Starting phenix.real_space_refine on Sun May 25 02:00:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uun_42591/05_2025/8uun_42591.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uun_42591/05_2025/8uun_42591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uun_42591/05_2025/8uun_42591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uun_42591/05_2025/8uun_42591.map" model { file = "/net/cci-nas-00/data/ceres_data/8uun_42591/05_2025/8uun_42591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uun_42591/05_2025/8uun_42591.cif" } resolution = 3.8 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= 0.016 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: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16461 2.51 5 N 4263 2.21 5 O 4988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25829 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8458 Classifications: {'peptide': 1083} Link IDs: {'PTRANS': 57, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8472 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 57, 'TRANS': 1026} Chain breaks: 5 Chain: "C" Number of atoms: 8493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8493 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 58, 'TRANS': 1028} Chain breaks: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 15.38, per 1000 atoms: 0.60 Number of scatterers: 25829 At special positions: 0 Unit cell: (147.851, 154.933, 177.067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4988 8.00 N 4263 7.00 C 16461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B1303 " - " ASN B 709 " " NAG C1301 " - " ASN C 709 " " NAG D 1 " - " ASN B 801 " " NAG E 1 " - " ASN B 717 " " NAG G 1 " - " ASN C 717 " " NAG H 1 " - " ASN C 801 " Time building additional restraints: 6.34 Conformation dependent library (CDL) restraints added in 3.4 seconds 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6094 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 50 sheets defined 25.2% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.684A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.810A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.347A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.677A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.858A pdb=" N VAL A 622 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.682A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.528A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.598A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 868 through 885 removed outlier: 3.555A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.466A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.505A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.391A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.292A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.797A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.762A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.162A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.655A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.270A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.915A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.592A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 869 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.695A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 964 removed outlier: 4.450A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.584A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.762A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.894A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.721A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.620A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.516A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 removed outlier: 4.290A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 618 through 623' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.643A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.684A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.777A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.608A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.413A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.548A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.424A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.267A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.712A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.944A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.564A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.485A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.303A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.566A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 11.527A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.300A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.144A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.656A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.686A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.540A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.922A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.373A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1087 through 1088 