Starting phenix.real_space_refine on Thu Jun 19 04:06:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tey_25855/06_2025/7tey_25855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tey_25855/06_2025/7tey_25855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tey_25855/06_2025/7tey_25855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tey_25855/06_2025/7tey_25855.map" model { file = "/net/cci-nas-00/data/ceres_data/7tey_25855/06_2025/7tey_25855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tey_25855/06_2025/7tey_25855.cif" } resolution = 2.25 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= 0.024 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 92 5.16 5 C 13904 2.51 5 N 3584 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21867 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6496 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "B" Number of atoms: 6496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6496 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "C" Number of atoms: 8091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8091 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 56, 'TRANS': 978} Chain breaks: 7 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: "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: "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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" 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 Time building chain proxies: 13.21, per 1000 atoms: 0.60 Number of scatterers: 21867 At special positions: 0 Unit cell: (140, 147, 174, 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 92 16.00 O 4287 8.00 N 3584 7.00 C 13904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, 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=2.04 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " 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=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.03 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=2.03 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 2.7 seconds 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5064 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 44 sheets defined 26.1% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.052A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.700A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.913A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.564A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.062A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.595A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.952A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 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: 3.615A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.910A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.539A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.038A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.533A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.897A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.646A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.886A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.564A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.892A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 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: 3.656A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.956A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.521A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.229A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.897A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.568A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.963A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.605A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 144 removed outlier: 7.067A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.650A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.080A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.051A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.694A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.505A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.505A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.283A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.660A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.324A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.114A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.741A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.713A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.674A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.560A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.973A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.624A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.211A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.146A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.021A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.452A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 