Starting phenix.real_space_refine on Thu Jun 26 02:47:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gto_34259/06_2025/8gto_34259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gto_34259/06_2025/8gto_34259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gto_34259/06_2025/8gto_34259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gto_34259/06_2025/8gto_34259.map" model { file = "/net/cci-nas-00/data/ceres_data/8gto_34259/06_2025/8gto_34259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gto_34259/06_2025/8gto_34259.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 19227 2.51 5 N 4959 2.21 5 O 5919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.78s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30234 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "N" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 20.17, per 1000 atoms: 0.67 Number of scatterers: 30234 At special positions: 0 Unit cell: (138.933, 184.167, 202.476, 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 129 16.00 O 5919 8.00 N 4959 7.00 C 19227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.84 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.07 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=1.96 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.20 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.18 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.99 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.59 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=1.97 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.17 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.10 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.08 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.61 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.75 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=1.97 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=2.11 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.08 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.76 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.14 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=2.51 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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=1.99 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.26 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.97 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.17 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " 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 A1410 " - " NAG A1411 " " NAG B1410 " - " NAG B1411 " " NAG C1410 " - " NAG C1411 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG A1410 " - " ASN A1074 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG C1409 " - " ASN C 709 " " NAG C1410 " - " ASN C1074 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 7.54 Conformation dependent library (CDL) restraints added in 3.5 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6978 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 60 sheets defined 18.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.629A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.057A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.542A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.591A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.592A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 4.057A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.393A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 295 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.629A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.056A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.513A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.652A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.079A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.573A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.417A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 295 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.628A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.056A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.700A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.528A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.814A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 595 through 598 removed outlier: 4.080A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.938A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.384A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.611A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 310 through 313 removed outlier: 5.662A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.529A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.815A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 655 through 656 removed outlier: 4.014A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.869A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.133A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.562A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.562A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 325 removed outlier: 3.991A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.528A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.563A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 670 through 673 Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.375A pdb=" N GLU H 10 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.152A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.152A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AF7, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.375A pdb=" N GLU I 10 " --> pdb=" O ALA I 118 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 18 through 22 Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.375A pdb=" N GLU J 10 " --> pdb=" O ALA J 118 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 18 through 22 1111 hydrogen bonds defined for protein. 