REVERT: D 518 ASP cc_start: 0.7675 (m-30) cc_final: 0.7285 (m-30) REVERT: D 615 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7517 (tp30) REVERT: D 779 PHE cc_start: 0.8446 (t80) cc_final: 0.8209 (t80) outliers start: 20 outliers final: 8 residues processed: 788 average time/residue: 1.5021 time to fit residues: 1373.7548 Evaluate side-chains 384 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 376 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 1012 PRO Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 1012 PRO Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 1012 PRO Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 1012 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.7980 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 40.0000 chunk 150 optimal weight: 3.9990 chunk 291 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 217 optimal weight: 0.0470 chunk 337 optimal weight: 0.7980 overall best weight: 1.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 HIS A 279 ASN A 406 ASN A 510 GLN A 517 ASN A 671 GLN A 675 GLN A 681 GLN A 765 HIS A 987 GLN A 997 GLN A1007 ASN A1047 ASN A1090 ASN B 136 HIS ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 HIS B 279 ASN B 406 ASN B 510 GLN B 517 ASN B 619 ASN B 671 GLN B 675 GLN B 681 GLN B 765 HIS B 987 GLN B 997 GLN B1047 ASN B1090 ASN C 136 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 HIS C 279 ASN C 510 GLN C 517 ASN C 671 GLN C 675 GLN C 681 GLN C 987 GLN C 997 GLN C1007 ASN C1047 ASN C1090 ASN D 136 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 HIS D 279 ASN D 406 ASN D 510 GLN D 517 ASN D 619 ASN D 671 GLN D 675 GLN D 681 GLN D 987 GLN D 997 GLN D1047 ASN D1090 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2603 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= 0.226 Angle : 0.688 10.191 42112 Z= 0.361 Chirality : 0.042 0.174 4708 Planarity : 0.005 0.067 5264 Dihedral : 5.682 35.159 4020 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.19 % Allowed : 13.25 % Favored : 83.56 % 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: -2.03 (0.12), residues: 3656 helix: -0.52 (0.10), residues: 2460 sheet: -1.48 (0.36), residues: 188 loop : -3.23 (0.15), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 453 HIS 0.003 0.001 HIS B 136 PHE 0.017 0.001 PHE D1082 TYR 0.013 0.002 TYR C1005 ARG 0.005 0.001 ARG C 507 *********************** 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 590 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 484 time to evaluate : 4.268 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: A 185 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.6934 (t-90) REVERT: A 396 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7165 (mpm) REVERT: A 731 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6664 (t80) REVERT: A 779 PHE cc_start: 0.8486 (t80) cc_final: 0.8284 (t80) REVERT: A 920 ASP cc_start: 0.7895 (t0) cc_final: 0.7671 (t0) REVERT: A 1069 THR cc_start: 0.8268 (p) cc_final: 0.7955 (m) REVERT: B 185 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6901 (t-90) REVERT: B 189 MET cc_start: 0.7615 (mpp) cc_final: 0.6977 (mtt) REVERT: B 396 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7172 (mpm) REVERT: B 615 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7415 (tp30) REVERT: B 731 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6657 (t80) REVERT: B 920 ASP cc_start: 0.7898 (t0) cc_final: 0.7672 (t0) REVERT: B 1069 THR cc_start: 0.8266 (p) cc_final: 0.7951 (m) REVERT: C 185 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.6923 (t-90) REVERT: C 396 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7171 (mpm) REVERT: C 731 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6658 (t80) REVERT: C 779 PHE cc_start: 0.8491 (t80) cc_final: 0.8289 (t80) REVERT: C 920 ASP cc_start: 0.7906 (t0) cc_final: 0.7680 (t0) REVERT: C 1069 THR cc_start: 0.8263 (p) cc_final: 0.7948 (m) REVERT: D 185 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6902 (t-90) REVERT: D 396 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7158 (mpm) REVERT: D 615 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7410 (tp30) REVERT: D 731 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6660 (t80) REVERT: D 779 PHE cc_start: 0.8491 (t80) cc_final: 0.8288 (t80) REVERT: D 920 ASP cc_start: 0.7903 (t0) cc_final: 0.7679 (t0) REVERT: D 1069 THR cc_start: 0.8270 (p) cc_final: 0.7954 (m) outliers start: 106 outliers final: 12 residues processed: 565 average time/residue: 1.3288 time to fit residues: 888.0717 Evaluate side-chains 382 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 358 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 731 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 93 optimal weight: 30.0000 chunk 338 optimal weight: 7.9990 chunk 365 optimal weight: 9.9990 chunk 