144 removed outlier: 6.857A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.205A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.574A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.449A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.449A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.278A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 1006 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.10 Time building geometry restraints manager: 6.62 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: 6755 1.34 - 1.46: 5506 1.46 - 1.59: 9960 1.59 - 1.71: 0 1.71 - 1.83: 116 Bond restraints: 22337 Sorted by residual: bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.36e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.99e+00 ... (remaining 22332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 29139 1.89 - 3.77: 1124 3.77 - 5.66: 99 5.66 - 7.54: 32 7.54 - 9.43: 7 Bond angle restraints: 30401 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.38 -5.68 1.22e+00 6.72e-01 2.17e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.28 -5.58 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.09 -5.39 1.22e+00 6.72e-01 1.95e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.42 -4.49 1.20e+00 6.94e-01 1.40e+01 ... (remaining 30396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12970 17.92 - 35.84: 867 35.84 - 53.76: 146 53.76 - 71.68: 56 71.68 - 89.60: 25 Dihedral angle restraints: 14064 sinusoidal: 6215 harmonic: 7849 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -58.25 -27.75 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA ASP C 994 " pdb=" CB ASP C 994 " pdb=" CG ASP C 994 " pdb=" OD1 ASP C 994 " ideal model delta sinusoidal sigma weight residual -30.00 -86.93 56.93 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 14061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3072 0.081 - 0.163: 539 0.163 - 0.244: 33 0.244 - 0.325: 2 0.325 - 0.407: 1 Chirality restraints: 3647 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3644 not shown) Planarity restraints: 3899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.016 2.00e-02 2.50e+03 1.63e-02 6.63e+00 pdb=" CG TRP C 886 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 886 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 551 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C VAL C 551 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL C 551 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 552 " 0.014 2.00e-02 2.50e+03 ... (remaining 3896 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6022 2.81 - 3.34: 18440 3.34 - 3.86: 37594 3.86 - 4.38: 43056 4.38 - 4.90: 73807 Nonbonded interactions: 178919 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.294 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.303 3.040 nonbonded pdb=" OE1 GLN C 115 " pdb=" OG1 THR C 167 " model vdw 2.303 3.040 ... (remaining 178914 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' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 52.640 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.005 0.068 22427 Z= 0.247 Angle : 0.851 15.349 30637 Z= 0.449 Chirality : 0.057 0.407 3647 Planarity : 0.006 0.054 3861 Dihedral : 12.951 89.598 8898 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 0.06 (0.15), residues: 2651 helix: 1.22 (0.19), residues: 612 sheet: 0.75 (0.20), residues: 581 loop : -0.78 (0.14), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 886 HIS 0.005 0.001 HIS C 66 PHE 0.036 0.002 PHE A 275 TYR 0.036 0.003 TYR C1067 ARG 0.006 0.001 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00788 ( 38) link_NAG-ASN : angle 3.69572 ( 114) link_BETA1-4 : bond 0.00683 ( 18) link_BETA1-4 : angle 1.57074 ( 54) hydrogen bonds : bond 0.11897 ( 953) hydrogen bonds : angle 7.35085 ( 2793) SS BOND : bond 0.00288 ( 34) SS BOND : angle 1.21401 ( 68) covalent geometry : bond 0.00522 (22337) covalent geometry : angle 