Starting phenix.real_space_refine on Sun Jun 22 03:00:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxr_25503/06_2025/7sxr_25503.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxr_25503/06_2025/7sxr_25503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sxr_25503/06_2025/7sxr_25503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxr_25503/06_2025/7sxr_25503.map" model { file = "/net/cci-nas-00/data/ceres_data/7sxr_25503/06_2025/7sxr_25503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxr_25503/06_2025/7sxr_25503.cif" } resolution = 3.0 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= -0.001 sd= 0.033 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 111 5.16 5 C 16059 2.51 5 N 4128 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25236 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8132 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8132 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8132 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 15.47, per 1000 atoms: 0.61 Number of scatterers: 25236 At special positions: 0 Unit cell: (141, 147, 196, 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 111 16.00 O 4938 8.00 N 4128 7.00 C 16059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " 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 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " 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: 6.40 Conformation dependent library (CDL) restraints added in 3.5 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 41 sheets defined 24.7% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.086A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.627A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.456A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.090A 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: 3.626A 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: 3.902A 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 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 1032 removed outlier: 4.071A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.553A 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 337 through 343 removed outlier: 4.051A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.854A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.612A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.021A 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: 3.584A 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 removed outlier: 3.546A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.891A 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 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 1033 removed outlier: 4.007A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.518A 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: 3.852A 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: 3.692A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.870A 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) removed outlier: 3.588A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.600A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.936A 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: 3.676A 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: 3.950A 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: 3.590A 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: 4.288A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 5.535A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.620A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.031A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 11.408A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.066A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 154 through 172 current: chain 'A' and resid 259 through 260 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.686A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.201A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.520A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.101A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.829A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.919A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.348A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.802A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.039A 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: 4.181A 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 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 6.846A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.712A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.596A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 354 through 358 current: chain 'B' and resid 508 through 516 