2934 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: 15.23 Time building geometry restraints manager: 8.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5481 1.32 - 1.45: 8562 1.45 - 1.57: 16721 1.57 - 1.70: 1 1.70 - 1.83: 165 Bond restraints: 30930 Sorted by residual: bond pdb=" CA TYR B 369 " pdb=" C TYR B 369 " ideal model delta sigma weight residual 1.523 1.437 0.086 1.34e-02 5.57e+03 4.13e+01 bond pdb=" CA TYR A 369 " pdb=" C TYR A 369 " ideal model delta sigma weight residual 1.523 1.437 0.086 1.34e-02 5.57e+03 4.11e+01 bond pdb=" CA TYR C 369 " pdb=" C TYR C 369 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.34e-02 5.57e+03 4.04e+01 bond pdb=" CA TYR B 365 " pdb=" C TYR B 365 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.56e-02 4.11e+03 2.69e+01 bond pdb=" C PRO C 862 " pdb=" N PRO C 863 " ideal model delta sigma weight residual 1.329 1.391 -0.062 1.20e-02 6.94e+03 2.65e+01 ... (remaining 30925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 40833 2.71 - 5.42: 1062 5.42 - 8.13: 134 8.13 - 10.84: 25 10.84 - 13.56: 15 Bond angle restraints: 42069 Sorted by residual: angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 110.21 99.55 10.66 1.13e+00 7.83e-01 8.89e+01 angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 110.21 99.57 10.64 1.13e+00 7.83e-01 8.87e+01 angle pdb=" N VAL C 367 " pdb=" CA VAL C 367 " pdb=" C VAL C 367 " ideal model delta sigma weight residual 110.21 99.63 10.58 1.13e+00 7.83e-01 8.77e+01 angle pdb=" N SER B 366 " pdb=" CA SER B 366 " pdb=" C SER B 366 " ideal model delta sigma weight residual 111.07 103.23 7.84 1.07e+00 8.73e-01 5.37e+01 angle pdb=" N SER C 366 " pdb=" CA SER C 366 " pdb=" C SER C 366 " ideal model delta sigma weight residual 111.07 103.27 7.80 1.07e+00 8.73e-01 5.31e+01 ... (remaining 42064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17452 17.93 - 35.86: 1295 35.86 - 53.79: 391 53.79 - 71.72: 80 71.72 - 89.65: 42 Dihedral angle restraints: 19260 sinusoidal: 8382 harmonic: 10878 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -174.61 88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 20.60 72.40 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 163.42 -70.42 1 1.00e+01 1.00e-02 6.38e+01 ... (remaining 19257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 4890 0.326 - 0.652: 12 0.652 - 0.978: 4 0.978 - 1.304: 1 1.304 - 1.630: 1 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.20e+03 chirality pdb=" C1 NAG C1411 " pdb=" O4 NAG C1410 " pdb=" C2 NAG C1411 " pdb=" O5 NAG C1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.18e+03 chirality pdb=" C1 NAG A1411 " pdb=" O4 NAG A1410 " pdb=" C2 NAG A1411 " pdb=" O5 NAG A1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.17e+03 ... (remaining 4905 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.151 2.00e-02 2.50e+03 1.99e-01 4.95e+02 pdb=" CG ASN A 331 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.341 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.234 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " 0.095 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" CG ASN A 603 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.192 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.071 2.00e-02 2.50e+03 9.57e-02 1.14e+02 pdb=" CG ASN B 603 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.165 2.00e-02 2.50e+03 pdb=" C1 NAG B1406 " 0.112 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 199 2.47 - 3.08: 20470 3.08 - 3.69: 42611 3.69 - 4.29: 63507 4.29 - 4.90: 104714 Nonbonded interactions: 231501 Sorted by model distance: nonbonded pdb=" N GLU A 309 " pdb=" OE1 GLU A 309 " model vdw 1.865 3.120 nonbonded pdb=" O SER A 530 " pdb=" OG1 THR A 531 " model vdw 1.915 3.040 nonbonded pdb=" OD1 ASN C 317 " pdb=" N PHE C 318 " model vdw 1.930 3.120 nonbonded pdb=" O SER C 530 " pdb=" CG2 THR C 531 " model vdw 1.961 3.460 nonbonded pdb=" O ASN A 603 " pdb=" OG1 THR A 604 " model vdw 1.988 3.040 ... (remaining 231496 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 71.600 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 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 : 0.013 0.805 31041 Z= 0.673 Angle : 1.411 56.720 42360 Z= 0.740 Chirality : 0.079 1.630 4908 Planarity : 0.008 0.104 5358 Dihedral : 14.253 89.654 12156 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 2.41 % Allowed : 8.72 % Favored : 88.87 % Rotamer: Outliers : 4.19 % Allowed : 9.27 % Favored : 86.54 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.12), residues: 3693 helix: -1.01 (0.18), residues: 583 sheet: -1.36 (0.15), residues: 998 loop : -3.05 (0.11), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP I 47 HIS 0.004 0.001 HIS C 207 PHE 0.025 0.002 PHE A 86 TYR 0.019 0.002 TYR B 265 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.02602 ( 48) link_NAG-ASN : angle 9.24082 ( 144) link_BETA1-4 : bond 0.07718 ( 21) link_BETA1-4 : angle 9.86636 ( 63) hydrogen bonds : bond 0.19303 ( 1032) hydrogen bonds : angle 8.04803 ( 2934) SS BOND : bond 0.23445 ( 42) SS BOND : angle 14.01316 ( 84) covalent geometry : bond 0.00880 (30930) covalent geometry : angle 1.08346 (42069) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 579 time to evaluate : 3.