0.81934 (30401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7771 (tp-100) REVERT: A 88 ASP cc_start: 0.8420 (m-30) cc_final: 0.8216 (m-30) REVERT: A 205 SER cc_start: 0.8476 (t) cc_final: 0.8242 (m) REVERT: A 591 SER cc_start: 0.8322 (m) cc_final: 0.7938 (p) REVERT: B 54 LEU cc_start: 0.7467 (mm) cc_final: 0.7187 (mp) REVERT: B 287 ASP cc_start: 0.7968 (t0) cc_final: 0.7668 (m-30) REVERT: B 553 THR cc_start: 0.6995 (p) cc_final: 0.6781 (p) REVERT: B 592 PHE cc_start: 0.7294 (p90) cc_final: 0.6884 (p90) REVERT: B 1029 MET cc_start: 0.9141 (tpp) cc_final: 0.8886 (tpp) REVERT: C 129 LYS cc_start: 0.6968 (mtmt) cc_final: 0.6218 (mmtm) REVERT: C 347 PHE cc_start: 0.6661 (m-10) cc_final: 0.6396 (m-10) REVERT: C 396 TYR cc_start: 0.6830 (m-80) cc_final: 0.6586 (m-80) REVERT: C 421 TYR cc_start: 0.8323 (m-10) cc_final: 0.8022 (m-10) REVERT: C 436 TRP cc_start: 0.7005 (p90) cc_final: 0.6577 (p90) REVERT: C 437 ASN cc_start: 0.6398 (t0) cc_final: 0.6174 (m-40) REVERT: C 453 TYR cc_start: 0.7156 (p90) cc_final: 0.6673 (p90) REVERT: C 508 TYR cc_start: 0.7844 (m-80) cc_final: 0.7041 (m-80) outliers start: 0 outliers final: 1 residues processed: 310 average time/residue: 1.3133 time to fit residues: 468.4741 Evaluate side-chains 156 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 81 optimal weight: 0.0060 chunk 128 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 244 optimal weight: 0.3980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN B 901 GLN B 955 ASN B1002 GLN B1011 GLN C 321 GLN C 556 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.155636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.093132 restraints weight = 33615.400| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.46 r_work: 0.3149 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22427 Z= 0.121 Angle : 0.594 20.956 30637 Z= 0.291 Chirality : 0.045 0.391 3647 Planarity : 0.004 0.046 3861 Dihedral : 6.328 59.606 4054 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.18 % Allowed : 7.39 % Favored : 91.42 % 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: 0.61 (0.16), residues: 2651 helix: 2.24 (0.21), residues: 615 sheet: 0.80 (0.21), residues: 605 loop : -0.59 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 886 HIS 0.003 0.001 HIS C1048 PHE 0.025 0.001 PHE C 238 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 38) link_NAG-ASN : angle 3.93872 ( 114) link_BETA1-4 : bond 0.00344 ( 18) link_BETA1-4 : angle 1.13128 ( 54) hydrogen bonds : bond 0.04335 ( 953) hydrogen bonds : angle 5.94566 ( 2793) SS BOND : bond 0.00129 ( 34) SS BOND : angle 0.72287 ( 68) covalent geometry : bond 0.00257 (22337) covalent geometry : angle 0.54243 (30401) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7929 (tm-30) REVERT: A 205 SER cc_start: 0.8717 (t) cc_final: 0.8446 (m) REVERT: A 569 ILE cc_start: 0.8636 (mp) cc_final: 0.8424 (tp) REVERT: A 591 SER cc_start: 0.8534 (m) cc_final: 0.7739 (p) REVERT: A 868 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7613 (tp30) REVERT: A 1010 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8422 (mp10) REVERT: B 287 ASP cc_start: 0.7965 (t0) cc_final: 0.7653 (m-30) REVERT: B 592 PHE cc_start: 0.7493 (p90) cc_final: 0.7044 (p90) REVERT: B 1029 MET cc_start: 0.9434 (tpp) cc_final: 0.9159 (tpp) REVERT: C 129 LYS cc_start: 0.6841 (mtmt) cc_final: 0.6239 (mmtt) REVERT: C 421 TYR cc_start: 0.8224 (m-10) cc_final: 0.7932 (m-10) REVERT: C 436 TRP cc_start: 0.6538 (p90) cc_final: 0.6008 (p90) REVERT: C 453 TYR cc_start: 0.6811 (p90) cc_final: 0.6397 (p90) REVERT: C 508 TYR cc_start: 0.7599 (m-80) cc_final: 0.7239 (m-80) REVERT: C 740 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7965 (ttt) outliers start: 28 outliers final: 11 residues processed: 194 average time/residue: 1.1063 time to fit residues: 253.7379 Evaluate side-chains 158 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 138 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 172 optimal weight: 0.0470 chunk 250 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 239 GLN A 762 GLN A 955 ASN B1002 GLN C 121 ASN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.152466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089000 restraints weight = 33539.965| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.52 r_work: 0.3070 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22427 Z= 0.199 Angle : 0.610 14.659 30637 Z= 0.300 Chirality : 0.047 0.391 3647 Planarity : 0.004 0.042 3861 Dihedral : 5.833 59.030 4052 