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.029A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.674A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.939A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.354A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 6.496A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.646A 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: 4.161A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.927A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.483A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.294A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 354 through 358 current: chain 'C' and resid 508 through 516 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.263A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.932A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.333A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 852 hydrogen bonds defined for protein. 2373 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.46 Time building geometry restraints manager: 7.57 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: 7762 1.34 - 1.46: 6538 1.46 - 1.59: 11365 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 25803 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.23e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.83e+00 ... (remaining 25798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 33605 1.82 - 3.64: 1367 3.64 - 5.46: 107 5.46 - 7.28: 34 7.28 - 9.10: 11 Bond angle restraints: 35124 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 110.70 116.21 -5.51 1.22e+00 6.72e-01 2.04e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.19 -5.49 1.22e+00 6.72e-01 2.03e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.06 -5.36 1.22e+00 6.72e-01 1.93e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.43 -4.50 1.20e+00 6.94e-01 1.40e+01 ... (remaining 35119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14908 17.93 - 35.86: 1024 35.86 - 53.79: 153 53.79 - 71.72: 57 71.72 - 89.65: 28 Dihedral angle restraints: 16170 sinusoidal: 7092 harmonic: 9078 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 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+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 -57.51 -28.49 1 1.00e+01 1.00e-02 1.16e+01 ... (remaining 16167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3227 0.063 - 0.125: 800 0.125 - 0.188: 114 0.188 - 0.251: 13 0.251 - 0.314: 4 Chirality restraints: 4158 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 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+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 -2.09 -0.31 2.00e-01 2.50e+01 2.38e+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 -2.14 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 4155 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C MET C 902 " 0.051 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C GLN C 920 " 0.043 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.014 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 2.37e-02 5.63e+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 4515 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6869 2.81 - 3.33: 21263 3.33 - 3.85: 43118 3.85 - 4.38: 49692 4.38 - 4.90: 84644 Nonbonded interactions: 205586 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.310 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.313 3.040 ... (remaining 205581 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' selection = chain 'C' } 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: 4.080 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: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 61.620 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.180 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 0.067 25905 Z= 0.226 Angle : 0.822 15.070 35388 Z= 0.436 Chirality : 0.055 0.314 4158 Planarity : 0.006 0.055 4476 Dihedral : 12.745 89.650 10200 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: -0.27 (0.14), residues: 3072 helix: 0.71 (0.18), residues: 670 sheet: 0.42 (0.19), residues: 686 loop : -0.78 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 886 HIS 0.004 0.001 HIS A 66 PHE 0.033 0.002 PHE B 135 TYR 0.025 0.002 TYR C1067 ARG 0.007 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 42) link_NAG-ASN : angle 3.46825 ( 126) link_BETA1-4 : bond 0.00685 ( 18) link_BETA1-4 : angle 1.42996 ( 54) hydrogen bonds : bond 0.12917 ( 852) hydrogen bonds : angle 7.05191 ( 2373) SS BOND : bond 0.00274 ( 42) SS BOND : angle 1.34706 ( 84) covalent geometry : bond 0.00463 (25803) covalent geometry : angle 0.79415 (35124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.9410 (Cg_exo) cc_final: 0.9190 (Cg_endo) REVERT: A 153 MET cc_start: 0.4599 (ptt) cc_final: 0.3915 (tpt) REVERT: A 436 TRP cc_start: 0.6779 (p90) cc_final: 