Starting phenix.real_space_refine on Tue Aug 26 07:19:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhd_60099/08_2025/8zhd_60099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhd_60099/08_2025/8zhd_60099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zhd_60099/08_2025/8zhd_60099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhd_60099/08_2025/8zhd_60099.map" model { file = "/net/cci-nas-00/data/ceres_data/8zhd_60099/08_2025/8zhd_60099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhd_60099/08_2025/8zhd_60099.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6168 atoms to isotropic. 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 128 5.16 5 C 18594 2.51 5 N 4812 2.21 5 O 5772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29306 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8326 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 8326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8326 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8326 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 920 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 824 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 920 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "G" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 824 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "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: "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: "V" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.52, per 1000 atoms: 0.22 Number of scatterers: 29306 At special positions: 0 Unit cell: (161.518, 187.526, 202.582, 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 128 16.00 O 5772 8.00 N 4812 7.00 C 18594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, 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=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 91 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 V 1 " - " NAG V 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 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " 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 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " 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 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 343 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6804 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 59 sheets defined 19.7% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.754A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.513A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.002A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 778 removed outlier: 3.948A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.036A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.658A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.866A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 6.700A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.400A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.525A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.716A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.563A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.070A pdb=" N ILE B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 411' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 753 removed outlier: 4.125A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.546A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.715A pdb=" N VAL B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 916 " --> pdb=" O GLN B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 916' Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.893A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.198A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.014A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.127A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.632A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.260A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.859A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 778 removed outlier: 3.802A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.011A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.721A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.957A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (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 removed outlier: 4.171A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.116A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.758A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.828A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.894A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.676A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.731A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.593A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.638A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.573A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.340A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.539A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.602A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.078A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 3.624A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.503A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1094 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.762A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.272A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.729A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.586A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.745A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 152 through 154 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.407A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 327 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.648A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.578A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.402A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.505A pdb=" N ILE C 788 