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.94 % Allowed : 8.15 % Favored : 89.90 % 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: 0.69 (0.16), residues: 2651 helix: 2.42 (0.20), residues: 621 sheet: 0.68 (0.20), residues: 650 loop : -0.57 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 886 HIS 0.004 0.001 HIS C1048 PHE 0.027 0.002 PHE C 238 TYR 0.024 0.002 TYR C1067 ARG 0.005 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 38) link_NAG-ASN : angle 3.52377 ( 114) link_BETA1-4 : bond 0.00291 ( 18) link_BETA1-4 : angle 1.21964 ( 54) hydrogen bonds : bond 0.04717 ( 953) hydrogen bonds : angle 5.79350 ( 2793) SS BOND : bond 0.00181 ( 34) SS BOND : angle 0.68551 ( 68) covalent geometry : bond 0.00451 (22337) covalent geometry : angle 0.56941 (30401) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 200 TYR cc_start: 0.7613 (m-80) cc_final: 0.7374 (t80) REVERT: A 205 SER cc_start: 0.8792 (t) cc_final: 0.8524 (m) REVERT: A 569 ILE cc_start: 0.8706 (mp) cc_final: 0.8450 (tp) REVERT: A 591 SER cc_start: 0.8841 (m) cc_final: 0.8549 (p) REVERT: A 868 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: A 964 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8557 (tttm) REVERT: A 1010 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8426 (mp10) REVERT: B 565 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6690 (p90) REVERT: C 129 LYS cc_start: 0.6811 (mtmt) cc_final: 0.6111 (mmtt) REVERT: C 421 TYR cc_start: 0.8128 (m-10) cc_final: 0.7928 (m-10) REVERT: C 436 TRP cc_start: 0.6419 (p90) cc_final: 0.6082 (p90) REVERT: C 740 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8048 (ttt) REVERT: C 1141 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7332 (tm) outliers start: 46 outliers final: 18 residues processed: 186 average time/residue: 1.0165 time to fit residues: 225.9597 Evaluate side-chains 169 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 0.0070 chunk 258 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 260 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN A1011 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.153368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090607 restraints weight = 33926.582| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.46 r_work: 0.3097 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22427 Z= 0.121 Angle : 0.542 11.812 30637 Z= 0.269 Chirality : 0.045 0.357 3647 Planarity : 0.004 0.041 3861 Dihedral : 5.398 59.297 4052 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.65 % Allowed : 8.83 % Favored : 89.52 % 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: 0.85 (0.16), residues: 2651 helix: 2.63 (0.21), residues: 621 sheet: 0.73 (0.21), residues: 617 loop : -0.46 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.006 0.001 HIS A 66 PHE 0.029 0.001 PHE C 238 TYR 0.022 0.001 TYR C 28 ARG 0.005 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 38) link_NAG-ASN : angle 3.03010 ( 114) link_BETA1-4 : bond 0.00322 ( 18) link_BETA1-4 : angle 1.09759 ( 54) hydrogen bonds : bond 0.04172 ( 953) hydrogen bonds : angle 5.56530 ( 2793) SS BOND : bond 0.00091 ( 34) SS BOND : angle 0.56821 ( 68) covalent geometry : bond 0.00262 (22337) covalent geometry : angle 0.50838 (30401) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 205 SER cc_start: 0.8782 (t) cc_final: 0.8450 (m) REVERT: A 569 ILE cc_start: 0.8685 (mp) cc_final: 0.8422 (tp) REVERT: A 591 SER cc_start: 0.8832 (m) cc_final: 0.8492 (p) REVERT: A 868 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7739 (tp30) REVERT: A 964 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8551 (tttm) REVERT: B 565 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6841 (p90) REVERT: B 780 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8911 (mt-10) REVERT: C 129 LYS cc_start: 0.6878 (mtmt) cc_final: 0.6268 (mmtt) REVERT: C 421 TYR cc_start: 0.8142 (m-10) cc_final: 0.7935 (m-10) REVERT: C 436 TRP cc_start: 0.6694 (p90) cc_final: 0.6126 (p90) REVERT: C 740 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8025 (ttt) outliers start: 39 outliers final: 17 residues processed: 176 average time/residue: 0.9752 time to fit residues: 205.5303 Evaluate side-chains 158 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 214 optimal weight: 6.