0.6472 (p-90) REVERT: A 755 GLN cc_start: 0.8430 (mm110) cc_final: 0.8091 (mm110) REVERT: A 1002 GLN cc_start: 0.8596 (tt0) cc_final: 0.8262 (tm-30) REVERT: B 135 PHE cc_start: 0.7695 (m-10) cc_final: 0.7485 (m-80) REVERT: B 421 TYR cc_start: 0.8528 (m-10) cc_final: 0.7939 (m-10) REVERT: B 512 VAL cc_start: 0.9252 (t) cc_final: 0.8695 (p) REVERT: B 985 ASP cc_start: 0.8136 (p0) cc_final: 0.7197 (p0) REVERT: C 378 LYS cc_start: 0.9262 (ttmt) cc_final: 0.8953 (ttpp) REVERT: C 456 PHE cc_start: 0.8351 (m-10) cc_final: 0.8046 (m-10) REVERT: C 497 PHE cc_start: 0.4573 (m-10) cc_final: 0.4339 (m-10) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 1.4488 time to fit residues: 283.3248 Evaluate side-chains 77 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 283 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN B 901 GLN B 955 ASN C1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.076121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.048180 restraints weight = 97820.928| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.68 r_work: 0.2892 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25905 Z= 0.121 Angle : 0.537 10.721 35388 Z= 0.271 Chirality : 0.043 0.242 4158 Planarity : 0.004 0.047 4476 Dihedral : 5.845 57.204 4602 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.91 % Allowed : 5.27 % Favored : 93.82 % 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: 0.33 (0.14), residues: 3072 helix: 1.79 (0.20), residues: 687 sheet: 0.53 (0.19), residues: 708 loop : -0.57 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.003 0.001 HIS A 207 PHE 0.015 0.001 PHE A 347 TYR 0.017 0.001 TYR C 489 ARG 0.008 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 42) link_NAG-ASN : angle 2.62766 ( 126) link_BETA1-4 : bond 0.00205 ( 18) link_BETA1-4 : angle 1.11080 ( 54) hydrogen bonds : bond 0.03992 ( 852) hydrogen bonds : angle 5.62993 ( 2373) SS BOND : bond 0.00183 ( 42) SS BOND : angle 0.69876 ( 84) covalent geometry : bond 0.00264 (25803) covalent geometry : angle 0.51288 (35124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4787 (ptt) cc_final: 0.4007 (tpt) REVERT: A 755 GLN cc_start: 0.8901 (mm110) cc_final: 0.8548 (mm110) REVERT: A 1002 GLN cc_start: 0.9176 (tt0) cc_final: 0.8674 (tm-30) REVERT: A 1145 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8285 (tm) REVERT: B 135 PHE cc_start: 0.7788 (m-10) cc_final: 0.7521 (m-80) REVERT: B 421 TYR cc_start: 0.8839 (m-10) cc_final: 0.8263 (m-10) REVERT: B 512 VAL cc_start: 0.9072 (t) cc_final: 0.8588 (p) REVERT: B 985 ASP cc_start: 0.8249 (p0) cc_final: 0.7925 (p0) REVERT: C 456 PHE cc_start: 0.8510 (m-10) cc_final: 0.8216 (m-10) REVERT: C 571 ASP cc_start: 0.7935 (m-30) cc_final: 0.7638 (p0) REVERT: C 1010 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8739 (mp10) outliers start: 25 outliers final: 4 residues processed: 104 average time/residue: 1.3707 time to fit residues: 168.3674 Evaluate side-chains 79 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 106 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 62 optimal weight: 0.2980 chunk 206 optimal weight: 0.9990 chunk 39 optimal weight: 40.0000 chunk 232 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 158 optimal weight: 0.3980 chunk 148 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 580 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.075751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.047894 restraints weight = 97398.100| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.58 r_work: 0.2880 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25905 Z= 0.115 Angle : 0.505 10.522 35388 Z= 0.252 Chirality : 0.043 0.262 4158 Planarity : 0.004 0.040 4476 Dihedral : 5.193 54.897 4602 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.77 % Allowed : 6.59 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3072 helix: 2.23 (0.20), residues: 679 sheet: 0.58 (0.19), residues: 715 loop : -0.45 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.002 0.000 HIS A 207 PHE 0.024 0.001 PHE B 157 TYR 0.013 0.001 TYR B1067 ARG 0.006 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 42) link_NAG-ASN : angle 2.49358 ( 126) link_BETA1-4 : bond 0.00293 ( 18) link_BETA1-4 : angle 1.08352 ( 54) hydrogen bonds : bond 0.03824 ( 852) hydrogen bonds : angle 5.29062 ( 2373) SS BOND : bond 0.00150 ( 42) SS BOND : angle 0.60685 ( 84) covalent geometry : bond 0.00254 (25803) covalent geometry : angle 0.48156 (35124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4702 (ptt) cc_final: 0.3969 (tpt) REVERT: A 1002 GLN cc_start: 0.9167 (tt0) cc_final: 0.8651 (tm-30) REVERT: A 1010 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8407 (mp10) REVERT: B 135 PHE cc_start: 0.7825 (m-10) cc_final: 0.7555 (m-80) REVERT: B 200 TYR cc_start: 0.8908 (m-80) cc_final: 0.8675 (m-80) REVERT: B 985 ASP cc_start: 0.8146 (p0) cc_final: 0.7831 (p0) REVERT: B 1145 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8582 (tm) REVERT: C 378 LYS cc_start: 0.9047 (mtpm) cc_final: 0.8563 (ttpt) REVERT: C 414 GLN cc_start: 0.8834 (mm-40) cc_final: 0.7929 (tm130) REVERT: C 456 PHE cc_start: 0.8537 (m-10) cc_final: 0.8238 (m-10) REVERT: C 571 ASP cc_start: 0.7907 (m-30) cc_final: 0.7487 (t0) REVERT: C 1010 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8745 (mp10) outliers start: 21 outliers final: 6 residues processed: 91 average time/residue: 1.3203 time to fit residues: 142.3636 Evaluate side-chains 81 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 159 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 824 ASN B 872 GLN C 394 ASN C 580 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.073489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.045723 restraints weight = 98304.616| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.47 r_work: 0.2803 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 25905 Z= 0.255 Angle : 0.587 10.126 35388 Z= 0.292 Chirality : 0.045 0.237 4158 Planarity : 0.004 0.040 4476 Dihedral : 5.275 58.421 4602 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.02 % Allowed : 7.14 % Favored : 91.84 % 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: 0.37 (0.15), residues: 3072 helix: 2.00 (0.20), residues: 695 sheet: 0.16 (0.19), residues: 680 loop : -0.44 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 886 HIS 0.004 0.001 HIS C1088 PHE 0.016 0.002 PHE A 238 TYR 0.020 0.001 TYR C 756 ARG 0.008 0.001 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 42) link_NAG-ASN : angle 2.60109 ( 126) link_BETA1-4 : bond 0.00212 ( 18) link_BETA1-4 : angle 1.31865 ( 54) hydrogen bonds : bond 0.04459 ( 852) hydrogen bonds : angle 5.36199 ( 2373) SS BOND : bond 0.00188 ( 42) SS BOND : angle 0.65616 ( 84) covalent geometry : bond 0.00571 (25803) covalent geometry : angle 0.56488 (35124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.7965 (p) cc_final: 0.7722 (p) REVERT: A 153 MET cc_start: 0.4780 (ptt) cc_final: 0.3868 (tpt) REVERT: A 1002 GLN cc_start: 0.9214 (tt0) cc_final: 0.8726 (tm-30) REVERT: A 1010 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8483 (mp10) REVERT: A 1145 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8300 (tm) REVERT: B 104 TRP cc_start: 0.7808 (m-90) cc_final: 0.7514 (m-90) REVERT: B 200 TYR cc_start: 0.8993 (m-80) cc_final: 0.8745 (m-80) REVERT: B 985 ASP cc_start: 0.8190 (p0) cc_final: 0.7958 (p0) REVERT: C 414 GLN cc_start: 0.9005 (mm-40) cc_final: 0.7864 (tm130) REVERT: C 456 PHE cc_start: 0.8619 (m-10) cc_final: 0.8295 (m-10) REVERT: C 571 ASP cc_start: 0.8027 (m-30) cc_final: 0.7641 (p0) outliers start: 28 outliers final: 6 residues processed: 91 average time/residue: 1.2339 time to fit residues: 134.8834 Evaluate side-chains 78 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 320 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 260 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 309 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 221 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 907 ASN B 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.074564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.046850 restraints weight = 97155.407| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.49 r_work: 0.2842 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25905 Z= 0.105 Angle : 0.503 10.178 35388 Z= 0.249 Chirality : 0.043 0.258 4158 Planarity : 0.003 0.052 4476 Dihedral : 4.928 57.630 4602 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.77 % Allowed : 8.20 % Favored : 91.04 % 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: 0.55 (0.15), residues: 3072 helix: 2.24 (0.20), residues: 695 sheet: 0.35 (0.20), residues: 669 loop : -0.40 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.002 0.000 HIS A 207 PHE 0.016 0.001 PHE A 392 TYR 0.015 0.001 TYR B 449 ARG 0.004 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 42) link_NAG-ASN : angle 2.38389 ( 126) link_BETA1-4 : bond 0.00311 ( 18) link_BETA1-4 : angle 0.98269 ( 54) hydrogen bonds : bond 0.03804 ( 852) hydrogen bonds : angle 5.07640 ( 2373) SS BOND : bond 0.00134 ( 42) SS BOND : angle 0.50951 ( 84) covalent geometry : bond 0.00229 (25803) covalent geometry : angle 0.48231 (35124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4663 (ptt) cc_final: 0.3892 (tpt) REVERT: A 347 PHE cc_start: 0.5539 (t80) cc_final: 0.5314 (t80) REVERT: A 740 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8739 (tmm) REVERT: A 1002 GLN cc_start: 0.9223 (tt0) cc_final: 0.8711 (tm-30) REVERT: A 1010 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8421 (mp10) REVERT: A 1145 