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.572A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.572A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.664A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.574A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 49 through 55 removed outlier: 4.153A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.549A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.175A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 152 through 158 removed outlier: 6.613A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.542A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.594A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.808A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.258A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.770A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.537A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.317A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.911A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP H 73 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.176A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR H 94 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR H 114 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.612A pdb=" N VAL L 18 " --> pdb=" O ILE L 78 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE L 78 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 45 through 49 removed outlier: 3.575A pdb=" N VAL L 48 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN L 39 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP L 88 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER L 93 " --> pdb=" O VAL L 100 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 45 through 49 removed outlier: 3.575A pdb=" N VAL L 48 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN L 39 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP L 88 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.663A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP F 73 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN F 82 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR F 69 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 58 through 60 removed outlier: 4.834A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR F 94 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR F 114 " --> pdb=" O TYR F 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.695A pdb=" N VAL G 18 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 45 through 49 removed outlier: 6.879A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN G 92 " --> pdb=" O GLN G 35 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR G 37 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP G 88 " --> pdb=" O GLN G 39 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2646 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: 6.48 Time building geometry restraints manager: 3.55 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: 9298 1.34 - 1.46: 7338 1.46 - 1.59: 13175 1.59 - 1.71: 1 1.71 - 1.83: 164 Bond restraints: 29976 Sorted by residual: bond pdb=" N ILE L 49 " pdb=" CA ILE L 49 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.88e+00 bond pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 8.86e+00 bond pdb=" N CYS B 379 " pdb=" CA CYS B 379 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.21e-02 6.83e+03 8.29e+00 bond pdb=" N ILE B 410 " pdb=" CA ILE B 410 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.22e+00 bond pdb=" N VAL B 433 " pdb=" CA VAL B 433 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.25e-02 6.40e+03 7.99e+00 ... (remaining 29971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 39829 2.03 - 4.05: 842 4.05 - 6.08: 101 6.08 - 8.10: 32 8.10 - 10.13: 7 Bond angle restraints: 40811 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.08 127.61 -5.53 1.47e+00 4.63e-01 1.41e+01 angle pdb=" N THR C 523 " pdb=" CA THR C 523 " pdb=" C THR C 523 " ideal model delta sigma weight residual 113.88 109.30 4.58 1.23e+00 6.61e-01 1.39e+01 angle pdb=" CA GLU A 132 " pdb=" C GLU A 132 " pdb=" O GLU A 132 " ideal model delta sigma weight residual 122.64 118.10 4.54 1.25e+00 6.40e-01 1.32e+01 angle pdb=" CA ASN B 388 " pdb=" C ASN B 388 " pdb=" O ASN B 388 " ideal model delta sigma weight residual 121.94 117.89 4.05 1.15e+00 7.56e-01 1.24e+01 angle pdb=" CA LYS A 202 " pdb=" CB LYS A 202 " pdb=" CG LYS A 202 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 ... (remaining 40806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16198 17.92 - 35.85: 1837 35.85 - 53.77: 431 53.77 - 71.69: 84 71.69 - 89.62: 38 Dihedral angle restraints: 18588 sinusoidal: 7983 harmonic: 10605 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -169.18 83.18 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -167.42 81.42 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -166.39 80.39 1 1.00e+01 1.00e-02 8.00e+01 ... (remaining 18585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 4748 0.201 - 0.402: 7 0.402 - 0.603: 2 0.603 - 0.804: 1 0.804 - 1.005: 1 Chirality restraints: 4759 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.53e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.97e+00 ... (remaining 4756 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 664 " 0.088 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO B 665 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 429 " -0.033 2.00e-02 2.50e+03 2.89e-02 1.46e+01 pdb=" CG PHE B 429 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE B 429 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 429 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 429 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 429 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 429 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 81 " -0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO B 82 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.048 5.00e-02 4.00e+02 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2636 2.75 - 3.29: 27118 3.29 - 3.82: 48424 3.82 - 4.36: 53254 4.36 - 4.90: 94509 Nonbonded interactions: 225941 Sorted by model distance: nonbonded pdb=" O VAL C 130 " pdb=" OG1 THR