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 81 ASN A 762 GLN A 824 ASN B 245 HIS B 824 ASN B1002 GLN C 779 GLN C 824 ASN C 978 ASN C1010 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.151655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.087997 restraints weight = 33798.579| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.55 r_work: 0.3053 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22427 Z= 0.186 Angle : 0.580 10.651 30637 Z= 0.287 Chirality : 0.046 0.342 3647 Planarity : 0.004 0.047 3861 Dihedral : 5.375 56.878 4052 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.69 % Allowed : 9.25 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2651 helix: 2.45 (0.21), residues: 629 sheet: 0.59 (0.21), residues: 587 loop : -0.49 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.003 0.001 HIS C1048 PHE 0.028 0.001 PHE C 238 TYR 0.023 0.001 TYR C1067 ARG 0.004 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 38) link_NAG-ASN : angle 3.09683 ( 114) link_BETA1-4 : bond 0.00270 ( 18) link_BETA1-4 : angle 1.18051 ( 54) hydrogen bonds : bond 0.04554 ( 953) hydrogen bonds : angle 5.61538 ( 2793) SS BOND : bond 0.00200 ( 34) SS BOND : angle 0.69128 ( 68) covalent geometry : bond 0.00425 (22337) covalent geometry : angle 0.54719 (30401) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 569 ILE cc_start: 0.8691 (mp) cc_final: 0.8392 (tp) REVERT: A 577 ARG cc_start: 0.5365 (OUTLIER) cc_final: 0.5069 (ptp-110) REVERT: A 591 SER cc_start: 0.8883 (m) cc_final: 0.8525 (p) REVERT: A 858 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8806 (mt) REVERT: A 868 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7780 (tp30) REVERT: A 964 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8606 (tttm) REVERT: B 565 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6900 (p90) REVERT: B 780 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8883 (mt-10) REVERT: B 983 ARG cc_start: 0.7766 (ttm170) cc_final: 0.7526 (mtp180) REVERT: C 52 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8631 (tm-30) REVERT: C 129 LYS cc_start: 0.6935 (mtmt) cc_final: 0.6284 (mmtt) REVERT: C 238 PHE cc_start: 0.6182 (p90) cc_final: 0.5040 (p90) REVERT: C 421 TYR cc_start: 0.8144 (m-10) cc_final: 0.7845 (m-10) REVERT: C 436 TRP cc_start: 0.6746 (p90) cc_final: 0.6215 (p90) REVERT: C 509 ARG cc_start: 0.5684 (mtt180) cc_final: 0.5448 (ttt180) REVERT: C 740 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8049 (ttt) outliers start: 40 outliers final: 20 residues processed: 174 average time/residue: 1.0472 time to fit residues: 217.8895 Evaluate side-chains 164 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 258 optimal weight: 2.9990 chunk 6 optimal weight: 0.0040 chunk 116 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN B 955 ASN B1002 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.151838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089275 restraints weight = 33525.878| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.41 r_work: 0.3072 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22427 Z= 0.146 Angle : 0.553 12.377 30637 Z= 0.274 Chirality : 0.045 0.329 3647 Planarity : 0.004 0.044 3861 Dihedral : 5.099 53.684 4052 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.82 % Allowed : 9.72 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2651 helix: 2.52 (0.21), residues: 628 sheet: 0.41 (0.21), residues: 597 loop : -0.43 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.002 0.001 HIS C1048 PHE 0.024 0.001 PHE C 238 TYR 0.022 0.001 TYR C1067 ARG 0.008 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 38) link_NAG-ASN : angle 2.90150 ( 114) link_BETA1-4 : bond 0.00319 ( 18) link_BETA1-4 : angle 1.08415 ( 54) hydrogen bonds : bond 0.04235 ( 953) hydrogen bonds : angle 5.49785 ( 2793) SS BOND : bond 0.00113 ( 34) SS BOND : angle 0.58567 ( 68) covalent geometry : bond 0.00328 (22337) covalent geometry : angle 0.52346 (30401) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 200 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6251 (t80) REVERT: A 569 ILE cc_start: 0.8694 (mp) cc_final: 0.8359 (tp) REVERT: A 577 ARG cc_start: 0.5425 (OUTLIER) cc_final: 0.5128 (ptp-110) REVERT: A 591 SER cc_start: 0.8875 (m) cc_final: 0.8466 (p) REVERT: A 858 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (mt) REVERT: A 868 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7758 (tp30) REVERT: A 964 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8579 (tttm) REVERT: B 565 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.7008 (p90) REVERT: B 780 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8908 (mt-10) REVERT: B 983 ARG cc_start: 0.7761 (ttm170) cc_final: 0.7549 (mtp180) REVERT: C 