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6682 (mp10) REVERT: A 388 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8085 (m-40) REVERT: A 759 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7757 (m-10) REVERT: A 764 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8556 (ttpp) REVERT: A 819 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7052 (mt-10) REVERT: A 1081 ILE cc_start: 0.8075 (mm) cc_final: 0.7821 (mm) REVERT: B 314 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: B 529 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8079 (mtmm) REVERT: B 695 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8967 (p90) REVERT: C 864 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8285 (tp) REVERT: H 11 VAL cc_start: 0.5001 (t) cc_final: 0.4784 (p) outliers start: 136 outliers final: 60 residues processed: 695 average time/residue: 0.6235 time to fit residues: 690.6634 Evaluate side-chains 329 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 261 time to evaluate : 8.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 30.0000 chunk 281 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 150 optimal weight: 0.0870 chunk 291 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 217 optimal weight: 6.9990 chunk 337 optimal weight: 50.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 173 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 606 ASN A 607 GLN A 755 GLN A 762 GLN A 935 GLN B 121 ASN B 164 ASN B 207 HIS B 321 GLN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 532 ASN B 564 GLN B 607 GLN B1119 ASN C 121 ASN C 164 ASN C 173 GLN C 360 ASN C 422 ASN C 439 ASN C 532 ASN C 607 GLN C 907 ASN H 100 GLN L 35 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 HIS M 52 ASN M 88 HIS N 52 ASN N 88 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.204801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.142571 restraints weight = 45151.857| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.09 r_work: 0.3581 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 31041 Z= 0.153 Angle : 0.793 16.458 42360 Z= 0.388 Chirality : 0.049 0.568 4908 Planarity : 0.006 0.071 5358 Dihedral : 8.439 80.963 5629 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.93 % Favored : 92.66 % Rotamer: Outliers : 3.42 % Allowed : 13.96 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.13), residues: 3693 helix: 0.60 (0.21), residues: 600 sheet: -0.96 (0.16), residues: 1000 loop : -2.49 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 111 HIS 0.016 0.001 HIS I 110 PHE 0.020 0.001 PHE C 86 TYR 0.024 0.001 TYR H 107 ARG 0.006 0.001 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 48) link_NAG-ASN : angle 4.39868 ( 144) link_BETA1-4 : bond 0.01083 ( 21) link_BETA1-4 : angle 3.24551 ( 63) hydrogen bonds : bond 0.04955 ( 1032) hydrogen bonds : angle 5.70515 ( 2934) SS BOND : bond 0.00818 ( 42) SS BOND : angle 2.31717 ( 84) covalent geometry : bond 0.00328 (30930) covalent geometry : angle 0.73490 (42069) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 308 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6860 (OUTLIER) cc_final: 0.6094 (m-40) REVERT: A 129 LYS cc_start: 0.7371 (ptmt) cc_final: 0.7098 (pttt) REVERT: A 501 TYR cc_start: 0.7154 (m-10) cc_final: 0.6830 (m-10) REVERT: A 525 CYS cc_start: 0.4701 (OUTLIER) cc_final: 0.4007 (m) REVERT: A 982 SER cc_start: 0.8830 (t) cc_final: 0.8492 (m) REVERT: B 517 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6856 (pp) REVERT: B 529 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8348 (mtmm) REVERT: B 731 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8204 (ptm) REVERT: B 869 MET cc_start: 0.8218 (mtp) cc_final: 0.7814 (mtt) REVERT: B 904 TYR cc_start: 0.7771 (m-10) cc_final: 0.7423 (m-10) REVERT: B 1073 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6857 (tttm) REVERT: C 303 LEU cc_start: 0.8388 (mt) cc_final: 0.8172 (mt) REVERT: C 328 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7622 (mmp80) REVERT: C 346 ARG cc_start: 0.8012 (ptm-80) cc_final: 0.7750 (ptm160) REVERT: C 568 ASP cc_start: 0.7542 (p0) cc_final: 0.7317 (p0) REVERT: C 675 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7666 (mm-40) REVERT: C 693 ILE cc_start: 0.8235 (tt) cc_final: 0.7978 (tt) REVERT: H 100 GLN cc_start: 0.5000 (OUTLIER) cc_final: 0.4780 (pp30) REVERT: I 111 TRP cc_start: 0.0792 (OUTLIER) cc_final: 0.0417 (t-100) REVERT: J 107 TYR cc_start: 0.5412 (t80) cc_final: 0.4922 (t80) outliers start: 111 outliers final: 49 residues processed: 401 average time/residue: 0.4078 time to fit residues: 272.0296 Evaluate side-chains 279 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 220 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain I residue 111 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 229 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 342 optimal weight: 40.0000 chunk 258 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1101 HIS B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 762 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 121 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS N 35 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.198996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.133288 