301 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 271 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 406 ASN A 438 GLN A 572 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 438 GLN B 572 ASN B 619 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 572 ASN ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN D 438 GLN D 572 ASN D 619 ASN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 31088 Z= 0.469 Angle : 0.779 8.167 42112 Z= 0.410 Chirality : 0.047 0.181 4708 Planarity : 0.006 0.063 5264 Dihedral : 5.565 29.155 4000 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.36 % Allowed : 15.41 % Favored : 80.23 % 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: -1.63 (0.13), residues: 3656 helix: -0.12 (0.10), residues: 2460 sheet: -1.81 (0.32), residues: 192 loop : -3.25 (0.15), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 426 HIS 0.006 0.001 HIS D 765 PHE 0.025 0.002 PHE D 155 TYR 0.029 0.002 TYR A1005 ARG 0.007 0.001 ARG A 507 *********************** 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 531 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 386 time to evaluate : 3.753 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 616 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: A 731 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6746 (t80) REVERT: A 779 PHE cc_start: 0.8554 (t80) cc_final: 0.8335 (t80) REVERT: A 920 ASP cc_start: 0.8017 (t0) cc_final: 0.7802 (t0) REVERT: B 615 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7594 (tp30) REVERT: B 616 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: B 731 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6743 (t80) REVERT: B 920 ASP cc_start: 0.8025 (t0) cc_final: 0.7811 (t0) REVERT: C 616 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: C 731 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6743 (t80) REVERT: C 779 PHE cc_start: 0.8559 (t80) cc_final: 0.8338 (t80) REVERT: C 920 ASP cc_start: 0.8029 (t0) cc_final: 0.7814 (t0) REVERT: D 185 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.7088 (t-90) REVERT: D 615 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7593 (tp30) REVERT: D 616 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: D 731 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6745 (t80) REVERT: D 920 ASP cc_start: 0.8021 (t0) cc_final: 0.7806 (t0) outliers start: 145 outliers final: 50 residues processed: 485 average time/residue: 1.2912 time to fit residues: 746.8143 Evaluate side-chains 388 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 329 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 801 MET Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 801 MET Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 850 SER Chi-restraints excluded: chain D residue 940 CYS 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: 1.9990 chunk 175 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 0.0770 chunk 227 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 359 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 321 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- 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 517 ASN A 973 ASN A 990 ASN ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 ASN B 619 ASN B 973 ASN B 990 ASN ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 438 GLN C 517 ASN C 973 ASN C 990 ASN C1007 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 517 ASN D 619 ASN D 973 ASN D 990 ASN ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31088 Z= 0.200 Angle : 0.655 9.051 42112 Z= 0.341 Chirality : 0.042 0.175 4708 Planarity : 0.005 0.064 5264 Dihedral : 5.169 28.629 4000 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.88 % Allowed : 15.66 % Favored : 80.47 % 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: -0.89 (0.13), residues: 3656 helix: 0.49 (0.10), residues: 2468 sheet: -1.62 (0.37), residues: 180 loop : -3.08 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 453 HIS 0.003 0.001 HIS C 138 PHE 0.027 0.001 PHE D 779 TYR 0.020 0.002 TYR C 727 ARG 0.006 0.001 ARG B 507 *********************** 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 504 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 375 time to evaluate : 3.535 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: A 385 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7508 (mm) REVERT: A 616 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: A 731 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6731 (t80) REVERT: A 779 PHE cc_start: 0.8512 (t80) cc_final: 0.8293 (t80) REVERT: A 989 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.7215 (t0) REVERT: B 385 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7506 (mm) REVERT: B 616 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: B 731 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6729 (t80) REVERT: B 989 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7202 (t0) REVERT: C 385 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7510 (mm) REVERT: C 616 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: C 731 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6728 (t80) REVERT: C 779 PHE cc_start: 0.8514 (t80) cc_final: 0.8297 (t80) REVERT: C 989 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7202 (t0) REVERT: D 189 MET cc_start: 0.7608 (mpp) cc_final: 0.7022 (mtt) REVERT: D 385 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7507 (mm) REVERT: D 616 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: D 731 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6727 (t80) REVERT: D 989 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7210 (t0) outliers start: 129 outliers final: 34 residues processed: 473 average time/residue: 1.2162 time to fit residues: 694.3869 Evaluate side-chains 377 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 327 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 183 optimal weight: 20.0000 chunk 322 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 635 ASN A 886 GLN A 973 ASN ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 ASN ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN C 886 GLN C 973 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 ASN ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 31088 Z= 0.357 Angle : 0.712 7.546 42112 Z= 0.372 Chirality : 0.045 0.173 4708 Planarity : 0.005 0.065 5264 Dihedral : 5.183 27.878 4000 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.61 % Allowed : 18.27 % Favored : 78.12 % 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: -0.90 (0.13), residues: 3656 helix: 0.49 (0.10), residues: 2460 sheet: -1.41 (0.35), residues: 192 loop : -3.14 (0.16), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 453 HIS 0.005 0.001 HIS C 765 PHE 0.023 0.002 PHE B 779 TYR 0.020 0.002 TYR D 787 ARG 0.007 0.001 ARG A 507 *********************** 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 464 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 344 time to evaluate : 3.355 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 179 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8619 (pt) REVERT: A 385 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7636 (mm) REVERT: A 616 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: A 731 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6864 (t80) REVERT: A 779 PHE cc_start: 0.8586 (t80) cc_final: 0.8353 (t80) REVERT: A 989 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7194 (t0) REVERT: B 179 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8491 (pt) REVERT: B 385 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7633 (mm) REVERT: B 616 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: B 731 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6864 (t80) REVERT: B 989 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.7183 (t0) REVERT: C 179 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8631 (pt) REVERT: C 385 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7639 (mm) REVERT: C 616 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: C 731 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6860 (t80) REVERT: C 779 PHE cc_start: 0.8590 (t80) cc_final: 0.8358 (t80) REVERT: C 989 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.7181 (t0) REVERT: D 179 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8535 (pt) REVERT: D 188 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8478 (tm) REVERT: D 385 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7637 (mm) REVERT: D 616 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: D 731 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6840 (t80) REVERT: D 989 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7186 (t0) outliers start: 120 outliers final: 62 residues processed: 429 average time/residue: 1.1442 time to fit residues: 596.5513 Evaluate side-chains 403 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 320 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 5.9990 chunk 323 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 359 optimal weight: 0.6980 chunk 298 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 ASN ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 ASN ** D 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 886 GLN D 973 ASN ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31088 Z= 0.265 Angle : 0.661 8.220 42112 Z= 0.346 Chirality : 0.043 0.169 4708 Planarity : 0.005 0.064 5264 Dihedral : 5.054 26.681 4000 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.97 % Allowed : 20.01 % Favored : 77.01 % 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: -0.68 (0.14), residues: 3656 helix: 0.65 (0.10), residues: 2460 sheet: -1.32 (0.36), residues: 192 loop : -3.06 (0.16), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 453 HIS 0.003 0.001 HIS D 765 PHE 0.028 0.001 PHE D1082 TYR 0.020 0.002 TYR B 787 ARG 0.007 0.001 ARG A 507 *********************** 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 442 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 343 time to evaluate : 3.904 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 179 ILE cc_start: 0.8912 (mt) cc_final: 0.8599 (pt) REVERT: A 385 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 605 LYS cc_start: 0.8812 (tppp) cc_final: 0.8445 (tppp) REVERT: A 616 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: A 731 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6909 (t80) REVERT: A 779 PHE cc_start: 0.8578 (t80) cc_final: 0.8340 (t80) REVERT: A 989 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.7161 (t0) REVERT: B 179 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8447 (pt) REVERT: B 385 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7601 (mm) REVERT: B 605 LYS cc_start: 0.8812 (tppp) cc_final: 0.8444 (tppp) REVERT: B 616 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: B 731 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6907 (t80) REVERT: B 989 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7155 (t0) REVERT: C 179 ILE cc_start: 0.8912 (mt) cc_final: 0.8596 (pt) REVERT: C 188 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8402 (tm) REVERT: C 385 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7602 (mm) REVERT: C 426 TRP cc_start: 0.6511 (p-90) cc_final: 0.5994 (p-90) REVERT: C 605 LYS cc_start: 0.8810 (tppp) cc_final: 0.8444 (tppp) REVERT: C 616 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7020 (tm-30) REVERT: C 731 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6905 (t80) REVERT: C 779 PHE cc_start: 0.8584 (t80) cc_final: 0.8343 (t80) REVERT: C 989 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7154 (t0) REVERT: D 179 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8522 (pt) REVERT: D 188 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8543 (tm) REVERT: D 189 MET cc_start: 0.7425 (mpp) cc_final: 0.7096 (mtt) REVERT: D 385 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7597 (mm) REVERT: D 605 LYS cc_start: 0.8811 (tppp) cc_final: 0.8441 (tppp) REVERT: D 616 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: D 731 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6906 (t80) REVERT: D 989 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7153 (t0) outliers start: 99 outliers final: 59 residues processed: 411 average time/residue: 1.1767 time to fit residues: 588.4990 Evaluate side-chains 408 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 329 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 787 TYR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 787 TYR Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 262 optimal weight: 0.0970 chunk 203 optimal weight: 9.9990 chunk 302 optimal weight: 6.9990 chunk 200 optimal weight: 0.0870 chunk 358 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.0158 ------------------------------------------------------------------------------- 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 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31088 Z= 0.174 Angle : 0.631 9.184 42112 Z= 0.328 Chirality : 0.041 0.194 4708 Planarity : 0.004 0.064 5264 Dihedral : 4.799 25.786 4000 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.88 % Allowed : 20.40 % Favored : 76.71 % 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: -0.43 (0.14), residues: 3656 helix: 0.81 (0.10), residues: 2472 sheet: -1.16 (0.37), residues: 192 loop : -2.91 (0.16), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 525 HIS 0.002 0.000 HIS B 257 PHE 0.028 0.001 PHE B 779 TYR 0.022 0.001 TYR C 787 ARG 0.005 0.000 ARG C 688 *********************** 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 468 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 372 time to evaluate : 3.439 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: A 179 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8571 (pt) REVERT: A 385 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7505 (mm) REVERT: A 605 LYS cc_start: 0.8694 (tppp) cc_final: 0.8490 (tppp) REVERT: A 731 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.7074 (t80) REVERT: A 779 PHE cc_start: 0.8575 (t80) cc_final: 0.8325 (t80) REVERT: B 385 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7507 (mm) REVERT: B 605 LYS cc_start: 0.8703 (tppp) cc_final: 0.8501 (tppp) REVERT: B 619 ASN cc_start: 0.7679 (m110) cc_final: 0.7409 (m-40) REVERT: B 731 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.7075 (t80) REVERT: B 989 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.7101 (t0) REVERT: C 179 ILE cc_start: 0.8896 (mt) cc_final: 0.8564 (pt) REVERT: C 189 MET cc_start: 0.7456 (mpm) cc_final: 0.6631 (mmt) REVERT: C 385 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7506 (mm) REVERT: C 451 ARG cc_start: 0.6453 (OUTLIER) cc_final: 0.5482 (pmt-80) REVERT: C 605 LYS cc_start: 0.8690 (tppp) cc_final: 0.8487 (tppp) REVERT: C 731 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.7071 (t80) REVERT: C 779 PHE cc_start: 0.8581 (t80) cc_final: 0.8327 (t80) REVERT: C 989 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.7102 (t0) REVERT: D 189 MET cc_start: 0.7424 (mpp) cc_final: 0.7004 (mtt) REVERT: D 385 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7505 (mm) REVERT: D 605 LYS cc_start: 0.8701 (tppp) cc_final: 0.8497 (tppp) REVERT: D 619 ASN cc_start: 0.7673 (m110) cc_final: 0.7404 (m-40) REVERT: D 731 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.7070 (t80) REVERT: D 989 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.7099 (t0) outliers start: 96 outliers final: 52 residues processed: 440 average time/residue: 1.1274 time to fit residues: 604.8228 Evaluate side-chains 386 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 321 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1091 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 281 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 886 GLN ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN ** D 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31088 Z= 0.203 Angle : 0.649 10.042 42112 Z= 0.335 Chirality : 0.042 0.169 4708 Planarity : 0.004 0.065 5264 Dihedral : 4.736 26.535 4000 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.85 % Allowed : 21.39 % Favored : 75.75 % 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: 0.77 (0.10), residues: 2476 sheet: -1.13 (0.37), residues: 192 loop : -2.79 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 453 HIS 0.002 0.001 HIS B 257 PHE 0.032 0.001 PHE D 779 TYR 0.020 0.001 TYR D 727 ARG 0.005 0.000 ARG C 368 *********************** 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 414 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 319 time to evaluate : 3.768 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 179 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8552 (pt) REVERT: A 189 MET cc_start: 0.7356 (mpm) cc_final: 0.6701 (mmt) REVERT: A 385 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7503 (mm) REVERT: A 616 GLU cc_start: 0.7467 (pp20) cc_final: 0.7123 (tm-30) REVERT: A 779 PHE cc_start: 0.8591 (t80) cc_final: 0.8333 (t80) REVERT: A 787 TYR cc_start: 0.6994 (t80) cc_final: 0.6748 (OUTLIER) REVERT: B 189 MET cc_start: 0.7369 (mpm) cc_final: 0.6655 (mmt) REVERT: B 385 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7458 (mm) REVERT: B 616 GLU cc_start: 0.7544 (pp20) cc_final: 0.6999 (tm-30) REVERT: B 787 TYR cc_start: 0.6897 (t80) cc_final: 0.6683 (OUTLIER) REVERT: C 179 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8554 (pt) REVERT: C 188 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8449 (tm) REVERT: C 385 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7505 (mm) REVERT: C 616 GLU cc_start: 0.7469 (pp20) cc_final: 0.7121 (tm-30) REVERT: C 731 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.7079 (t80) REVERT: C 779 PHE cc_start: 0.8595 (t80) cc_final: 0.8334 (t80) REVERT: C 787 TYR cc_start: 0.6996 (t80) cc_final: 0.6746 (OUTLIER) REVERT: D 188 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8600 (tm) REVERT: D 189 MET cc_start: 0.7465 (mpp) cc_final: 0.7010 (mtt) REVERT: D 385 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7460 (mm) REVERT: D 616 GLU cc_start: 0.7534 (pp20) cc_final: 0.7003 (tm-30) REVERT: D 787 TYR cc_start: 0.6910 (t80) cc_final: 0.6694 (OUTLIER) outliers start: 95 outliers final: 63 residues processed: 387 average time/residue: 1.1162 time to fit residues: 528.8837 Evaluate side-chains 375 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 307 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1091 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 8.9990 chunk 313 optimal weight: 2.9990 chunk 334 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 301 optimal weight: 7.9990 chunk 316 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31088 Z= 0.344 Angle : 0.721 10.718 42112 Z= 0.373 Chirality : 0.045 0.191 4708 Planarity : 0.005 0.066 5264 Dihedral : 4.924 27.235 4000 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.73 % Allowed : 21.63 % Favored : 75.63 % 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: -0.64 (0.13), residues: 3656 helix: 0.59 (0.10), residues: 2468 sheet: -1.31 (0.37), residues: 192 loop : -2.80 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 453 HIS 0.003 0.001 HIS A 268 PHE 0.037 0.002 PHE D1082 TYR 0.018 0.002 TYR B 727 ARG 0.006 0.001 ARG B 507 *********************** 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 418 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 327 time to evaluate : 3.629 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: A 162 ARG cc_start: 0.7028 (ttm110) cc_final: 0.6821 (ttp-110) REVERT: A 179 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8573 (pt) REVERT: A 385 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7683 (mm) REVERT: A 616 GLU cc_start: 0.7582 (pp20) cc_final: 0.7362 (tm-30) REVERT: B 179 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8403 (pt) REVERT: B 385 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7659 (mm) REVERT: C 179 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8567 (pt) REVERT: C 189 MET cc_start: 0.7328 (mpm) cc_final: 0.6573 (mmt) REVERT: C 385 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7687 (mm) REVERT: C 616 GLU cc_start: 0.7584 (pp20) cc_final: 0.7357 (tm-30) REVERT: C 731 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6962 (t80) REVERT: D 189 MET cc_start: 0.7497 (mpp) cc_final: 0.6940 (mtt) REVERT: D 385 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7659 (mm) outliers start: 91 outliers final: 49 residues processed: 390 average time/residue: 1.0151 time to fit residues: 496.1418 Evaluate side-chains 364 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 307 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1091 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 370 optimal weight: 20.0000 chunk 341 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 180 optimal weight: 20.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31088 Z= 0.210 Angle : 0.672 9.940 42112 Z= 0.349 Chirality : 0.042 0.162 4708 Planarity : 0.005 0.098 5264 Dihedral : 4.785 27.660 4000 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.86 % Allowed : 23.08 % Favored : 75.06 % 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: -0.41 (0.14), residues: 3656 helix: 0.75 (0.10), residues: 2472 sheet: -1.19 (0.38), residues: 192 loop : -2.69 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 453 HIS 0.003 0.001 HIS B 257 PHE 0.035 0.001 PHE D 487 TYR 0.027 0.001 TYR A 808 ARG 0.009 0.001 ARG B 507 ********************** 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 380 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 318 time to evaluate : 3.398 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: A 179 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8549 (pt) REVERT: A 385 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7569 (mm) REVERT: A 616 GLU cc_start: 0.7472 (pp20) cc_final: 0.7215 (tm-30) REVERT: B 179 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8420 (pt) REVERT: B 189 MET cc_start: 0.7395 (mpm) cc_final: 0.6610 (mmt) REVERT: B 252 ILE cc_start: 0.8263 (mm) cc_final: 0.8031 (mm) REVERT: B 385 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7597 (mm) REVERT: C 179 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8534 (pt) REVERT: C 385 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7639 (mm) REVERT: C 616 GLU cc_start: 0.7474 (pp20) cc_final: 0.7213 (tm-30) REVERT: C 779 PHE cc_start: 0.8626 (t80) cc_final: 0.8426 (t80) REVERT: D 179 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8394 (pt) REVERT: D 189 MET cc_start: 0.7512 (mpp) cc_final: 0.6966 (mtt) REVERT: D 252 ILE cc_start: 0.8262 (mm) cc_final: 0.8024 (mm) REVERT: D 385 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7598 (mm) outliers start: 62 outliers final: 44 residues processed: 361 average time/residue: 1.1149 time to fit residues: 493.0668 Evaluate side-chains 355 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 303 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 940 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 9.9990 chunk 314 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 295 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.145606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.104346 restraints weight = 62022.603| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.65 r_work: 0.3402 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31088 Z= 0.245 Angle : 0.670 9.718 42112 Z= 0.348 Chirality : 0.042 0.165 4708 Planarity : 0.005 0.085 5264 Dihedral : 4.745 27.604 4000 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.01 % Allowed : 23.08 % Favored : 74.91 % 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: -0.38 (0.14), residues: 3656 helix: 0.78 (0.10), residues: 2472 sheet: -1.20 (0.38), residues: 192 loop : -2.67 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 453 HIS 0.002 0.001 HIS B 257 PHE 0.040 0.001 PHE A 779 TYR 0.023 0.001 TYR A 646 ARG 0.005 0.000 ARG D 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10920.54 seconds wall clock time: 196 minutes 50.92 seconds (11810.92 seconds total)