52 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8597 (tm-30) REVERT: C 129 LYS cc_start: 0.6833 (mtmt) cc_final: 0.6161 (mmtt) REVERT: C 238 PHE cc_start: 0.5965 (p90) cc_final: 0.4755 (p90) REVERT: C 269 TYR cc_start: 0.7252 (m-80) cc_final: 0.6960 (m-80) REVERT: C 421 TYR cc_start: 0.8101 (m-10) cc_final: 0.7766 (m-10) REVERT: C 436 TRP cc_start: 0.6883 (p90) cc_final: 0.6224 (p90) REVERT: C 740 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8018 (ttt) outliers start: 43 outliers final: 20 residues processed: 171 average time/residue: 0.9745 time to fit residues: 199.7497 Evaluate side-chains 163 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 86 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 125 ASN A 762 GLN B1002 GLN C 115 GLN C 321 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.150810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087696 restraints weight = 33672.322| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.50 r_work: 0.3054 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22427 Z= 0.188 Angle : 0.574 10.066 30637 Z= 0.287 Chirality : 0.046 0.321 3647 Planarity : 0.004 0.047 3861 Dihedral : 5.088 53.848 4052 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.73 % Allowed : 9.84 % Favored : 88.42 % 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 (0.16), residues: 2651 helix: 2.43 (0.21), residues: 630 sheet: 0.23 (0.21), residues: 594 loop : -0.48 (0.15), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.003 0.001 HIS C1048 PHE 0.022 0.001 PHE C 238 TYR 0.023 0.001 TYR C1067 ARG 0.005 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 38) link_NAG-ASN : angle 2.84644 ( 114) link_BETA1-4 : bond 0.00298 ( 18) link_BETA1-4 : angle 1.15645 ( 54) hydrogen bonds : bond 0.04534 ( 953) hydrogen bonds : angle 5.57985 ( 2793) SS BOND : bond 0.00146 ( 34) SS BOND : angle 0.59704 ( 68) covalent geometry : bond 0.00429 (22337) covalent geometry : angle 0.54650 (30401) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7811 (tm-30) REVERT: A 125 ASN cc_start: 0.5316 (OUTLIER) cc_final: 0.4844 (p0) REVERT: A 200 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6241 (t80) REVERT: A 569 ILE cc_start: 0.8598 (mp) cc_final: 0.8211 (tp) REVERT: A 591 SER cc_start: 0.8789 (m) cc_final: 0.8410 (p) REVERT: A 858 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8825 (mt) REVERT: A 868 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7779 (tp30) REVERT: A 964 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8621 (tttm) REVERT: B 565 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7075 (p90) REVERT: B 780 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8889 (mt-10) REVERT: C 52 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8619 (tm-30) REVERT: C 129 LYS cc_start: 0.6761 (mtmt) cc_final: 0.6165 (mmtt) REVERT: C 238 PHE cc_start: 0.6055 (p90) cc_final: 0.4824 (p90) REVERT: C 269 TYR cc_start: 0.7246 (m-80) cc_final: 0.6961 (m-80) REVERT: C 436 TRP cc_start: 0.6875 (p90) cc_final: 0.6200 (p90) REVERT: C 509 ARG cc_start: 0.5669 (mtt180) cc_final: 0.5386 (ttt180) REVERT: C 516 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6610 (pp20) REVERT: C 740 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8013 (ttt) outliers start: 41 outliers final: 20 residues processed: 185 average time/residue: 1.4136 time to fit residues: 310.9841 Evaluate side-chains 164 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 20 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.151112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088623 restraints weight = 33294.659| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.46 r_work: 0.3061 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22427 Z= 0.136 Angle : 0.549 10.392 30637 Z= 0.273 Chirality : 0.045 0.318 3647 Planarity : 0.004 0.049 3861 Dihedral : 4.907 53.722 4052 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.65 % Allowed : 10.35 % Favored : 88.00 % 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: 0.67 (0.16), residues: 2651 helix: 2.55 (0.21), residues: 629 sheet: 0.31 (0.21), residues: 579 loop : -0.45 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.002 0.001 HIS B1088 PHE 0.025 0.001 PHE A 168 TYR 0.034 0.001 TYR C 421 ARG 0.007 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 38) link_NAG-ASN : angle 2.74616 ( 114) link_BETA1-4 : bond 0.00309 ( 18) link_BETA1-4 : angle 1.06394 ( 54) hydrogen bonds : bond 0.04174 ( 953) hydrogen bonds : angle 5.46544 ( 2793) SS