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.727A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.219A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.384A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.463A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.695A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.531A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.521A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.678A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.574A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.655A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.266A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.610A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.901A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.983A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.082A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.097A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.814A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.089A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.043A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.097A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.822A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 318 " --> pdb=" O GLY C 593 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.562A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 328 Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.619A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.950A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.950A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.577A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1054 hydrogen bonds defined for protein. 2865 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.91 Time building geometry restraints manager: 7.47 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: 8231 1.34 - 1.47: 6668 1.47 - 1.59: 11378 1.59 - 1.72: 1 1.72 - 1.84: 147 Bond restraints: 26425 Sorted by residual: bond pdb=" CA GLN A 474 " pdb=" CB GLN A 474 " ideal model delta sigma weight residual 1.524 1.610 -0.086 1.30e-02 5.92e+03 4.42e+01 bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.10e+00 bond pdb=" N THR A 599 " pdb=" CA THR A 599 " ideal model delta sigma weight residual 1.453 1.419 0.034 1.18e-02 7.18e+03 8.29e+00 bond pdb=" C ASN B 331 " pdb=" N ILE B 332 " ideal model delta sigma weight residual 1.334 1.299 0.035 1.24e-02 6.50e+03 7.84e+00 bond pdb=" C VAL C 860 " pdb=" N LEU C 861 " ideal model delta sigma weight residual 1.327 1.264 0.063 2.31e-02 1.87e+03 7.42e+00 ... (remaining 26420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 34142 2.21 - 4.42: 1583 4.42 - 6.64: 197 6.64 - 8.85: 43 8.85 - 11.06: 13 Bond angle restraints: 35978 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.84 -7.14 1.22e+00 6.72e-01 3.43e+01 angle pdb=" C ILE B 714 " pdb=" CA ILE B 714 " pdb=" CB ILE B 714 " ideal model delta sigma weight residual 109.33 114.66 -5.33 9.80e-01 1.04e+00 2.96e+01 angle pdb=" C GLN A 913 " pdb=" N ASN A 914 " pdb=" CA ASN A 914 " ideal model delta sigma weight residual 120.82 128.46 -7.64 1.50e+00 4.44e-01 2.60e+01 angle pdb=" C ALA B1070 " pdb=" N GLN B1071 " pdb=" CA GLN B1071 " ideal model delta sigma weight residual 121.33 128.45 -7.12 1.40e+00 5.10e-01 2.59e+01 angle pdb=" N ILE B 714 " pdb=" CA ILE B 714 " pdb=" C ILE B 714 " ideal model delta sigma weight residual 109.19 105.23 3.96 8.20e-01 1.49e+00 2.33e+01 ... (remaining 35973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 15219 23.65 - 47.30: 793 47.30 - 70.95: 89 70.95 - 94.60: 29 94.60 - 118.25: 16 Dihedral angle restraints: 16146 sinusoidal: 6675 harmonic: 9471 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 2.57 -88.57 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -174.26 88.26 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -174.01 88.01 1 1.00e+01 1.00e-02 9.27e+01 ... (remaining 16143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3290 0.077 - 0.154: 759 0.154 - 0.230: 84 0.230 - 0.307: 7 0.307 - 0.384: 2 Chirality restraints: 4142 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 5.23e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 5.16e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.90e+00 ... (remaining 4139 not shown) Planarity restraints: 4639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.066 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO B 987 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 956 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ALA C 956 " 0.057 2.00e-02 2.50e+03 pdb=" O ALA C 956 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN C 957 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 955 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ASN A 955 " -0.057 2.00e-02 2.50e+03 pdb=" O ASN A 955 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA A 956 " 0.019 2.00e-02 2.50e+03 ... (remaining 4636 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6573 2.79 - 3.32: 22683 3.32 - 3.84: 41915 3.84 - 4.37: 45745 4.37 - 4.90: 80201 Nonbonded interactions: 197117 Sorted by model distance: nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.262 3.040 nonbonded pdb=" OE1 GLN A 498 " pdb=" OG1 THR A 500 " model vdw 2.277 3.040 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR B 20 " pdb=" OG SER B 256 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.281 3.040 ... (remaining 197112 