restraints weight = 44634.560| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.30 r_work: 0.3404 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 31041 Z= 0.166 Angle : 0.746 21.534 42360 Z= 0.361 Chirality : 0.050 0.789 4908 Planarity : 0.005 0.071 5358 Dihedral : 6.834 70.346 5535 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.61 % Favored : 93.04 % Rotamer: Outliers : 3.14 % Allowed : 14.91 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.13), residues: 3693 helix: 0.98 (0.21), residues: 599 sheet: -0.73 (0.15), residues: 1043 loop : -2.18 (0.12), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 111 HIS 0.007 0.001 HIS A1058 PHE 0.026 0.002 PHE C 86 TYR 0.018 0.001 TYR J 108 ARG 0.006 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.01059 ( 48) link_NAG-ASN : angle 4.53876 ( 144) link_BETA1-4 : bond 0.00940 ( 21) link_BETA1-4 : angle 2.87972 ( 63) hydrogen bonds : bond 0.04543 ( 1032) hydrogen bonds : angle 5.33978 ( 2934) SS BOND : bond 0.00519 ( 42) SS BOND : angle 2.37241 ( 84) covalent geometry : bond 0.00379 (30930) covalent geometry : angle 0.68313 (42069) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 241 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7198 (ptmt) cc_final: 0.6852 (pttt) REVERT: A 153 MET cc_start: 0.5166 (mpp) cc_final: 0.4668 (mpp) REVERT: A 278 LYS cc_start: 0.8451 (tttt) cc_final: 0.8148 (ttpt) REVERT: A 298 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 405 ASN cc_start: 0.8457 (m110) cc_final: 0.7818 (p0) REVERT: A 764 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8681 (ttpp) REVERT: A 1029 MET cc_start: 0.9049 (tpp) cc_final: 0.8754 (tpt) REVERT: B 529 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8283 (mtmm) REVERT: B 859 THR cc_start: 0.8306 (t) cc_final: 0.8077 (p) REVERT: B 869 MET cc_start: 0.8533 (mtp) cc_final: 0.8314 (mtt) REVERT: B 904 TYR cc_start: 0.8148 (m-10) cc_final: 0.7371 (m-10) REVERT: C 468 ILE cc_start: 0.4594 (OUTLIER) cc_final: 0.4267 (mp) REVERT: C 568 ASP cc_start: 0.7656 (p0) cc_final: 0.7417 (p0) REVERT: C 602 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.7010 (m) REVERT: L 22 CYS cc_start: 0.4358 (OUTLIER) cc_final: 0.4028 (m) REVERT: L 37 TYR cc_start: 0.5161 (m-80) cc_final: 0.4896 (m-80) REVERT: I 81 MET cc_start: -0.0009 (ttp) cc_final: -0.1000 (tmm) REVERT: I 111 TRP cc_start: 0.0694 (OUTLIER) cc_final: 0.0466 (t-100) REVERT: J 48 MET cc_start: 0.1759 (mmm) cc_final: 0.0220 (ptt) REVERT: J 107 TYR cc_start: 0.5713 (t80) cc_final: 0.5369 (t80) REVERT: N 71 SER cc_start: 0.6229 (t) cc_final: 0.5967 (p) outliers start: 102 outliers final: 57 residues processed: 326 average time/residue: 0.3717 time to fit residues: 205.2097 Evaluate side-chains 257 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 194 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain I residue 111 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 273 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 332 optimal weight: 50.0000 chunk 266 optimal weight: 0.9990 chunk 359 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 348 optimal weight: 20.0000 chunk 199 optimal weight: 0.9980 chunk 300 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 935 GLN A1101 HIS B 207 HIS B 422 ASN B 505 HIS B 762 GLN B 856 ASN B 901 GLN B 965 GLN C 188 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN H 43 GLN M 35 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.190330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148346 restraints weight = 44266.107| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.51 r_work: 0.3363 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 31041 Z= 0.240 Angle : 0.774 19.277 42360 Z= 0.379 Chirality : 0.051 0.713 4908 Planarity : 0.005 0.057 5358 Dihedral : 6.515 59.899 5520 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.58 % Favored : 93.10 % Rotamer: Outliers : 3.57 % Allowed : 15.62 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 3693 helix: 0.83 (0.21), residues: 600 sheet: -0.50 (0.16), residues: 1022 loop : -2.18 (0.12), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 111 HIS 0.010 0.002 HIS A1058 PHE 0.036 0.002 PHE C 86 TYR 0.023 0.002 TYR H 108 ARG 0.009 0.001 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00938 ( 48) link_NAG-ASN : angle 4.27150 ( 144) link_BETA1-4 : bond 0.00799 ( 21) link_BETA1-4 : angle 2.72640 ( 63) hydrogen bonds : bond 0.04864 ( 1032) hydrogen bonds : angle 5.29028 ( 2934) SS BOND : bond 0.00564 ( 42) SS BOND : angle 2.20957 ( 84) covalent geometry : bond 0.00578 (30930) covalent geometry : angle 0.72109 (42069) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 209 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7276 (OUTLIER) cc_final: 0.6903 (m) REVERT: A 129 LYS cc_start: 0.7668 (ptmt) cc_final: 0.7378 (pttt) REVERT: A 176 LEU cc_start: 0.6222 (tp) cc_final: 0.5911 (tt) REVERT: A 298 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7464 (tp30) REVERT: A 366 SER cc_start: 0.7453 (OUTLIER) cc_final: 0.6998 (t) REVERT: A 405 ASN cc_start: 0.8183 (m110) cc_final: 0.7811 (p0) REVERT: A 764 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8562 (ttpp) REVERT: A 914 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8710 (p0) REVERT: B 318 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8414 (p90) REVERT: B 755 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: B 859 THR cc_start: 0.8467 (t) cc_final: 0.8257 (p) REVERT: C 63 THR cc_start: 0.6824 (OUTLIER) cc_final: 0.6604 (m) REVERT: C 238 PHE cc_start: 0.7013 (p90) cc_final: 0.6217 (p90) REVERT: C 568 ASP cc_start: 0.7670 (p0) cc_final: 0.7436 (p0) REVERT: C 904 TYR cc_start: 0.8110 (m-10) cc_final: 0.7814 (m-10) REVERT: N 71 SER cc_start: 0.6121 (t) cc_final: 0.5736 (p) outliers start: 116 outliers final: 71 residues processed: 306 average time/residue: 0.3559 time to fit residues: 185.9548 Evaluate side-chains 250 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 25 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 333 optimal weight: 30.0000 chunk 361 optimal weight: 0.4980 chunk 104 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 236 optimal weight: 4.9990 chunk 355 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 388 ASN B 505 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1010 GLN L 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.191437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.145621 restraints weight = 43889.556| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.50 r_work: 0.3377 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31041 Z= 0.150 Angle : 0.693 19.792 42360 Z= 0.334 Chirality : 0.047 0.308 4908 Planarity : 0.004 0.053 5358 Dihedral : 6.337 59.777 5515 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.12 % Favored : 93.56 % Rotamer: Outliers : 3.02 % Allowed : 16.64 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3693 helix: 1.16 (0.21), residues: 591 sheet: -0.37 (0.15), residues: 1045 loop : -2.07 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 111 HIS 0.006 0.001 HIS C 207 PHE 0.029 0.001 PHE H 29 TYR 0.043 0.001 TYR H 107 ARG 0.006 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 48) link_NAG-ASN : angle 4.00263 ( 144) link_BETA1-4 : bond 0.00822 ( 21) link_BETA1-4 : angle 2.62194 ( 63) hydrogen bonds : bond 0.04202 ( 1032) hydrogen bonds : angle 5.08710 ( 2934) SS BOND : bond 0.00598 ( 42) SS BOND : angle 2.02097 ( 84) covalent geometry : bond 0.00350 (30930) covalent geometry : angle 0.64060 (42069) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 193 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7377 (OUTLIER) cc_final: 0.7014 (m) REVERT: A 129 LYS cc_start: 0.7568 (ptmt) cc_final: 0.7280 (pttt) REVERT: A 153 MET cc_start: 0.5204 (mpp) cc_final: 0.4476 (ptm) REVERT: A 176 LEU cc_start: 0.6272 (tp) cc_final: 0.5950 (tt) REVERT: A 298 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7425 (tp30) REVERT: A 405 ASN cc_start: 0.8183 (m110) cc_final: 0.7390 (p0) REVERT: B 318 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8209 (p90) REVERT: B 613 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: C 52 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7716 (tp-100) REVERT: C 63 THR cc_start: 0.6804 (OUTLIER) cc_final: 0.6589 (m) REVERT: C 238 PHE cc_start: 0.7038 (p90) cc_final: 0.6175 (p90) REVERT: C 568 ASP cc_start: 0.7623 (p0) cc_final: 0.7342 (p0) REVERT: I 81 MET cc_start: 0.0326 (ttp) cc_final: -0.0704 (tmm) REVERT: J 48 MET cc_start: 0.2153 (mmm) cc_final: 0.0062 (mtt) REVERT: J 107 TYR cc_start: 0.5916 (t80) cc_final: 0.5702 (t80) REVERT: N 71 SER cc_start: 0.6180 (t) cc_final: 0.5801 (p) outliers start: 98 outliers final: 64 residues processed: 278 average time/residue: 0.4157 time to fit residues: 201.0968 Evaluate side-chains 233 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 232 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 chunk 352 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 288 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 258 optimal weight: 0.0670 chunk 4 optimal weight: 7.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 914 ASN B 505 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN L 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.188666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138144 restraints weight = 44022.121| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.56 r_work: 0.3328 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 31041 Z= 0.223 Angle : 0.730 19.808 42360 Z= 0.356 Chirality : 0.049 0.328 4908 Planarity : 0.005 0.052 5358 Dihedral : 6.189 57.217 5506 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.50 % Favored : 93.23 % Rotamer: Outliers : 3.33 % Allowed : 16.61 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3693 helix: 1.05 (0.21), residues: 585 sheet: -0.44 (0.15), residues: 1061 loop : -2.05 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 111 HIS 0.009 0.002 HIS C1064 PHE 0.034 0.002 PHE C 86 TYR 0.033 0.002 TYR H 107 ARG 0.006 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00715 ( 48) link_NAG-ASN : angle 3.98198 ( 144) link_BETA1-4 : bond 0.00720 ( 21) link_BETA1-4 : angle 2.55392 ( 63) hydrogen bonds : bond 0.04614 ( 1032) hydrogen bonds : angle 5.13732 ( 2934) SS BOND : bond 0.00677 ( 42) SS BOND : angle 2.16227 ( 84) covalent geometry : bond 0.00540 (30930) covalent geometry : angle 0.68069 (42069) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 177 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7768 (ptmt) cc_final: 0.7494 (pttt) REVERT: A 153 MET cc_start: 0.5831 (mpp) cc_final: 0.4926 (ptm) REVERT: A 176 LEU cc_start: 0.6481 (tp) cc_final: 0.6151 (tt) REVERT: A 298 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7754 (tp30) REVERT: A 501 TYR cc_start: 0.7470 (m-80) cc_final: 0.7230 (m-10) REVERT: A 574 ASP cc_start: 0.7934 (m-30) cc_final: 