BOND : bond 0.00098 ( 34) SS BOND : angle 0.57633 ( 68) covalent geometry : bond 0.00303 (22337) covalent geometry : angle 0.52206 (30401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 200 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.6213 (t80) REVERT: A 569 ILE cc_start: 0.8597 (mp) cc_final: 0.8185 (tp) REVERT: A 577 ARG cc_start: 0.5303 (OUTLIER) cc_final: 0.5070 (ptp-110) REVERT: A 591 SER cc_start: 0.8907 (m) cc_final: 0.8470 (p) REVERT: A 858 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8828 (mt) REVERT: A 868 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: A 964 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8609 (tttm) REVERT: B 565 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7106 (p90) REVERT: B 780 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8891 (mt-10) REVERT: C 52 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8620 (tm-30) REVERT: C 129 LYS cc_start: 0.6780 (mtmt) cc_final: 0.6156 (mmtt) REVERT: C 238 PHE cc_start: 0.6018 (p90) cc_final: 0.4805 (p90) REVERT: C 269 TYR cc_start: 0.7254 (m-80) cc_final: 0.6962 (m-80) REVERT: C 436 TRP cc_start: 0.6878 (p90) cc_final: 0.6464 (p90) REVERT: C 509 ARG cc_start: 0.5666 (mtt180) cc_final: 0.5445 (ttt180) REVERT: C 516 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6602 (pp20) REVERT: C 532 ASN cc_start: 0.8967 (m-40) cc_final: 0.8694 (t0) REVERT: C 740 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8040 (ttt) REVERT: C 940 SER cc_start: 0.7110 (OUTLIER) cc_final: 0.6891 (p) outliers start: 39 outliers final: 17 residues processed: 170 average time/residue: 1.2415 time to fit residues: 251.7082 Evaluate side-chains 164 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 130 optimal weight: 0.7980 chunk 221 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 255 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN B1002 GLN C 978 ASN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.151882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089666 restraints weight = 33339.055| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.48 r_work: 0.3078 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22427 Z= 0.111 Angle : 0.532 10.496 30637 Z= 0.264 Chirality : 0.045 0.314 3647 Planarity : 0.004 0.049 3861 Dihedral : 4.689 53.732 4052 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.10 % Allowed : 10.90 % Favored : 88.00 % 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: 0.75 (0.16), residues: 2651 helix: 2.65 (0.21), residues: 629 sheet: 0.39 (0.21), residues: 579 loop : -0.43 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 104 HIS 0.002 0.000 HIS C 66 PHE 0.022 0.001 PHE C 194 TYR 0.021 0.001 TYR C1067 ARG 0.008 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 38) link_NAG-ASN : angle 2.66955 ( 114) link_BETA1-4 : bond 0.00318 ( 18) link_BETA1-4 : angle 1.04239 ( 54) hydrogen bonds : bond 0.03913 ( 953) hydrogen bonds : angle 5.32530 ( 2793) SS BOND : bond 0.00077 ( 34) SS BOND : angle 0.57331 ( 68) covalent geometry : bond 0.00241 (22337) covalent geometry : angle 0.50613 (30401) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 200 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6246 (t80) REVERT: A 221 SER cc_start: 0.8686 (t) cc_final: 0.8306 (p) REVERT: A 231 ILE cc_start: 0.8599 (pt) cc_final: 0.8332 (pp) REVERT: A 569 ILE cc_start: 0.8658 (mp) cc_final: 0.8254 (tp) REVERT: A 591 SER cc_start: 0.8870 (m) cc_final: 0.8445 (p) REVERT: A 773 GLU cc_start: 0.8849 (tt0) cc_final: 0.8610 (tt0) REVERT: A 868 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7735 (tp30) REVERT: A 964 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8603 (tttm) REVERT: B 565 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7057 (p90) REVERT: B 780 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8907 (mt-10) REVERT: B 983 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7539 (mtp180) REVERT: C 52 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8615 (tm-30) REVERT: C 129 LYS cc_start: 0.6694 (mtmt) cc_final: 0.6134 (mmtt) REVERT: C 238 PHE cc_start: 0.5926 (p90) cc_final: 0.4727 (p90) REVERT: C 269 TYR cc_start: 0.7190 (m-80) cc_final: 0.6872 (m-80) REVERT: C 353 TRP cc_start: 0.6973 (p-90) cc_final: 0.6763 (p-90) REVERT: C 586 ASP cc_start: 0.7555 (t0) cc_final: 0.7226 (t0) REVERT: C 740 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7978 (ttt) REVERT: C 940 SER cc_start: 0.7082 (OUTLIER) cc_final: 0.6876 (p) outliers start: 26 outliers final: 15 residues