C 167 " model vdw 2.211 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.250 3.040 nonbonded pdb=" NH2 ARG C 273 " pdb=" OD2 ASP C 290 " model vdw 2.265 3.120 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.277 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.283 3.040 ... (remaining 225936 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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' selection = chain 'V' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'L' } 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=0.00 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.170 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 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 : 0.004 0.085 30082 Z= 0.220 Angle : 0.716 12.749 41083 Z= 0.365 Chirality : 0.052 1.005 4759 Planarity : 0.005 0.132 5223 Dihedral : 15.619 89.617 11646 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.91 % Allowed : 24.34 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.13), residues: 3612 helix: 0.74 (0.20), residues: 641 sheet: 0.15 (0.18), residues: 842 loop : -1.83 (0.12), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 214 TYR 0.029 0.001 TYR B 160 PHE 0.066 0.001 PHE B 429 TRP 0.039 0.002 TRP B 353 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00403 (29976) covalent geometry : angle 0.68656 (40811) SS BOND : bond 0.00215 ( 46) SS BOND : angle 1.02675 ( 92) hydrogen bonds : bond 0.23352 ( 940) hydrogen bonds : angle 9.25729 ( 2646) link_BETA1-4 : bond 0.00456 ( 15) link_BETA1-4 : angle 1.30500 ( 45) link_NAG-ASN : bond 0.00713 ( 45) link_NAG-ASN : angle 3.51215 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.6969 (m-30) cc_final: 0.6584 (m-30) REVERT: B 386 LYS cc_start: 0.5041 (OUTLIER) cc_final: 0.4125 (mmtp) REVERT: B 390 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8198 (mp) REVERT: B 406 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6465 (mt-10) REVERT: B 410 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8352 (mm) REVERT: C 133 PHE cc_start: 0.7314 (m-80) cc_final: 0.6792 (m-10) REVERT: L 51 GLU cc_start: 0.5514 (mm-30) cc_final: 0.5104 (mm-30) outliers start: 29 outliers final: 6 residues processed: 172 average time/residue: 0.1671 time to fit residues: 48.0273 Evaluate side-chains 127 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain L residue 48 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN A 580 GLN A 804 GLN A 901 GLN A 935 GLN B 52 GLN B 321 GLN B 540 ASN B 563 GLN B 751 ASN B 872 GLN B 901 GLN B1054 GLN C 49 HIS C 804 GLN C 895 GLN C 935 GLN F 53 GLN F 112 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.146384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091642 restraints weight = 86006.972| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.76 r_work: 0.2973 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 30082 Z= 0.303 Angle : 0.774 12.361 41083 Z= 0.393 Chirality : 0.052 0.498 4759 Planarity : 0.006 0.088 5223 Dihedral : 6.345 74.618 5205 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.35 % Allowed : 20.65 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.13), residues: 3612 helix: 0.79 (0.20), residues: 627 sheet: -0.03 (0.17), residues: 906 loop : -1.78 (0.12), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 408 TYR 0.028 0.002 TYR L 33 PHE 0.028 0.003 PHE B1103 TRP 0.019 0.002 TRP C1102 HIS 0.012 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00705 (29976) covalent geometry : angle 0.74575 (40811) SS BOND : bond 0.01746 ( 46) SS BOND : angle 2.10579 ( 92) hydrogen bonds : bond 0.05951 ( 940) hydrogen bonds : angle 6.39049 ( 2646) link_BETA1-4 : bond 0.00527 ( 15) link_BETA1-4 : angle 1.74515 ( 45) link_NAG-ASN : bond 0.00770 ( 45) link_NAG-ASN : angle 3.16894 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 119 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8649 (m) REVERT: A 238 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.6309 (p90) REVERT: A 900 MET cc_start: 0.8551 (mmm) cc_final: 0.8268 (mtp) REVERT: A 919 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.7728 (p0) REVERT: A 1106 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8665 (mt0) REVERT: B 160 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7480 (p90) REVERT: B 197 ILE cc_start: 0.8123 (tp) cc_final: 0.7797 (tp) REVERT: B 201 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6722 (t80) REVERT: B 242 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6640 (tp) REVERT: B 425 LEU cc_start: 0.8090 (tp) cc_final: 0.7773 (tp) REVERT: B 429 PHE cc_start: 0.6799 (t80) cc_final: 0.6374 (t80) REVERT: B 514 SER cc_start: 0.6373 (OUTLIER) cc_final: 0.5516 (p) REVERT: C 51 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7828 (p) REVERT: C 133 PHE cc_start: 0.8444 (m-80) cc_final: 0.7433 (m-10) REVERT: C 250 THR cc_start: 0.0315 (OUTLIER) cc_final: 0.0103 (p) REVERT: C 270 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7958 (mt) REVERT: C 737 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.7691 (p0) REVERT: C 740 MET cc_start: 0.8532 (mmm) cc_final: 0.8272 (mmm) REVERT: C 878 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8437 (tt) REVERT: L 33 TYR cc_start: 0.5155 (m-80) cc_final: 0.4930 (m-80) REVERT: L 50 TYR cc_start: 0.6897 (p90) cc_final: 0.6499 (p90) REVERT: G 22 CYS cc_start: 0.4215 (OUTLIER) cc_final: 0.3189 (t) outliers start: 138 outliers final: 63 residues processed: 248 average time/residue: 0.1634 time to fit residues: 68.6358 Evaluate side-chains 175 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 98 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 256 optimal weight: 7.9990 chunk 35 optimal weight: 0.0870 chunk 266 optimal weight: 1.9990 chunk 179 optimal weight: 0.0000 chunk 353 optimal weight: 0.3980 chunk 359 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 288 optimal weight: 0.6980 chunk 223 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 338 optimal weight: 7.9990 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 544 ASN B 564 GLN B 919 ASN B 965 GLN ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.141016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087165 