0.7319 (t0) REVERT: B 318 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8270 (p90) REVERT: B 388 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.4922 (t0) REVERT: B 495 TYR cc_start: 0.3855 (OUTLIER) cc_final: 0.2567 (m-10) REVERT: B 613 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7556 (mp10) REVERT: B 988 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: C 52 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7916 (tp-100) REVERT: C 63 THR cc_start: 0.7139 (OUTLIER) cc_final: 0.6899 (m) REVERT: C 65 PHE cc_start: 0.7113 (m-80) cc_final: 0.6913 (m-80) REVERT: C 421 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5993 (p90) REVERT: C 519 HIS cc_start: 0.1675 (OUTLIER) cc_final: 0.0668 (t70) REVERT: C 568 ASP cc_start: 0.8060 (p0) cc_final: 0.7768 (p0) REVERT: H 37 VAL cc_start: 0.4022 (OUTLIER) cc_final: 0.3408 (m) REVERT: I 81 MET cc_start: 0.0485 (ttp) cc_final: -0.0724 (tmm) REVERT: J 48 MET cc_start: 0.2031 (mmm) cc_final: 0.0216 (mtm) REVERT: J 107 TYR cc_start: 0.6020 (t80) cc_final: 0.5470 (t80) REVERT: N 71 SER cc_start: 0.6154 (t) cc_final: 0.5740 (p) outliers start: 108 outliers final: 78 residues processed: 269 average time/residue: 0.3530 time to fit residues: 165.3352 Evaluate side-chains 251 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 164 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 338 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 340 optimal weight: 40.0000 chunk 3 optimal weight: 2.9990 chunk 254 optimal weight: 0.0980 chunk 225 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 409 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 505 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.187337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118993 restraints weight = 44104.562| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.18 r_work: 0.3243 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31041 Z= 0.208 Angle : 0.709 19.933 42360 Z= 0.346 Chirality : 0.048 0.352 4908 Planarity : 0.005 0.061 5358 Dihedral : 6.016 59.444 5505 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.61 % Favored : 93.12 % Rotamer: Outliers : 3.17 % Allowed : 16.91 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 3693 helix: 1.09 (0.22), residues: 584 sheet: -0.41 (0.15), residues: 1050 loop : -2.03 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 111 HIS 0.010 0.001 HIS C 207 PHE 0.034 0.002 PHE H 106 TYR 0.036 0.002 TYR H 107 ARG 0.006 0.000 ARG H 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 48) link_NAG-ASN : angle 3.84149 ( 144) link_BETA1-4 : bond 0.00810 ( 21) link_BETA1-4 : angle 2.47485 ( 63) hydrogen bonds : bond 0.04422 ( 1032) hydrogen bonds : angle 5.08744 ( 2934) SS BOND : bond 0.00631 ( 42) SS BOND : angle 2.00782 ( 84) covalent geometry : bond 0.00502 (30930) covalent geometry : angle 0.66224 (42069) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 184 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7503 (ptmt) cc_final: 0.7095 (pttt) REVERT: A 153 MET cc_start: 0.5725 (mpp) cc_final: 0.4874 (ptm) REVERT: A 176 LEU cc_start: 0.6440 (tp) cc_final: 0.5944 (tt) REVERT: A 298 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7473 (tp30) REVERT: A 369 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: A 574 ASP cc_start: 0.7748 (m-30) cc_final: 0.7119 (t0) REVERT: B 318 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8190 (p90) REVERT: B 495 TYR cc_start: 0.4007 (OUTLIER) cc_final: 0.2344 (m-10) REVERT: B 613 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7563 (mp10) REVERT: B 988 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: B 1041 ASP cc_start: 0.7788 (t0) cc_final: 0.7574 (m-30) REVERT: C 63 THR cc_start: 0.6783 (OUTLIER) cc_final: 0.6548 (m) REVERT: C 65 PHE cc_start: 0.7121 (m-80) cc_final: 0.6841 (m-80) REVERT: C 238 PHE cc_start: 0.6974 (p90) cc_final: 0.6028 (p90) REVERT: C 421 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5984 (p90) REVERT: C 516 GLU cc_start: 0.7526 (tp30) cc_final: 0.7240 (mp0) REVERT: C 568 ASP cc_start: 0.7870 (p0) cc_final: 0.7647 (p0) REVERT: H 37 VAL cc_start: 0.3530 (OUTLIER) cc_final: 0.3245 (m) REVERT: L 92 TRP cc_start: 0.5973 (t-100) cc_final: 0.5028 (t-100) REVERT: J 48 MET cc_start: 0.1816 (mmm) cc_final: 0.0332 (mtm) REVERT: J 107 TYR cc_start: 0.5569 (t80) cc_final: 0.5045 (t80) REVERT: N 71 SER cc_start: 0.6374 (t) cc_final: 0.6080 (p) outliers start: 103 outliers final: 75 residues processed: 270 average time/residue: 0.3473 time to fit residues: 161.8080 Evaluate side-chains 253 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 170 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 25 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 163 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 317 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 324 optimal weight: 20.0000 chunk 262 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.188765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119869 restraints weight = 44418.961| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.14 r_work: 0.3284 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 31041 Z= 0.136 Angle : 0.675 19.755 42360 Z= 0.327 Chirality : 0.046 0.349 4908 Planarity : 0.004 0.052 5358 Dihedral : 5.749 57.958 5503 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.96 % Favored : 93.77 % Rotamer: Outliers : 2.71 % Allowed : 17.56 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 3693 helix: 