processed: 165 average time/residue: 1.0681 time to fit residues: 208.6488 Evaluate side-chains 160 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 153 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 215 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 252 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 762 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.151333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.088796 restraints weight = 33421.015| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.50 r_work: 0.3062 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22427 Z= 0.138 Angle : 0.548 11.931 30637 Z= 0.272 Chirality : 0.045 0.312 3647 Planarity : 0.004 0.049 3861 Dihedral : 4.677 53.875 4052 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.31 % Allowed : 10.98 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2651 helix: 2.63 (0.21), residues: 621 sheet: 0.37 (0.21), residues: 575 loop : -0.44 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 436 HIS 0.002 0.001 HIS B1088 PHE 0.023 0.001 PHE A 168 TYR 0.025 0.001 TYR B 170 ARG 0.004 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 38) link_NAG-ASN : angle 2.66361 ( 114) link_BETA1-4 : bond 0.00322 ( 18) link_BETA1-4 : angle 1.06746 ( 54) hydrogen bonds : bond 0.04092 ( 953) hydrogen bonds : angle 5.38583 ( 2793) SS BOND : bond 0.00134 ( 34) SS BOND : angle 1.18900 ( 68) covalent geometry : bond 0.00310 (22337) covalent geometry : angle 0.52021 (30401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 200 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6260 (t80) REVERT: A 221 SER cc_start: 0.8688 (t) cc_final: 0.8312 (p) REVERT: A 231 ILE cc_start: 0.8631 (pt) cc_final: 0.8376 (pp) REVERT: A 569 ILE cc_start: 0.8583 (mp) cc_final: 0.8163 (tp) REVERT: A 591 SER cc_start: 0.8881 (m) cc_final: 0.8441 (p) REVERT: A 773 GLU cc_start: 0.8893 (tt0) cc_final: 0.8639 (tt0) REVERT: A 858 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8783 (mt) REVERT: A 868 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7771 (tp30) REVERT: A 964 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8613 (tttm) REVERT: B 565 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.7082 (p90) REVERT: B 780 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8900 (mt-10) REVERT: B 983 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7619 (mtp180) REVERT: C 52 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8587 (tm-30) REVERT: C 129 LYS cc_start: 0.6645 (mtmt) cc_final: 0.6109 (mmtt) REVERT: C 238 PHE cc_start: 0.5904 (p90) cc_final: 0.4710 (p90) REVERT: C 269 TYR cc_start: 0.7148 (m-80) cc_final: 0.6844 (m-80) REVERT: C 353 TRP cc_start: 0.6939 (p-90) cc_final: 0.6694 (p-90) REVERT: C 516 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6624 (pp20) REVERT: C 740 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7988 (ttt) outliers start: 31 outliers final: 18 residues processed: 163 average time/residue: 1.0867 time to fit residues: 211.5526 Evaluate side-chains 163 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 120 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 209 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 762 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.151048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.088640 restraints weight = 33454.380| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.47 r_work: 0.3061 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22427 Z= 0.143 Angle : 0.547 10.617 30637 Z= 0.273 Chirality : 0.045 0.310 3647 Planarity : 0.004 0.053 3861 Dihedral : 4.695 53.864 4052 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.18 % Allowed : 11.24 % Favored : 87.58 % 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: 0.70 (0.16), residues: 2651 helix: 2.63 (0.21), residues: 622 sheet: 0.36 (0.21), residues: 581 loop : -0.44 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 104 HIS 0.002 0.001 HIS C1048 PHE 0.019 0.001 PHE C 238 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 38) link_NAG-ASN : angle 2.64686 ( 114) link_BETA1-4 : bond 0.00303 ( 18) link_BETA1-4 : angle 1.06296 ( 54) hydrogen bonds : bond 0.04116 ( 953) hydrogen bonds : angle 5.39235 ( 2793) SS BOND : bond 0.00118 ( 34) SS BOND : angle 1.05807 ( 68) covalent geometry : bond 0.00322 (22337) covalent geometry : angle 0.52066 (30401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31917.47 seconds wall clock time: 550 minutes 51.40 seconds (33051.40 seconds total)