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1146 or resid 1301 through 1304)) selection = (chain 'B' and (resid 14 through 623 or resid 634 through 1146 or resid 1301 thr \ ough 1304)) selection = (chain 'C' and (resid 14 through 623 or resid 634 through 1146 or resid 1301 thr \ ough 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.170 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 60.970 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.140 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.009 0.100 26478 Z= 0.412 Angle : 1.074 11.062 36095 Z= 0.603 Chirality : 0.063 0.384 4142 Planarity : 0.007 0.097 4633 Dihedral : 14.538 118.251 9926 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.78 (0.14), residues: 3218 helix: -0.22 (0.18), residues: 670 sheet: 0.02 (0.19), residues: 706 loop : -2.14 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 633 HIS 0.018 0.003 HIS A 655 PHE 0.047 0.003 PHE C 906 TYR 0.024 0.003 TYR A 380 ARG 0.012 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01094 ( 6) link_NAG-ASN : angle 3.06776 ( 18) link_BETA1-4 : bond 0.01072 ( 5) link_BETA1-4 : angle 1.56168 ( 15) hydrogen bonds : bond 0.14380 ( 1021) hydrogen bonds : angle 7.40117 ( 2865) SS BOND : bond 0.00551 ( 42) SS BOND : angle 2.33893 ( 84) covalent geometry : bond 0.00894 (26425) covalent geometry : angle 1.06739 (35978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.828 Fit side-chains revert: symmetry clash REVERT: A 519 HIS cc_start: 0.8093 (m90) cc_final: 0.7790 (m90) REVERT: B 988 GLU cc_start: 0.8995 (mp0) cc_final: 0.8632 (mp0) REVERT: C 238 PHE cc_start: 0.7870 (p90) cc_final: 0.7634 (p90) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3166 time to fit residues: 41.7792 Evaluate side-chains 57 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 9.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 801 ASN A 804 GLN A1101 HIS B 282 ASN B 616 ASN C 804 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.055003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038624 restraints weight = 154614.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.039939 restraints weight = 83238.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.040823 restraints weight = 55470.936| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26478 Z= 0.137 Angle : 0.614 13.756 36095 Z= 0.322 Chirality : 0.045 0.259 4142 Planarity : 0.005 0.069 4633 Dihedral : 9.233 95.147 4094 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.18 % Allowed : 4.64 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.23 (0.14), residues: 3218 helix: 1.19 (0.20), residues: 666 sheet: -0.02 (0.19), residues: 633 loop : -1.94 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 633 HIS 0.004 0.001 HIS C 146 PHE 0.013 0.001 PHE C 79 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 6) link_NAG-ASN : angle 1.84498 ( 18) link_BETA1-4 : bond 0.00340 ( 5) link_BETA1-4 : angle 1.01984 ( 15) hydrogen bonds : bond 0.05372 ( 1021) hydrogen bonds : angle 5.96634 ( 2865) SS BOND : bond 0.00333 ( 42) SS BOND : angle 1.48399 ( 84) covalent geometry : bond 0.00292 (26425) covalent geometry : angle 0.60911 (35978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 2.822 Fit side-chains REVERT: A 519 HIS cc_start: 0.7859 (m90) cc_final: 0.7603 (m90) REVERT: B 773 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8954 (tt0) REVERT: B 988 GLU cc_start: 0.8933 (mp0) cc_final: 0.8621 (mp0) REVERT: C 238 PHE cc_start: 0.7926 (p90) cc_final: 0.7695 (p90) REVERT: C 780 GLU cc_start: 0.9083 (tp30) cc_final: 0.8807 (tm-30) outliers start: 5 outliers final: 0 residues processed: 77 average time/residue: 0.3014 time to fit residues: 42.9179 Evaluate side-chains 60 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 chunk 288 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.053448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.037163 restraints weight = 157289.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.038408 restraints weight = 86113.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.039256 restraints weight = 58096.843| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 26478 Z= 0.257 Angle : 0.675 14.111 36095 Z= 0.347 Chirality : 0.045 0.233 4142 Planarity : 0.004 0.060 4633 Dihedral : 7.932 78.899 4094 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.32 % Allowed : 6.82 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.07 (0.14), residues: 3218 helix: 1.63 (0.21), residues: 654 sheet: -0.10 (0.19), residues: 682 loop : -1.92 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.007 0.002 HIS C 519 PHE 0.014 0.001 PHE C 906 TYR 0.021 0.001 TYR A1067 ARG 0.003 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 6) link_NAG-ASN : angle 1.89399 ( 18) link_BETA1-4 : bond 0.00324 ( 5) link_BETA1-4 : angle 1.32483 ( 15) hydrogen bonds : bond 0.05279 ( 1021) hydrogen bonds : angle 5.80033 ( 2865) SS BOND : bond 0.00359 ( 42) SS BOND : angle 1.43837 ( 84) covalent geometry : bond 0.00571 (26425) covalent geometry : angle 0.67078 (35978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 3.185 Fit side-chains REVERT: A 519 HIS cc_start: 0.7873 (m90) cc_final: 0.7605 (m90) REVERT: B 988 GLU cc_start: 0.8979 (mp0) cc_final: 0.8729 (mp0) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.3165 time to fit residues: 39.1810 Evaluate side-chains 61 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain C residue 33 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 188 optimal weight: 0.6980 chunk 256 optimal weight: 8.9990 chunk 228 optimal weight: 0.0670 chunk 216 optimal weight: 40.0000 chunk 45 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.055385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.039088 restraints weight = 155844.