1.26 (0.22), residues: 588 sheet: -0.28 (0.15), residues: 1062 loop : -1.94 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.009 0.001 HIS C 207 PHE 0.028 0.001 PHE C 565 TYR 0.035 0.001 TYR L 50 ARG 0.005 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 48) link_NAG-ASN : angle 3.63593 ( 144) link_BETA1-4 : bond 0.00792 ( 21) link_BETA1-4 : angle 2.39824 ( 63) hydrogen bonds : bond 0.03944 ( 1032) hydrogen bonds : angle 4.97508 ( 2934) SS BOND : bond 0.00620 ( 42) SS BOND : angle 2.23984 ( 84) covalent geometry : bond 0.00318 (30930) covalent geometry : angle 0.62842 (42069) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 175 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.6966 (OUTLIER) cc_final: 0.6618 (m) REVERT: A 129 LYS cc_start: 0.7301 (ptmt) cc_final: 0.6888 (pttt) REVERT: A 153 MET cc_start: 0.5787 (mpp) cc_final: 0.4876 (ptp) REVERT: A 176 LEU cc_start: 0.6290 (tp) cc_final: 0.5770 (tt) REVERT: A 298 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7380 (tp30) REVERT: A 369 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: A 405 ASN cc_start: 0.8328 (m110) cc_final: 0.7544 (p0) REVERT: A 501 TYR cc_start: 0.7629 (m-80) cc_final: 0.7156 (m-10) REVERT: A 574 ASP cc_start: 0.7701 (m-30) cc_final: 0.7054 (t0) REVERT: B 88 ASP cc_start: 0.7745 (m-30) cc_final: 0.7362 (m-30) REVERT: B 318 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8219 (p90) REVERT: B 495 TYR cc_start: 0.3995 (OUTLIER) cc_final: 0.2207 (m-10) REVERT: B 613 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: B 762 GLN cc_start: 0.7849 (mp10) cc_final: 0.7591 (mp10) REVERT: B 988 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: B 1041 ASP cc_start: 0.7725 (t0) cc_final: 0.7505 (m-30) REVERT: C 52 GLN cc_start: 0.8417 (tp40) cc_final: 0.8143 (tp-100) REVERT: C 63 THR cc_start: 0.6775 (OUTLIER) cc_final: 0.6551 (m) REVERT: C 65 PHE cc_start: 0.7065 (m-80) cc_final: 0.6815 (m-80) REVERT: C 421 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.5875 (p90) REVERT: C 516 GLU cc_start: 0.7501 (tp30) cc_final: 0.7224 (mp0) REVERT: C 568 ASP cc_start: 0.7763 (p0) cc_final: 0.7541 (p0) REVERT: H 111 TRP cc_start: 0.3972 (t60) cc_final: 0.3695 (t60) REVERT: J 48 MET cc_start: 0.1859 (mmm) cc_final: 0.0419 (mtm) REVERT: J 107 TYR cc_start: 0.5954 (t80) cc_final: 0.5432 (t80) REVERT: N 71 SER cc_start: 0.6375 (t) cc_final: 0.6091 (p) outliers start: 88 outliers final: 67 residues processed: 249 average time/residue: 0.3466 time to fit residues: 149.5842 Evaluate side-chains 246 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 171 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 174 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 339 optimal weight: 8.9990 chunk 124 optimal weight: 0.3980 chunk 118 optimal weight: 4.9990 chunk 327 optimal weight: 30.0000 chunk 69 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.190018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123519 restraints weight = 43997.604| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.01 r_work: 0.3311 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 31041 Z= 0.112 Angle : 0.642 19.454 42360 Z= 0.310 Chirality : 0.045 0.338 4908 Planarity : 0.004 0.052 5358 Dihedral : 5.448 54.854 5503 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.50 % Favored : 94.26 % Rotamer: Outliers : 2.13 % Allowed : 18.21 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3693 helix: 1.62 (0.22), residues: 582 sheet: -0.19 (0.15), residues: 1069 loop : -1.78 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP L 92 HIS 0.009 0.001 HIS C 207 PHE 0.026 0.001 PHE C 565 TYR 0.031 0.001 TYR L 50 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 48) link_NAG-ASN : angle 3.49192 ( 144) link_BETA1-4 : bond 0.00790 ( 21) link_BETA1-4 : angle 2.31739 ( 63) hydrogen bonds : bond 0.03524 ( 1032) hydrogen bonds : angle 4.80126 ( 2934) SS BOND : bond 0.00524 ( 42) SS BOND : angle 1.86480 ( 84) covalent geometry : bond 0.00251 (30930) covalent geometry : angle 0.59830 (42069) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 186 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.6763 (OUTLIER) cc_final: 0.6438 (m) REVERT: A 129 LYS cc_start: 0.7027 (ptmt) cc_final: 0.6628 (pttt) REVERT: A 153 MET cc_start: 0.5782 (mpp) cc_final: 0.4869 (ptp) REVERT: A 176 LEU cc_start: 0.6246 (tp) cc_final: 0.5656 (tt) REVERT: A 298 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7340 (tp30) REVERT: A 405 ASN cc_start: 0.8359 (m110) cc_final: 0.7581 (p0) REVERT: A 501 TYR cc_start: 0.7815 (m-80) cc_final: 0.7267 (m-10) REVERT: A 508 TYR cc_start: 0.7910 (m-80) cc_final: 0.7611 (m-80) REVERT: A 574 ASP cc_start: 0.7528 (m-30) cc_final: 0.6941 (t0) REVERT: B 88 ASP cc_start: 0.7750 (m-30) cc_final: 0.7368 (m-30) REVERT: B 318 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8141 (p90) REVERT: B 495 TYR cc_start: 0.3946 (OUTLIER) cc_final: 0.1855 (m-10) REVERT: B 762 GLN cc_start: 0.7709 (mp10) cc_final: 0.7389 (mp10) REVERT: B 1041 ASP cc_start: 0.7740 (t0) cc_final: 0.7447 (m-30) REVERT: C 52 GLN cc_start: 0.8379 (tp40) cc_final: 0.8093 (tp-100) REVERT: C 63 THR cc_start: 0.6624 (OUTLIER) cc_final: 0.6413 (m) REVERT: C 65 PHE cc_start: 0.7024 (m-80) cc_final: 0.6757 (m-80) REVERT: C 421 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.5934 (p90) REVERT: C 516 GLU cc_start: 0.7477 (tp30) cc_final: 0.7173 (mp0) REVERT: C 568 ASP cc_start: 0.7815 (p0) cc_final: 0.7568 (p0) REVERT: C 675 