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8458 (tm) REVERT: B 104 TRP cc_start: 0.7667 (m-90) cc_final: 0.7418 (m-90) REVERT: B 200 TYR cc_start: 0.8980 (m-80) cc_final: 0.8729 (m-80) REVERT: B 759 PHE cc_start: 0.8606 (m-10) cc_final: 0.8392 (m-10) REVERT: B 985 ASP cc_start: 0.8220 (p0) cc_final: 0.7972 (p0) REVERT: C 414 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8057 (tm130) REVERT: C 456 PHE cc_start: 0.8643 (m-10) cc_final: 0.8338 (m-10) REVERT: C 571 ASP cc_start: 0.7938 (m-30) cc_final: 0.7551 (p0) outliers start: 21 outliers final: 4 residues processed: 93 average time/residue: 1.3103 time to fit residues: 145.3078 Evaluate side-chains 77 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN C 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.073290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.045526 restraints weight = 97611.325| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.50 r_work: 0.2810 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 25905 Z= 0.220 Angle : 0.557 10.084 35388 Z= 0.276 Chirality : 0.044 0.238 4158 Planarity : 0.004 0.052 4476 Dihedral : 4.992 58.972 4602 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.80 % Allowed : 8.71 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3072 helix: 2.16 (0.20), residues: 697 sheet: 0.09 (0.19), residues: 678 loop : -0.41 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.003 0.001 HIS C1088 PHE 0.026 0.001 PHE A 347 TYR 0.016 0.001 TYR B1067 ARG 0.011 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 42) link_NAG-ASN : angle 2.46294 ( 126) link_BETA1-4 : bond 0.00159 ( 18) link_BETA1-4 : angle 1.18886 ( 54) hydrogen bonds : bond 0.04147 ( 852) hydrogen bonds : angle 5.16853 ( 2373) SS BOND : bond 0.00171 ( 42) SS BOND : angle 0.59913 ( 84) covalent geometry : bond 0.00496 (25803) covalent geometry : angle 0.53666 (35124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8164 (p) cc_final: 0.7909 (p) REVERT: A 153 MET cc_start: 0.4424 (ptt) cc_final: 0.3768 (tpt) REVERT: A 740 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8662 (tmm) REVERT: A 1002 GLN cc_start: 0.9287 (tt0) cc_final: 0.8762 (tm-30) REVERT: A 1010 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8514 (mp10) REVERT: A 1145 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8405 (tm) REVERT: B 104 TRP cc_start: 0.7805 (m-90) cc_final: 0.7556 (m-90) REVERT: B 200 TYR cc_start: 0.9019 (m-80) cc_final: 0.8768 (m-80) REVERT: C 378 LYS cc_start: 0.9060 (mtmm) cc_final: 0.8347 (ptmm) REVERT: C 414 GLN cc_start: 0.9079 (mm-40) cc_final: 0.7969 (tm130) REVERT: C 456 PHE cc_start: 0.8672 (m-10) cc_final: 0.8386 (m-10) REVERT: C 571 ASP cc_start: 0.8069 (m-30) cc_final: 0.7625 (p0) REVERT: C 779 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.9061 (tm-30) REVERT: C 981 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9235 (mm) REVERT: C 1010 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8759 (mp10) outliers start: 22 outliers final: 3 residues processed: 89 average time/residue: 1.2613 time to fit residues: 133.5807 Evaluate side-chains 76 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 260 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 296 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 253 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.073956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.046271 restraints weight = 97064.050| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.51 r_work: 0.2832 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25905 Z= 0.124 Angle : 0.505 10.333 35388 Z= 0.251 Chirality : 0.043 0.249 4158 Planarity : 0.003 0.054 4476 Dihedral : 4.809 58.460 4602 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.70 % Allowed : 8.96 % Favored : 90.34 % 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: 0.52 (0.15), residues: 3072 helix: 2.22 (0.20), residues: 706 sheet: 0.08 (0.19), residues: 686 loop : -0.32 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.002 0.000 HIS A 207 PHE 0.018 0.001 PHE A 392 TYR 0.015 0.001 TYR B 369 ARG 0.005 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 42) link_NAG-ASN : angle 2.34146 ( 126) link_BETA1-4 : bond 0.00269 ( 18) link_BETA1-4 : angle 1.00335 ( 54) hydrogen bonds : bond 0.03832 ( 852) hydrogen bonds : angle 5.03997 ( 2373) SS BOND : bond 0.00133 ( 42) SS BOND : angle 0.51806 ( 84) covalent geometry : bond 0.00274 (25803) covalent geometry : angle 0.48530 (35124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4615 (ptt) cc_final: 0.4025 (tpt) REVERT: A 740 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8750 (tmm) REVERT: A 1002 GLN cc_start: 0.9283 (tt0) cc_final: 0.8748 (tm-30) REVERT: A 1010 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8437 (mp10) REVERT: A 1145 