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.040418 restraints weight = 83767.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.041301 restraints weight = 55678.544| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26478 Z= 0.103 Angle : 0.535 11.983 36095 Z= 0.277 Chirality : 0.044 0.285 4142 Planarity : 0.004 0.058 4633 Dihedral : 6.164 58.485 4094 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.60 % Allowed : 7.62 % Favored : 91.78 % 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: -0.78 (0.15), residues: 3218 helix: 2.15 (0.21), residues: 653 sheet: 0.11 (0.20), residues: 634 loop : -1.81 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS A1101 PHE 0.012 0.001 PHE C 157 TYR 0.015 0.001 TYR C1067 ARG 0.002 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 6) link_NAG-ASN : angle 1.28206 ( 18) link_BETA1-4 : bond 0.00493 ( 5) link_BETA1-4 : angle 1.17734 ( 15) hydrogen bonds : bond 0.04283 ( 1021) hydrogen bonds : angle 5.28959 ( 2865) SS BOND : bond 0.00258 ( 42) SS BOND : angle 1.00829 ( 84) covalent geometry : bond 0.00220 (26425) covalent geometry : angle 0.53258 (35978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 3.067 Fit side-chains REVERT: A 519 HIS cc_start: 0.7830 (m90) cc_final: 0.7503 (m90) REVERT: A 1002 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8446 (tm-30) REVERT: B 387 LEU cc_start: 0.9488 (mt) cc_final: 0.9148 (mt) REVERT: B 988 GLU cc_start: 0.8994 (mp0) cc_final: 0.8695 (mp0) REVERT: B 1072 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8455 (pm20) outliers start: 17 outliers final: 4 residues processed: 85 average time/residue: 0.3070 time to fit residues: 48.4152 Evaluate side-chains 70 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 104 optimal weight: 2.9990 chunk 229 optimal weight: 30.0000 chunk 88 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 296 optimal weight: 6.9990 chunk 314 optimal weight: 7.9990 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.053439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.037187 restraints weight = 159905.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.038423 restraints weight = 87996.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039262 restraints weight = 59599.566| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26478 Z= 0.245 Angle : 0.627 10.726 36095 Z= 0.322 Chirality : 0.044 0.222 4142 Planarity : 0.004 0.055 4633 Dihedral : 6.171 59.837 4094 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.95 % Allowed : 9.38 % Favored : 89.67 % 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: -0.83 (0.15), residues: 3218 helix: 2.11 (0.21), residues: 648 sheet: -0.06 (0.19), residues: 665 loop : -1.80 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.006 0.001 HIS A 655 PHE 0.012 0.001 PHE A1121 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 6) link_NAG-ASN : angle 1.80721 ( 18) link_BETA1-4 : bond 0.00264 ( 5) link_BETA1-4 : angle 1.47678 ( 15) hydrogen bonds : bond 0.04840 ( 1021) hydrogen bonds : angle 5.48008 ( 2865) SS BOND : bond 0.00314 ( 42) SS BOND : angle 1.41759 ( 84) covalent geometry : bond 0.00549 (26425) covalent geometry : angle 0.62229 (35978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 3.233 Fit side-chains REVERT: A 519 HIS cc_start: 0.7909 (m90) cc_final: 0.7569 (m90) REVERT: B 387 LEU cc_start: 0.9512 (mt) cc_final: 0.9124 (mt) REVERT: B 988 GLU cc_start: 0.9019 (mp0) cc_final: 0.8689 (mp0) REVERT: C 780 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8646 (tm-30) outliers start: 27 outliers final: 10 residues processed: 86 average time/residue: 0.2952 time to fit residues: 47.4205 Evaluate side-chains 72 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 57 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 152 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN A1101 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN C 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.054418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.038149 restraints weight = 155919.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.039436 restraints weight = 85338.