restraints weight = 87432.022| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.13 r_work: 0.3058 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 30082 Z= 0.099 Angle : 0.538 12.313 41083 Z= 0.267 Chirality : 0.044 0.413 4759 Planarity : 0.004 0.067 5223 Dihedral : 5.323 58.273 5190 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.59 % Allowed : 21.63 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.13), residues: 3612 helix: 1.63 (0.22), residues: 630 sheet: 0.13 (0.17), residues: 879 loop : -1.68 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG L 40 TYR 0.019 0.001 TYR B 508 PHE 0.022 0.001 PHE C 168 TRP 0.012 0.001 TRP B 353 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00215 (29976) covalent geometry : angle 0.51132 (40811) SS BOND : bond 0.00241 ( 46) SS BOND : angle 1.60693 ( 92) hydrogen bonds : bond 0.04064 ( 940) hydrogen bonds : angle 5.60900 ( 2646) link_BETA1-4 : bond 0.00416 ( 15) link_BETA1-4 : angle 1.06251 ( 45) link_NAG-ASN : bond 0.00560 ( 45) link_NAG-ASN : angle 2.62124 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 112 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8522 (m) REVERT: A 726 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9167 (mm) REVERT: A 786 LYS cc_start: 0.8583 (mmtp) cc_final: 0.7988 (ptpp) REVERT: A 919 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7547 (p0) REVERT: B 201 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6696 (t80) REVERT: B 402 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6270 (pt) REVERT: B 439 ASN cc_start: 0.8951 (p0) cc_final: 0.8369 (m-40) REVERT: B 508 TYR cc_start: 0.9208 (m-80) cc_final: 0.8786 (m-80) REVERT: B 544 ASN cc_start: -0.3445 (OUTLIER) cc_final: -0.4024 (m-40) REVERT: B 855 PHE cc_start: 0.7532 (m-80) cc_final: 0.6557 (m-80) REVERT: C 133 PHE cc_start: 0.8496 (m-80) cc_final: 0.7453 (m-10) REVERT: C 250 THR cc_start: -0.0129 (OUTLIER) cc_final: -0.0361 (p) REVERT: C 737 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7696 (p0) REVERT: C 740 MET cc_start: 0.8520 (mmm) cc_final: 0.8229 (mmm) REVERT: L 33 TYR cc_start: 0.5088 (m-80) cc_final: 0.4573 (m-80) REVERT: L 50 TYR cc_start: 0.7111 (p90) cc_final: 0.6699 (p90) REVERT: L 92 GLN cc_start: 0.3003 (tm-30) cc_final: 0.1334 (mp10) REVERT: G 22 CYS cc_start: 0.4623 (OUTLIER) cc_final: 0.3587 (t) outliers start: 82 outliers final: 41 residues processed: 185 average time/residue: 0.1714 time to fit residues: 55.1809 Evaluate side-chains 154 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 104 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 83 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 350 optimal weight: 50.0000 chunk 338 optimal weight: 50.0000 chunk 255 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 353 optimal weight: 30.0000 chunk 131 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 211 ASN B 321 GLN B 481 ASN B 544 ASN B 901 GLN C 99 ASN C 919 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.134221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080135 restraints weight = 87705.449| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 5.10 r_work: 0.2797 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 30082 Z= 0.282 Angle : 0.721 11.968 41083 Z= 0.362 Chirality : 0.049 0.526 4759 Planarity : 0.005 0.054 5223 Dihedral : 5.555 59.837 5190 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.16 % Rotamer: Outliers : 4.26 % Allowed : 21.37 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.13), residues: 3612 helix: 1.06 (0.21), residues: 646 sheet: -0.01 (0.17), residues: 873 loop : -1.75 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 905 TYR 0.022 0.002 TYR B 904 PHE 0.023 0.002 PHE B1103 TRP 0.019 0.002 TRP B 353 HIS 0.010 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00673 (29976) covalent geometry : angle 0.69144 (40811) SS BOND : bond 0.00466 ( 46) SS BOND : angle 2.04343 ( 92) hydrogen bonds : bond 0.05907 ( 940) hydrogen bonds : angle 5.74665 ( 2646) link_BETA1-4 : bond 0.00311 ( 15) link_BETA1-4 : angle 1.50085 ( 45) link_NAG-ASN : bond 0.00645 ( 45) link_NAG-ASN : angle 3.16774 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 103 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7744 (t-90) REVERT: A 227 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8756 (m) REVERT: A 238 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.6306 (p90) REVERT: A 240 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8085 (t) REVERT: A 281 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8814 (pm20) REVERT: A 289 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.8054 (m) REVERT: A 726 ILE cc_start: 0.9564 (OUTLIER) cc_final: 0.9345 (mm) REVERT: A 753 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8511 (tt) REVERT: A 786 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8073 (ptpt) REVERT: A 919 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.7592 (p0) REVERT: A 1106 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8722 (mt0) REVERT: B 104 TRP cc_start: 0.6922 (m-90) cc_final: 0.6699 (m-90) REVERT: B 201 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6772 (t80) REVERT: B 293 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8955 (tp) REVERT: B 429 PHE cc_start: 0.7360 (t80) cc_final: 0.7064 (t80) REVERT: B 439 ASN cc_start: 0.8987 (p0) cc_final: 0.8385 (m-40) REVERT: B 492 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7259 (mm) REVERT: B 508 TYR cc_start: 0.9206 (m-80) cc_final: 0.8796 (m-80) REVERT: B 541 PHE cc_start: 0.4254 (m-80) cc_final: 0.3967 (m-10) REVERT: B 670 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8953 (mt) REVERT: B 855 PHE cc_start: 0.7741 (m-80) cc_final: 0.6843 (m-80) REVERT: B 856 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8413 (p0) REVERT: B 902 MET cc_start: 0.9369 (tpp) cc_final: 0.8940 (tpp) REVERT: C 133 PHE cc_start: 0.8759 (m-80) cc_final: 0.7943 (m-10) REVERT: C 141 LEU cc_start: 0.8741 (mm) cc_final: 0.8267 (tt) REVERT: C 250 THR cc_start: 0.0491 (OUTLIER) cc_final: 0.0260 (p) REVERT: C 434 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7398 (tp) REVERT: L 33 TYR