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8433 (tm) REVERT: B 104 TRP cc_start: 0.7724 (m-90) cc_final: 0.7458 (m-90) REVERT: B 200 TYR cc_start: 0.9005 (m-80) cc_final: 0.8751 (m-80) REVERT: B 1145 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8623 (tm) REVERT: C 414 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8193 (tm-30) REVERT: C 456 PHE cc_start: 0.8690 (m-10) cc_final: 0.8404 (m-10) REVERT: C 571 ASP cc_start: 0.8054 (m-30) cc_final: 0.7605 (p0) REVERT: C 981 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9238 (mm) REVERT: C 1010 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8740 (mp10) outliers start: 19 outliers final: 4 residues processed: 86 average time/residue: 2.2208 time to fit residues: 234.7959 Evaluate side-chains 74 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 5.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 131 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 256 optimal weight: 0.0870 chunk 261 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 179 optimal weight: 0.0370 chunk 216 optimal weight: 10.0000 chunk 229 optimal weight: 40.0000 chunk 162 optimal weight: 4.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.073585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.045961 restraints weight = 97360.841| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.49 r_work: 0.2821 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25905 Z= 0.160 Angle : 0.520 10.367 35388 Z= 0.258 Chirality : 0.044 0.333 4158 Planarity : 0.003 0.053 4476 Dihedral : 4.751 58.416 4602 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.84 % Allowed : 8.96 % Favored : 90.19 % 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: 0.52 (0.15), residues: 3072 helix: 2.27 (0.20), residues: 696 sheet: 0.05 (0.19), residues: 680 loop : -0.31 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.002 0.001 HIS A 207 PHE 0.019 0.001 PHE A 392 TYR 0.013 0.001 TYR B1067 ARG 0.005 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 42) link_NAG-ASN : angle 2.35317 ( 126) link_BETA1-4 : bond 0.00205 ( 18) link_BETA1-4 : angle 1.07462 ( 54) hydrogen bonds : bond 0.03868 ( 852) hydrogen bonds : angle 5.02593 ( 2373) SS BOND : bond 0.00140 ( 42) SS BOND : angle 0.54376 ( 84) covalent geometry : bond 0.00358 (25803) covalent geometry : angle 0.50026 (35124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4637 (ptt) cc_final: 0.4106 (tpt) REVERT: A 347 PHE cc_start: 0.5012 (t80) cc_final: 0.4732 (t80) REVERT: A 740 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8713 (tmm) REVERT: A 1002 GLN cc_start: 0.9284 (tt0) cc_final: 0.8735 (tm-30) REVERT: A 1010 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: A 1145 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8406 (tm) REVERT: B 200 TYR cc_start: 0.9009 (m-80) cc_final: 0.8760 (m-80) REVERT: C 414 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8213 (tm-30) REVERT: C 456 PHE cc_start: 0.8691 (m-10) cc_final: 0.8432 (m-10) REVERT: C 571 ASP cc_start: 0.8064 (m-30) cc_final: 0.7611 (p0) REVERT: C 779 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.9081 (tm-30) REVERT: C 981 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9282 (mm) REVERT: C 1010 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8753 (mp10) outliers start: 23 outliers final: 7 residues processed: 88 average time/residue: 1.2782 time to fit residues: 134.2846 Evaluate side-chains 81 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 0.0070 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 279 optimal weight: 0.0970 chunk 162 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.074259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.046654 restraints weight = 97288.458| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.55 r_work: 0.2853 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25905 Z= 0.097 Angle : 0.494 10.667 35388 Z= 0.245 Chirality : 0.043 0.287 4158 Planarity : 0.003 0.054 4476 Dihedral : 4.534 56.912 4602 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.73 % Allowed : 9.22 % Favored : 90.05 % 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: 0.65 (0.15), residues: 3072 helix: 2.38 (0.20), residues: 696 sheet: 0.16 (0.19), residues: 701 loop : -0.24 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 104 HIS 0.002 0.000 HIS A 207 PHE 0.019 0.001 PHE A 392 TYR 0.015 0.001 TYR B 449 ARG 0.003 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 42) link_NAG-ASN : angle 2.26560 ( 126) link_BETA1-4 : bond 0.00348 ( 18) link_BETA1-4 : angle 0.93206 ( 54) hydrogen bonds : bond 0.03560 ( 852) hydrogen bonds : angle 4.86144 ( 2373) SS BOND : bond 0.00118 ( 42) SS BOND : angle 0.50270 ( 84) covalent geometry : bond 0.00214 (25803) covalent geometry : angle 0.47503 (35124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4722 (ptt) cc_final: 0.4164 (tpt) REVERT: A 347 PHE cc_start: 0.5057 (t80) cc_final: 0.4694 (t80) REVERT: A 740 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8828 (tmm) REVERT: A 1002 GLN cc_start: 0.9254 (tt0) cc_final: 0.8717 (tm-30) REVERT: A 1010 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: A 1145 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8391 (tm) REVERT: C 414 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8072 (tm130) REVERT: C 456 PHE cc_start: 0.8683 (m-10) cc_final: 0.8428 (m-10) REVERT: C 571 ASP cc_start: 0.8083 (m-30) cc_final: 0.7644 (p0) REVERT: C 779 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.9100 (tm-30) REVERT: C 1010 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8738 (mp10) outliers start: 20 outliers final: 8 residues processed: 87 average time/residue: 1.3150 time to fit residues: 136.5367 Evaluate side-chains 79 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 0.0570 chunk 109 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 225 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.074092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.046519 restraints weight = 97102.722| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.48 r_work: 0.2843 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25905 Z= 0.118 Angle : 0.497 10.723 35388 Z= 0.246 Chirality : 0.043 0.308 4158 Planarity : 0.003 0.053 4476 Dihedral : 4.473 56.668 4602 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.70 % Allowed : 9.37 % Favored : 89.94 % 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 (0.15), residues: 3072 helix: 2.41 (0.20), residues: 702 sheet: 0.20 (0.19), residues: 716 loop : -0.23 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 104 HIS 0.003 0.000 HIS A 207 PHE 0.027 0.001 PHE C 497 TYR 0.014 0.001 TYR C 489 ARG 0.005 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 42) link_NAG-ASN : angle 2.27461 ( 126) link_BETA1-4 : bond 0.00262 ( 18) link_BETA1-4 : angle 1.00308 ( 54) hydrogen bonds : bond 0.03636 ( 852) hydrogen bonds : angle 4.85979 ( 2373) SS BOND : bond 0.00121 ( 42) SS BOND : angle 0.49209 ( 84) covalent geometry : bond 0.00265 (25803) covalent geometry : angle 0.47771 (35124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4715 (ptt) cc_final: 0.4161 (tpt) REVERT: A 347 PHE cc_start: 0.5015 (t80) cc_final: 0.4693 (t80) REVERT: A 740 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8790 (tmm) REVERT: A 1002 GLN cc_start: 0.9254 (tt0) cc_final: 0.8719 (tm-30) REVERT: A 1010 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8466 (mp10) REVERT: B 759 PHE cc_start: 0.8580 (m-10) cc_final: 0.8362 (m-10) REVERT: C 408 ARG cc_start: 0.9095 (tmm-80) cc_final: 0.8295 (ppt170) REVERT: C 414 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8593 (mm-40) REVERT: C 456 PHE cc_start: 0.8695 (m-10) cc_final: 0.8435 (m-10) REVERT: C 571 ASP cc_start: 0.8054 (m-30) cc_final: 0.7632 (p0) REVERT: C 779 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.9087 (tm-30) REVERT: C 1010 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8718 (mp10) outliers start: 19 outliers final: 8 residues processed: 84 average time/residue: 1.9337 time to fit residues: 197.2213 Evaluate side-chains 80 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 51 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 281 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 251 optimal weight: 3.9990 chunk 190 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.074300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.046851 restraints weight = 97128.344| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.44 r_work: 0.2856 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25905 Z= 0.105 Angle : 0.493 10.663 35388 Z= 0.243 Chirality : 0.043 0.308 4158 Planarity : 0.003 0.053 4476 Dihedral : 4.409 56.222 4602 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.51 % Allowed : 9.51 % Favored : 89.97 % 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: 0.71 (0.15), residues: 3072 helix: 2.37 (0.20), residues: 708 sheet: 0.11 (0.19), residues: 706 loop : -0.16 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 104 HIS 0.002 0.000 HIS A 207 PHE 0.021 0.001 PHE A 392 TYR 0.017 0.001 TYR B 449 ARG 0.004 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 42) link_NAG-ASN : angle 2.24617 ( 126) link_BETA1-4 : bond 0.00303 ( 18) link_BETA1-4 : angle 0.95249 ( 54) hydrogen bonds : bond 0.03553 ( 852) hydrogen bonds : angle 4.81601 ( 2373) SS BOND : bond 0.00116 ( 42) SS BOND : angle 0.47769 ( 84) covalent geometry : bond 0.00232 (25803) covalent geometry : angle 0.47394 (35124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16686.12 seconds wall clock time: 294 minutes 5.91 seconds (17645.91 seconds total)