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.040298 restraints weight = 57380.359| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26478 Z= 0.131 Angle : 0.537 9.706 36095 Z= 0.280 Chirality : 0.043 0.232 4142 Planarity : 0.004 0.056 4633 Dihedral : 5.790 56.080 4094 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.67 % Allowed : 10.68 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3218 helix: 2.26 (0.21), residues: 655 sheet: 0.14 (0.19), residues: 661 loop : -1.77 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS A 655 PHE 0.010 0.001 PHE C 157 TYR 0.019 0.001 TYR C1067 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 6) link_NAG-ASN : angle 1.40841 ( 18) link_BETA1-4 : bond 0.00332 ( 5) link_BETA1-4 : angle 1.21888 ( 15) hydrogen bonds : bond 0.04375 ( 1021) hydrogen bonds : angle 5.20973 ( 2865) SS BOND : bond 0.00289 ( 42) SS BOND : angle 1.21604 ( 84) covalent geometry : bond 0.00290 (26425) covalent geometry : angle 0.53315 (35978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 2.964 Fit side-chains REVERT: A 519 HIS cc_start: 0.7895 (m90) cc_final: 0.7541 (m90) REVERT: B 387 LEU cc_start: 0.9504 (mt) cc_final: 0.9115 (mt) REVERT: B 988 GLU cc_start: 0.9047 (mp0) cc_final: 0.8747 (mp0) REVERT: B 1072 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: C 780 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8715 (tm-30) outliers start: 19 outliers final: 8 residues processed: 81 average time/residue: 0.2944 time to fit residues: 44.4840 Evaluate side-chains 72 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 263 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 269 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 297 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 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 = 0.3406 r_free = 0.3406 target = 0.054037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.037827 restraints weight = 156473.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039110 restraints weight = 85196.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.039979 restraints weight = 56982.491| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26478 Z= 0.156 Angle : 0.546 9.439 36095 Z= 0.283 Chirality : 0.043 0.231 4142 Planarity : 0.004 0.059 4633 Dihedral : 5.661 56.303 4094 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.74 % Allowed : 11.00 % Favored : 88.26 % 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: -0.66 (0.15), residues: 3218 helix: 2.30 (0.21), residues: 657 sheet: 0.07 (0.19), residues: 670 loop : -1.74 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 655 PHE 0.009 0.001 PHE C 157 TYR 0.019 0.001 TYR C1067 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 6) link_NAG-ASN : angle 1.50434 ( 18) link_BETA1-4 : bond 0.00281 ( 5) link_BETA1-4 : angle 1.27771 ( 15) hydrogen bonds : bond 0.04365 ( 1021) hydrogen bonds : angle 5.20696 ( 2865) SS BOND : bond 0.00293 ( 42) SS BOND : angle 1.39909 ( 84) covalent geometry : bond 0.00348 (26425) covalent geometry : angle 0.54094 (35978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 2.859 Fit side-chains REVERT: A 519 HIS cc_start: 0.7890 (m90) cc_final: 0.7548 (m90) REVERT: A 869 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8454 (mtm) REVERT: B 387 LEU cc_start: 0.9514 (mt) cc_final: 0.9116 (mt) REVERT: B 988 GLU cc_start: 0.9050 (mp0) cc_final: 0.8753 (mp0) REVERT: B 1072 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8539 (pm20) outliers start: 21 outliers final: 12 residues processed: 80 average time/residue: 0.2924 time to fit residues: 43.3509 Evaluate side-chains 76 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 8 optimal weight: 30.0000 chunk 285 optimal weight: 0.9980 chunk 275 optimal weight: 20.0000 chunk 87 optimal weight: 0.4980 chunk 114 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 189 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.054520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038275 restraints weight = 156513.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.039568 restraints weight = 85483.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.040436 restraints weight = 57350.735| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26478 Z= 0.129 Angle : 0.522 14.134 36095 Z= 0.270 Chirality : 0.043 0.230 4142 Planarity : 0.004 0.060 4633 Dihedral : 5.323 55.690 4094 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.77 % Allowed : 11.42 % Favored : 87.81 % 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: -0.57 (0.15), residues: 3218 helix: 2.42 (0.21), residues: 660 sheet: 0.14 (0.20), residues: 627 loop : -1.68 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE C 157 TYR 0.017 0.001 TYR C1067 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 6) link_NAG-ASN : angle 1.33414 ( 18) link_BETA1-4 : bond 0.00314 ( 5) link_BETA1-4 : angle 1.13958 ( 15) hydrogen bonds : bond 0.04100 ( 1021) hydrogen bonds : angle 5.06639 ( 2865) SS BOND : bond 0.00285 ( 42) SS BOND : angle 1.17677 ( 84) covalent geometry : bond 0.00290 (26425) covalent geometry : angle 0.51882 (35978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 2.989 Fit side-chains REVERT: A 519 HIS cc_start: 0.7845 (m90) cc_final: 0.7496 (m90) REVERT: A 869 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8380 (mtm) REVERT: B 387 LEU cc_start: 0.9506 (mt) cc_final: 0.9103 (mt) REVERT: B 988 GLU cc_start: 0.9044 (mp0) cc_final: 0.8730 (mp0) REVERT: B 1072 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8528 (pm20) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 0.3034 time to fit residues: 46.5942 Evaluate side-chains 78 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 211 optimal weight: 0.9980 chunk 309 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 287 optimal weight: 0.7980 chunk 304 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 128 optimal weight: 30.0000 chunk 281 optimal weight: 0.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.054035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.037888 restraints weight = 158015.