cc_start: 0.5369 (m-80) cc_final: 0.4855 (m-80) REVERT: L 50 TYR cc_start: 0.7233 (p90) cc_final: 0.6711 (p90) REVERT: L 92 GLN cc_start: 0.3955 (tm-30) cc_final: 0.1967 (mp10) REVERT: G 22 CYS cc_start: 0.4239 (OUTLIER) cc_final: 0.3424 (t) outliers start: 135 outliers final: 69 residues processed: 231 average time/residue: 0.1676 time to fit residues: 67.0711 Evaluate side-chains 179 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 92 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 83 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 109 optimal weight: 2.9990 chunk 160 optimal weight: 0.3980 chunk 216 optimal weight: 0.7980 chunk 335 optimal weight: 50.0000 chunk 276 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 323 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 320 optimal weight: 40.0000 chunk 68 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.138131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082351 restraints weight = 86139.041| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.30 r_work: 0.2903 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30082 Z= 0.109 Angle : 0.551 12.032 41083 Z= 0.271 Chirality : 0.044 0.412 4759 Planarity : 0.004 0.051 5223 Dihedral : 4.940 53.470 5190 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.12 % Allowed : 22.32 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.14), residues: 3612 helix: 1.72 (0.22), residues: 638 sheet: 0.16 (0.17), residues: 849 loop : -1.68 (0.12), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.021 0.001 TYR A 170 PHE 0.019 0.001 PHE C 168 TRP 0.014 0.001 TRP B 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00248 (29976) covalent geometry : angle 0.52519 (40811) SS BOND : bond 0.00589 ( 46) SS BOND : angle 1.44534 ( 92) hydrogen bonds : bond 0.04227 ( 940) hydrogen bonds : angle 5.22794 ( 2646) link_BETA1-4 : bond 0.00310 ( 15) link_BETA1-4 : angle 1.06663 ( 45) link_NAG-ASN : bond 0.00496 ( 45) link_NAG-ASN : angle 2.70023 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 102 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7694 (t-90) REVERT: A 200 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7845 (t80) REVERT: A 227 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8762 (m) REVERT: A 238 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6454 (p90) REVERT: A 726 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9224 (mm) REVERT: A 786 LYS cc_start: 0.8553 (mmtp) cc_final: 0.7933 (ptpt) REVERT: A 919 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7606 (p0) REVERT: B 104 TRP cc_start: 0.6710 (m-90) cc_final: 0.6483 (m-90) REVERT: B 201 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6662 (t80) REVERT: B 242 LEU cc_start: 0.7700 (mm) cc_final: 0.7147 (tp) REVERT: B 429 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7041 (t80) REVERT: B 439 ASN cc_start: 0.8958 (p0) cc_final: 0.8362 (m-40) REVERT: B 508 TYR cc_start: 0.9171 (m-80) cc_final: 0.8732 (m-80) REVERT: B 543 PHE cc_start: 0.4802 (m-10) cc_final: 0.3955 (t80) REVERT: B 670 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8974 (mt) REVERT: B 855 PHE cc_start: 0.7485 (m-80) cc_final: 0.6543 (m-80) REVERT: B 856 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8242 (p0) REVERT: C 133 PHE cc_start: 0.8647 (m-80) cc_final: 0.7585 (m-10) REVERT: C 135 PHE cc_start: 0.7829 (m-80) cc_final: 0.7540 (m-10) REVERT: C 434 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7369 (tp) REVERT: C 737 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.7809 (p0) REVERT: L 33 TYR cc_start: 0.5133 (m-80) cc_final: 0.4691 (m-80) REVERT: L 50 TYR cc_start: 0.7258 (p90) cc_final: 0.6815 (p90) REVERT: L 92 GLN cc_start: 0.3270 (tm-30) cc_final: 0.1521 (mp10) REVERT: G 22 CYS cc_start: 0.4186 (OUTLIER) cc_final: 0.3499 (t) outliers start: 99 outliers final: 58 residues processed: 192 average time/residue: 0.1460 time to fit residues: 48.5658 Evaluate side-chains 168 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 97 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 83 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 264 optimal weight: 9.9990 chunk 239 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 355 optimal weight: 40.0000 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 315 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN B 211 ASN B 544 ASN B 804 GLN C 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.135667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080886 restraints weight = 86421.078| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 4.61 r_work: 0.2839 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30082 Z= 0.167 Angle : 0.572 11.846 41083 Z= 0.284 Chirality : 0.045 0.431 4759 Planarity : 0.004 0.048 5223 Dihedral : 4.563 43.376 5190 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.44 % Allowed : 21.53 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.14), residues: 3612 helix: 1.67 (0.21), residues: 645 sheet: 0.12 (0.18), residues: 834 loop : -1.61 (0.12), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 408 TYR 0.017 0.001 TYR B 369 PHE 0.026 0.001 PHE B 541 TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00397 (29976) covalent geometry : angle 0.54511 (40811) SS BOND : bond 0.00353 ( 46) SS BOND : angle 1.67124 ( 92) hydrogen bonds : bond 0.04570 ( 940) hydrogen bonds : angle 5.16168 ( 2646) link_BETA1-4 : bond 0.00242 ( 15) link_BETA1-4 : angle 1.17588 ( 45) link_NAG-ASN : bond 0.00498 ( 45) link_NAG-ASN : angle 2.74767 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 103 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7723 (t-90) REVERT: A 200 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7972 (t80) REVERT: A 238 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6350 (p90) REVERT: A 281 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8781 (pm20) REVERT: A 726 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9232 (mm) REVERT: A 753 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8376 (tt) REVERT: A 786 LYS cc_start: 0.8417 (mmtp) cc_final: 0.8004 (ptpt) REVERT: A 1106 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8555 (mt0) REVERT: B 201 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.6941 (t80) REVERT: B 319 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8496 (ttm-80) REVERT: B 429 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7082 (t80) REVERT: B 439 ASN cc_start: 0.8788 (p0) cc_final: 0.8109 (m-40) REVERT: B 508 TYR cc_start: 0.9157 (m-80) cc_final: 0.8708 (m-80) REVERT: B 532 ASN cc_start: 0.8991 (m110) cc_final: 0.8372 (t0) REVERT: B 543 PHE cc_start: 0.5288 (m-10) cc_final: 0.4275 (t80) REVERT: B 670 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9039 (mt) REVERT: B 814 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8980 (mmtm) REVERT: B 855 PHE cc_start: 0.7661 (m-80) cc_final: 0.6909 (m-10) REVERT: B 856 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8231 (p0) REVERT: C 133 PHE cc_start: 0.8663 (m-80) cc_final: 0.7659 (m-10) REVERT: C 135 PHE cc_start: 0.8019 (m-80) cc_final: 0.7720 (m-10) REVERT: C 141 LEU cc_start: 0.8759 (mm) cc_final: 0.8355 (tt) REVERT: C 434 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7566 (tp) REVERT: C 737 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.7838 (p0) REVERT: C 740 MET cc_start: 0.8964 (mmm) cc_final: 0.8701 (mmm) REVERT: C 821 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8401 (tp) REVERT: L 33 TYR cc_start: 0.5160 (m-80) cc_final: 0.4725 (m-80) REVERT: L 50 TYR cc_start: 0.7272 (p90) cc_final: 0.6820 (p90) REVERT: L 92 GLN cc_start: 0.3417 (tm-30) cc_final: 0.1633 (mp10) REVERT: G 22 CYS cc_start: 0.3984 (OUTLIER) cc_final: 0.3298 (t) outliers start: 109 outliers final: 68 residues processed: 206 average time/residue: 0.1624 time to fit residues: 57.6330 Evaluate side-chains 181 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 96 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 83 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 319 optimal weight: 8.9990 chunk 335 optimal weight: 8.9990 chunk 302 optimal weight: 0.8980 chunk 280 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 329 optimal weight: 30.0000 chunk 144 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 919 ASN B 211 ASN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.136141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.081993 restraints weight = 86698.989| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.56 r_work: 0.2844 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30082 Z= 0.167 Angle : 0.569 11.938 41083 Z= 0.281 Chirality : 0.044 0.425 4759 Planarity : 0.004 0.045 5223 Dihedral : 4.462 42.746 5189 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.12 % Allowed : 21.85 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.14), residues: 3612 helix: 1.72 (0.21), residues: 642 sheet: 0.18 (0.18), residues: 806 loop : -1.59 (0.12), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.015 0.001 TYR C 369 PHE 0.019 0.001 PHE C1121 TRP 0.016 0.001 TRP B 353 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00401 (29976) covalent geometry : angle 0.54316 (40811) SS BOND : bond 0.00317 ( 46) SS BOND : angle 1.56389 ( 92) hydrogen bonds : bond 0.04507 ( 940) hydrogen bonds : angle 5.10684 ( 2646) link_BETA1-4 : bond 0.00231 ( 15) link_BETA1-4 : angle 1.10413 ( 45) link_NAG-ASN : bond 0.00479 ( 45) link_NAG-ASN : angle 2.72646 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 99 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7622 (t-90) REVERT: A 200 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.7959 (t80) REVERT: A 238 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6662 (p90) REVERT: A 326 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7191 (tt) REVERT: A 726 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9209 (mm) REVERT: A 753 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8486 (tt) REVERT: A 786 LYS cc_start: 0.8412 (mmtp) cc_final: 0.8000 (ptpt) REVERT: A 919 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7722 (p0) REVERT: A 1106 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8560 (mt0) REVERT: B 160 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7532 (p90) REVERT: B 201 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7237 (t80) REVERT: B 429 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7147 (t80) REVERT: B 439 ASN cc_start: 0.8808 (p0) cc_final: 0.8101 (m-40) REVERT: B 508 TYR cc_start: 0.9179 (m-80) cc_final: 0.8729 (m-80) REVERT: B 532 ASN cc_start: 0.9062 (m110) cc_final: 0.8535 (t0) REVERT: B 543 PHE cc_start: 0.5427 (m-10) cc_final: 0.4455 (t80) REVERT: B 670 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9017 (mt) REVERT: B 855 PHE cc_start: 0.7654 (m-80) cc_final: 0.6697 (m-80) REVERT: B 856 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8290 (p0) REVERT: C 133 PHE cc_start: 0.8800 (m-80) cc_final: 0.7834 (m-10) REVERT: C 135 PHE cc_start: 0.8025 (m-80) cc_final: 0.7748 (m-10) REVERT: C 434 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7567 (tp) REVERT: C 737 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8215 (p0) REVERT: C 740 MET cc_start: 0.8976 (mmm) cc_final: 0.8694 (mmm) REVERT: L 33 TYR cc_start: 0.5260 (m-80) cc_final: 0.4781 (m-80) REVERT: L 50 TYR cc_start: 0.7236 (p90) cc_final: 0.6732 (p90) REVERT: L 92 GLN cc_start: 0.3603 (tm-30) cc_final: 0.1686 (mp10) REVERT: G 22 CYS cc_start: 0.4233 (OUTLIER) cc_final: 0.3401 (t) outliers start: 99 outliers final: 72 residues processed: 194 average time/residue: 0.1576 time to fit residues: 53.1017 Evaluate side-chains 185 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 97 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 83 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 264 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 258 optimal weight: 50.0000 chunk 95 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN B 211 ASN C 580 GLN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.135442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.081415 restraints weight = 86925.481| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.50 r_work: 0.2846 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30082 Z= 0.150 Angle : 0.558 11.952 41083 Z= 0.274 