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7307 (mm-40) REVERT: J 107 TYR cc_start: 0.6126 (t80) cc_final: 0.5556 (t80) REVERT: N 71 SER cc_start: 0.6378 (t) cc_final: 0.6078 (p) outliers start: 69 outliers final: 55 residues processed: 241 average time/residue: 0.3697 time to fit residues: 154.5968 Evaluate side-chains 227 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 343 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 188 optimal weight: 0.0770 chunk 47 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 357 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 505 HIS C 52 GLN C 207 HIS C 460 ASN L 35 ASN N 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.189621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117533 restraints weight = 44525.504| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.83 r_work: 0.3247 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31041 Z= 0.117 Angle : 0.644 19.425 42360 Z= 0.310 Chirality : 0.045 0.328 4908 Planarity : 0.004 0.050 5358 Dihedral : 5.312 53.492 5502 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.63 % Favored : 94.18 % Rotamer: Outliers : 2.25 % Allowed : 18.30 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3693 helix: 1.79 (0.22), residues: 582 sheet: -0.11 (0.16), residues: 1069 loop : -1.70 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 92 HIS 0.010 0.001 HIS C 207 PHE 0.017 0.001 PHE B 86 TYR 0.032 0.001 TYR L 50 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 48) link_NAG-ASN : angle 3.49293 ( 144) link_BETA1-4 : bond 0.00778 ( 21) link_BETA1-4 : angle 2.30424 ( 63) hydrogen bonds : bond 0.03479 ( 1032) hydrogen bonds : angle 4.74139 ( 2934) SS BOND : bond 0.00512 ( 42) SS BOND : angle 1.87756 ( 84) covalent geometry : bond 0.00267 (30930) covalent geometry : angle 0.60049 (42069) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 173 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.6680 (m-40) REVERT: A 126 VAL cc_start: 0.6681 (OUTLIER) cc_final: 0.6100 (m) REVERT: A 129 LYS cc_start: 0.6606 (ptmt) cc_final: 0.6194 (pttt) REVERT: A 153 MET cc_start: 0.5929 (mpp) cc_final: 0.5053 (ptp) REVERT: A 176 LEU cc_start: 0.6099 (tp) cc_final: 0.5020 (pp) REVERT: A 298 GLU cc_start: 0.7540 (tm-30) cc_final: 0.6943 (tp30) REVERT: A 405 ASN cc_start: 0.8386 (m110) cc_final: 0.7522 (p0) REVERT: A 501 TYR cc_start: 0.7807 (m-80) cc_final: 0.7239 (m-10) REVERT: A 508 TYR cc_start: 0.7711 (m-80) cc_final: 0.7474 (m-80) REVERT: A 574 ASP cc_start: 0.7175 (m-30) cc_final: 0.6343 (t0) REVERT: B 143 VAL cc_start: 0.6891 (OUTLIER) cc_final: 0.6641 (t) REVERT: B 318 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.7805 (p90) REVERT: B 495 TYR cc_start: 0.3818 (OUTLIER) cc_final: 0.1850 (m-10) REVERT: B 762 GLN cc_start: 0.7501 (mp10) cc_final: 0.7174 (mp10) REVERT: B 988 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: B 1041 ASP cc_start: 0.7545 (t0) cc_final: 0.7239 (m-30) REVERT: C 52 GLN cc_start: 0.8380 (tp-100) cc_final: 0.8034 (tp-100) REVERT: C 63 THR cc_start: 0.5912 (OUTLIER) cc_final: 0.5708 (m) REVERT: C 65 PHE cc_start: 0.6888 (m-80) cc_final: 0.6510 (m-80) REVERT: C 421 TYR cc_start: 0.6065 (OUTLIER) cc_final: 0.5773 (p90) REVERT: C 516 GLU cc_start: 0.7525 (tp30) cc_final: 0.7116 (mp0) REVERT: C 568 ASP cc_start: 0.7591 (p0) cc_final: 0.7309 (p0) REVERT: C 574 ASP cc_start: 0.6739 (p0) cc_final: 0.6484 (t70) REVERT: I 106 PHE cc_start: 0.6044 (OUTLIER) cc_final: 0.5744 (m-80) REVERT: J 107 TYR cc_start: 0.6228 (t80) cc_final: 0.5598 (t80) REVERT: N 71 SER cc_start: 0.6212 (t) cc_final: 0.5901 (p) outliers start: 73 outliers final: 59 residues processed: 235 average time/residue: 0.3504 time to fit residues: 142.9546 Evaluate side-chains 229 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 161 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 42 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 chunk 239 optimal weight: 0.1980 chunk 279 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 chunk 219 optimal weight: 0.0040 chunk 14 optimal weight: 0.5980 chunk 325 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 755 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.189822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117922 restraints weight = 44520.832| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.69 r_work: 0.3284 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 31041 Z= 0.108 Angle : 0.632 19.329 42360 Z= 0.304 Chirality : 0.045 0.327 4908 Planarity : 0.004 0.049 5358 Dihedral : 5.240 52.753 5502 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.33 % Favored : 94.50 % Rotamer: Outliers : 2.16 % Allowed : 18.48 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3693 helix: 1.89 (0.21), residues: 582 sheet: -0.04 (0.16), residues: 1065 loop : -1.67 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 92 HIS 0.018 0.001 HIS C 207 PHE 0.017 0.001 PHE B 86 TYR 0.031 0.001 TYR L 50 ARG 0.008 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 48) link_NAG-ASN : angle 3.43760 ( 144) link_BETA1-4 : bond 0.00731 ( 21) link_BETA1-4 : angle 2.25307 ( 63) hydrogen bonds : bond 0.03362 ( 1032) hydrogen bonds : angle 4.70312 ( 2934) SS BOND : bond 0.00499 ( 42) SS BOND : angle 1.83980 ( 84) covalent geometry : bond 0.00242 (30930) covalent geometry : angle 0.58930 (42069) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24381.67 seconds wall clock time: 429 minutes 3.83 seconds (25743.83 seconds total)