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.039161 restraints weight = 86215.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.040021 restraints weight = 57855.777| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26478 Z= 0.181 Angle : 0.567 12.985 36095 Z= 0.292 Chirality : 0.043 0.227 4142 Planarity : 0.004 0.056 4633 Dihedral : 5.426 56.458 4094 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.74 % Allowed : 11.74 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3218 helix: 2.36 (0.21), residues: 657 sheet: 0.02 (0.20), residues: 656 loop : -1.68 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS A 655 PHE 0.008 0.001 PHE B1089 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 6) link_NAG-ASN : angle 1.57094 ( 18) link_BETA1-4 : bond 0.00325 ( 5) link_BETA1-4 : angle 1.28544 ( 15) hydrogen bonds : bond 0.04413 ( 1021) hydrogen bonds : angle 5.17867 ( 2865) SS BOND : bond 0.00337 ( 42) SS BOND : angle 1.29830 ( 84) covalent geometry : bond 0.00404 (26425) covalent geometry : angle 0.56272 (35978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 2.891 Fit side-chains REVERT: A 519 HIS cc_start: 0.7900 (m90) cc_final: 0.7524 (m90) REVERT: A 869 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8417 (mtm) REVERT: B 387 LEU cc_start: 0.9519 (mt) cc_final: 0.9106 (mt) REVERT: B 988 GLU cc_start: 0.9040 (mp0) cc_final: 0.8701 (mp0) REVERT: B 1072 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8520 (pm20) outliers start: 21 outliers final: 14 residues processed: 82 average time/residue: 0.2994 time to fit residues: 45.4193 Evaluate side-chains 79 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 234 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 236 optimal weight: 20.0000 chunk 262 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 242 optimal weight: 0.8980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN C 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.053258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.037160 restraints weight = 157021.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.038416 restraints weight = 85838.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039274 restraints weight = 57761.190| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26478 Z= 0.207 Angle : 0.590 12.864 36095 Z= 0.303 Chirality : 0.044 0.225 4142 Planarity : 0.004 0.097 4633 Dihedral : 5.635 56.372 4094 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.74 % Allowed : 11.70 % Favored : 87.56 % 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: -0.68 (0.15), residues: 3218 helix: 2.27 (0.21), residues: 655 sheet: -0.08 (0.20), residues: 652 loop : -1.67 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS A 655 PHE 0.009 0.001 PHE B1089 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 6) link_NAG-ASN : angle 1.55329 ( 18) link_BETA1-4 : bond 0.00300 ( 5) link_BETA1-4 : angle 1.21353 ( 15) hydrogen bonds : bond 0.04625 ( 1021) hydrogen bonds : angle 5.29272 ( 2865) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.41254 ( 84) covalent geometry : bond 0.00461 (26425) covalent geometry : angle 0.58585 (35978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 2.849 Fit side-chains REVERT: A 519 HIS cc_start: 0.7983 (m90) cc_final: 0.7604 (m90) REVERT: B 387 LEU cc_start: 0.9534 (mt) cc_final: 0.9113 (mt) REVERT: B 988 GLU cc_start: 0.9053 (mp0) cc_final: 0.8696 (mp0) REVERT: B 1072 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: C 177 MET cc_start: -0.5457 (mtt) cc_final: -0.5755 (mtt) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 0.3068 time to fit residues: 47.3151 Evaluate side-chains 79 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 93 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 271 optimal weight: 0.6980 chunk 311 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 318 optimal weight: 8.9990 chunk 273 optimal weight: 0.4980 chunk 168 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN B 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.055023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038883 restraints weight = 154009.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040200 restraints weight = 83246.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.041084 restraints weight = 55419.104| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26478 Z= 0.097 Angle : 0.527 12.871 36095 Z= 0.271 Chirality : 0.043 0.238 4142 Planarity : 0.004 0.095 4633 Dihedral : 5.163 55.003 4094 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.67 % Allowed : 11.84 % Favored : 87.49 % 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: -0.51 (0.15), residues: 3218 helix: 2.50 (0.21), residues: 658 sheet: 0.14 (0.20), residues: 637 loop : -1.64 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS A 146 PHE 0.012 0.001 PHE C 157 TYR 0.016 0.001 TYR C1067 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00043 ( 6) link_NAG-ASN : angle 1.14374 ( 18) link_BETA1-4 : bond 0.00493 ( 5) link_BETA1-4 : angle 1.06063 ( 15) hydrogen bonds : bond 0.03992 ( 1021) hydrogen bonds : angle 4.98939 ( 2865) SS BOND : bond 0.00243 ( 42) SS BOND : angle 0.99644 ( 84) covalent geometry : bond 0.00206 (26425) covalent geometry : angle 0.52419 (35978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6795.87 seconds wall clock time: 120 minutes 45.32 seconds (7245.32 seconds total)