Chirality : 0.044 0.414 4759 Planarity : 0.004 0.044 5223 Dihedral : 4.356 40.413 5189 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.34 % Allowed : 21.78 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.14), residues: 3612 helix: 1.80 (0.22), residues: 642 sheet: 0.12 (0.18), residues: 823 loop : -1.58 (0.12), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.016 0.001 TYR B 369 PHE 0.019 0.001 PHE C1121 TRP 0.024 0.001 TRP B 353 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00358 (29976) covalent geometry : angle 0.53222 (40811) SS BOND : bond 0.00304 ( 46) SS BOND : angle 1.50551 ( 92) hydrogen bonds : bond 0.04362 ( 940) hydrogen bonds : angle 5.02963 ( 2646) link_BETA1-4 : bond 0.00236 ( 15) link_BETA1-4 : angle 1.08341 ( 45) link_NAG-ASN : bond 0.00475 ( 45) link_NAG-ASN : angle 2.68527 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 98 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7598 (t-90) REVERT: A 117 LEU cc_start: 0.8544 (tt) cc_final: 0.8039 (mp) REVERT: A 200 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 238 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6487 (p90) REVERT: A 281 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8767 (pm20) REVERT: A 326 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6933 (tt) REVERT: A 726 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9204 (mm) REVERT: A 753 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8621 (tt) REVERT: A 786 LYS cc_start: 0.8379 (mmtp) cc_final: 0.7979 (ptpt) REVERT: A 919 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7848 (p0) REVERT: A 1106 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8558 (mt0) REVERT: B 160 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7593 (p90) REVERT: B 201 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: B 429 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7095 (t80) REVERT: B 439 ASN cc_start: 0.8748 (p0) cc_final: 0.8002 (m-40) REVERT: B 508 TYR cc_start: 0.9186 (m-80) cc_final: 0.8715 (m-80) REVERT: B 532 ASN cc_start: 0.9127 (m110) cc_final: 0.8561 (t0) REVERT: B 543 PHE cc_start: 0.6241 (m-10) cc_final: 0.5022 (t80) REVERT: B 670 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9050 (mt) REVERT: B 814 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9002 (mmtm) REVERT: B 855 PHE cc_start: 0.7708 (m-80) cc_final: 0.6785 (m-80) REVERT: B 856 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8264 (p0) REVERT: C 133 PHE cc_start: 0.8852 (m-80) cc_final: 0.7857 (m-10) REVERT: C 135 PHE cc_start: 0.8130 (m-80) cc_final: 0.7868 (m-10) REVERT: C 434 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7557 (tp) REVERT: C 737 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8206 (p0) REVERT: C 740 MET cc_start: 0.8910 (mmm) cc_final: 0.8694 (mmm) REVERT: L 33 TYR cc_start: 0.5192 (m-80) cc_final: 0.4729 (m-80) REVERT: L 50 TYR cc_start: 0.7243 (p90) cc_final: 0.6752 (p90) REVERT: L 92 GLN cc_start: 0.3670 (tm-30) cc_final: 0.1814 (mp10) REVERT: G 22 CYS cc_start: 0.4629 (OUTLIER) cc_final: 0.3772 (t) outliers start: 106 outliers final: 73 residues processed: 198 average time/residue: 0.1775 time to fit residues: 60.1590 Evaluate side-chains 187 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 96 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 83 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 190 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 352 optimal weight: 0.0470 chunk 282 optimal weight: 3.9990 chunk 356 optimal weight: 9.9990 chunk 319 optimal weight: 0.3980 overall best weight: 1.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.135377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081357 restraints weight = 87235.795| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 4.60 r_work: 0.2847 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30082 Z= 0.145 Angle : 0.554 11.983 41083 Z= 0.272 Chirality : 0.044 0.411 4759 Planarity : 0.004 0.043 5223 Dihedral : 4.290 38.640 5189 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.09 % Allowed : 21.82 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.14), residues: 3612 helix: 1.82 (0.22), residues: 644 sheet: 0.17 (0.18), residues: 808 loop : -1.56 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.015 0.001 TYR C 369 PHE 0.018 0.001 PHE C1121 TRP 0.025 0.001 TRP B 353 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00347 (29976) covalent geometry : angle 0.52855 (40811) SS BOND : bond 0.00293 ( 46) SS BOND : angle 1.47929 ( 92) hydrogen bonds : bond 0.04313 ( 940) hydrogen bonds : angle 4.99157 ( 2646) link_BETA1-4 : bond 0.00256 ( 15) link_BETA1-4 : angle 1.07972 ( 45) link_NAG-ASN : bond 0.00474 ( 45) link_NAG-ASN : angle 2.66477 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 98 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7632 (t-90) REVERT: A 117 LEU cc_start: 0.8592 (tt) cc_final: 0.8069 (mp) REVERT: A 200 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7893 (t80) REVERT: A 238 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.7053 (p90) REVERT: A 281 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8801 (pm20) REVERT: A 726 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9189 (mm) REVERT: A 753 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8556 (tt) REVERT: A 786 LYS cc_start: 0.8406 (mmtp) cc_final: 0.8010 (ptpt) REVERT: A 919 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.7854 (p0) REVERT: A 1106 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: B 160 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7618 (p90) REVERT: B 201 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7138 (m-80) REVERT: B 429 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7054 (t80) REVERT: B 439 ASN cc_start: 0.8771 (p0) cc_final: 0.8038 (m-40) REVERT: B 508 TYR cc_start: 0.9185 (m-80) cc_final: 0.8712 (m-80) REVERT: B 532 ASN cc_start: 0.8942 (m110) cc_final: 0.8474 (t0) REVERT: B 543 PHE cc_start: 0.6548 (m-10) cc_final: 0.5142 (t80) REVERT: B 670 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9057 (mt) REVERT: B 814 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8993 (mmtm) REVERT: B 855 PHE cc_start: 0.7758 (m-80) cc_final: 0.6767 (m-80) REVERT: B 856 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8286 (p0) REVERT: C 133 PHE cc_start: 0.8805 (m-80) cc_final: 0.7822 (m-10) REVERT: C 135 PHE cc_start: 0.8110 (m-80) cc_final: 0.7887 (m-10) REVERT: C 737 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8345 (p0) REVERT: L 33 TYR cc_start: 0.5263 (m-80) cc_final: 0.4780 (m-80) REVERT: L 50 TYR cc_start: 0.7200 (p90) cc_final: 0.6606 (p90) REVERT: L 92 GLN cc_start: 0.4036 (tm-30) cc_final: 0.2085 (mp10) REVERT: G 22 CYS cc_start: 0.4490 (OUTLIER) cc_final: 0.3559 (t) outliers start: 98 outliers final: 73 residues processed: 191 average time/residue: 0.1692 time to fit residues: 56.0593 Evaluate side-chains 186 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 97 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 33 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 312 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 287 optimal weight: 0.9990 chunk 343 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN B 211 ASN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.135351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081615 restraints weight = 86382.885| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.56 r_work: 0.2854 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30082 Z= 0.128 Angle : 0.545 11.985 41083 Z= 0.268 Chirality : 0.044 0.399 4759 Planarity : 0.004 0.043 5223 Dihedral : 4.178 37.754 5189 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.87 % Allowed : 22.04 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.14), residues: 3612 helix: 1.87 (0.22), residues: 644 sheet: 0.19 (0.18), residues: 817 loop : -1.55 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.023 0.001 TYR A 170 PHE 0.017 0.001 PHE C1121 TRP 0.029 0.001 TRP B 353 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00303 (29976) covalent geometry : angle 0.52036 (40811) SS BOND : bond 0.00272 ( 46) SS BOND : angle 1.40033 ( 92) hydrogen bonds : bond 0.04137 ( 940) hydrogen bonds : angle 4.91329 ( 2646) link_BETA1-4 : bond 0.00280 ( 15) link_BETA1-4 : angle 1.04832 ( 45) link_NAG-ASN : bond 0.00477 ( 45) link_NAG-ASN : angle 2.61920 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 99 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7617 (t-90) REVERT: A 117 LEU cc_start: 0.8616 (tt) cc_final: 0.8047 (mp) REVERT: A 200 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7888 (t80) REVERT: A 238 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7194 (p90) REVERT: A 281 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8805 (pm20) REVERT: A 726 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9188 (mm) REVERT: A 753 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8513 (tt) REVERT: A 786 LYS cc_start: 0.8410 (mmtp) cc_final: 0.8013 (ptpt) REVERT: A 919 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7642 (p0) REVERT: A 1106 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: B 201 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7134 (m-80) REVERT: B 429 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6987 (t80) REVERT: B 439 ASN cc_start: 0.8681 (p0) cc_final: 0.7956 (m-40) REVERT: B 508 TYR cc_start: 0.9161 (m-80) cc_final: 0.8702 (m-80) REVERT: B 532 ASN cc_start: 0.8914 (m110) cc_final: 0.8452 (t0) REVERT: B 543 PHE cc_start: 0.6574 (m-10) cc_final: 0.5141 (t80) REVERT: B 670 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9037 (mt) REVERT: B 814 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8987 (mmtm) REVERT: B 855 PHE cc_start: 0.7778 (m-80) cc_final: 0.6731 (m-80) REVERT: B 856 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8223 (p0) REVERT: C 133 PHE cc_start: 0.8689 (m-80) cc_final: 0.7739 (m-10) REVERT: C 135 PHE cc_start: 0.8076 (m-80) cc_final: 0.7870 (m-10) REVERT: C 737 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8342 (p0) REVERT: C 988 GLU cc_start: 0.8666 (mp0) cc_final: 0.8271 (mp0) REVERT: L 33 TYR cc_start: 0.5131 (m-80) cc_final: 0.4719 (m-80) REVERT: L 50 TYR cc_start: 0.7294 (p90) cc_final: 0.6825 (p90) REVERT: L 92 GLN cc_start: 0.3453 (tm-30) cc_final: 0.1622 (mp10) REVERT: G 22 CYS cc_start: 0.4012 (OUTLIER) cc_final: 0.3279 (t) outliers start: 91 outliers final: 71 residues processed: 186 average time/residue: 0.1662 time to fit residues: 53.8053 Evaluate side-chains 183 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 97 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 308 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 38 optimal weight: 40.0000 chunk 220 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 276 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 231 optimal weight: 0.0070 chunk 230 optimal weight: 0.8980 chunk 37 optimal weight: 30.0000 chunk 218 optimal weight: 20.0000 overall best weight: 2.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.135468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.081473 restraints weight = 87766.537| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 4.60 r_work: 0.2836 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 30082 Z= 0.167 Angle : 0.671 59.184 41083 Z= 0.359 Chirality : 0.045 0.678 4759 Planarity : 0.004 0.058 5223 Dihedral : 4.214 41.223 5189 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.74 % Allowed : 22.26 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.14), residues: 3612 helix: 1.87 (0.22), residues: 644 sheet: 0.19 (0.18), residues: 817 loop : -1.55 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 34 TYR 0.022 0.001 TYR B 453 PHE 0.018 0.001 PHE C1121 TRP 0.024 0.001 TRP B 353 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00371 (29976) covalent geometry : angle 0.65172 (40811) SS BOND : bond 0.00277 ( 46) SS BOND : angle 1.39721 ( 92) hydrogen bonds : bond 0.04175 ( 940) hydrogen bonds : angle 4.91514 ( 2646) link_BETA1-4 : bond 0.00302 ( 15) link_BETA1-4 : angle 1.06432 ( 45) link_NAG-ASN : bond 0.00476 ( 45) link_NAG-ASN : angle 2.61766 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9813.82 seconds wall clock time: 167 minutes 57.67 seconds (10077.67 seconds total)