Starting phenix.real_space_refine on Tue Aug 26 15:41:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8top_41459/08_2025/8top_41459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8top_41459/08_2025/8top_41459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8top_41459/08_2025/8top_41459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8top_41459/08_2025/8top_41459.map" model { file = "/net/cci-nas-00/data/ceres_data/8top_41459/08_2025/8top_41459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8top_41459/08_2025/8top_41459.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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 252 5.16 5 C 24336 2.51 5 N 6606 2.21 5 O 7651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38845 Number of models: 1 Model: "" Number of chains: 49 Chain: "O" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3476 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Chain: "P" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "Q" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "S" Number of atoms: 3483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 442, 3476 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 442, 3476 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 bond proxies already assigned to first conformer: 3539 Chain: "T" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "J" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "K" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "M" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "N" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "U" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "V" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "W" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "X" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "Y" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "Z" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "C" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "E" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 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: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "Q" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "T" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.55, per 1000 atoms: 0.22 Number of scatterers: 38845 At special positions: 0 Unit cell: (154.38, 142.76, 223.27, 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 252 16.00 O 7651 8.00 N 6606 7.00 C 24336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=85, symmetry=0 Simple disulfide: pdb=" SG CYS O 54 " - pdb=" SG CYS O 74 " distance=2.04 Simple disulfide: pdb=" SG CYS O 119 " - pdb=" SG CYS O 205 " distance=2.03 Simple disulfide: pdb=" SG CYS O 126 " - pdb=" SG CYS O 196 " distance=2.03 Simple disulfide: pdb=" SG CYS O 131 " - pdb=" SG CYS O 157 " distance=2.03 Simple disulfide: pdb=" SG CYS O 201 " - pdb=" SG CYS O 433 " distance=2.03 Simple disulfide: pdb=" SG CYS O 218 " - pdb=" SG CYS O 247 " distance=2.03 Simple disulfide: pdb=" SG CYS O 228 " - pdb=" SG CYS O 239 " distance=2.03 Simple disulfide: pdb=" SG CYS O 296 " - pdb=" SG CYS O 331 " distance=2.03 Simple disulfide: pdb=" SG CYS O 378 " - pdb=" SG CYS O 445 " distance=2.03 Simple disulfide: pdb=" SG CYS O 385 " - pdb=" SG CYS O 418 " distance=2.03 Simple disulfide: pdb=" SG CYS O 501 " - pdb=" SG CYS P 605 " distance=2.03 Simple disulfide: pdb=" SG CYS P 598 " - pdb=" SG CYS P 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 54 " - pdb=" SG CYS Q 74 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 119 " - pdb=" SG CYS Q 205 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 126 " - pdb=" SG CYS Q 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 131 " - pdb=" SG CYS Q 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 201 " - pdb=" SG CYS Q 433 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 218 " - pdb=" SG CYS Q 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 228 " - pdb=" SG CYS Q 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 296 " - pdb=" SG CYS Q 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 378 " - pdb=" SG CYS Q 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 385 " - pdb=" SG CYS Q 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 501 " - pdb=" SG CYS R 605 " distance=2.03 Simple disulfide: pdb=" SG CYS R 598 " - pdb=" SG CYS R 604 " distance=2.03 Simple disulfide: pdb=" SG CYS S 54 " - pdb=" SG CYS S 74 " distance=2.04 Simple disulfide: pdb=" SG CYS S 119 " - pdb=" SG CYS S 205 " distance=2.03 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.04 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.03 Simple disulfide: pdb=" SG CYS S 201 " - pdb=" SG CYS S 433 " distance=2.03 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.03 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.03 Simple disulfide: pdb=" SG CYS S 296 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 331 " - pdb=" SG CYS S 385 " distance=2.03 Simple disulfide: pdb=" SG CYS S 378 " - pdb=" SG CYS S 445 " distance=2.04 Simple disulfide: pdb=" SG CYS S 385 " - pdb=" SG CYS S 418 " distance=2.03 Simple disulfide: pdb=" SG CYS S 501 " - pdb=" SG CYS T 605 " distance=2.03 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.05 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA l 3 " - " MAN l 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 363 " " NAG A 610 " - " ASN A 386 " " NAG A 611 " - " ASN A 392 " " NAG A 612 " - " ASN A 448 " " NAG A 613 " - " ASN A 339 " " NAG A 614 " - " ASN A 295 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 234 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 386 " " NAG C 608 " - " ASN C 448 " " NAG C 609 " - " ASN C 339 " " NAG C 610 " - " ASN C 295 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 363 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 276 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 332 " " NAG E 606 " - " ASN E 386 " " NAG E 607 " - " ASN E 392 " " NAG E 608 " - " ASN E 448 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 295 " " NAG E 611 " - " ASN E 156 " " NAG E 612 " - " ASN E 197 " " NAG F 701 " - " ASN F 637 " " NAG G 1 " - " ASN O 156 " " NAG I 1 " - " ASN O 262 " " NAG O 601 " - " ASN O 133 " " NAG O 602 " - " ASN O 160 " " NAG O 603 " - " ASN O 197 " " NAG O 604 " - " ASN O 234 " " NAG O 605 " - " ASN O 276 " " NAG O 606 " - " ASN O 332 " " NAG O 607 " - " ASN O 363 " " NAG O 608 " - " ASN O 386 " " NAG O 609 " - " ASN O 448 " " NAG O 610 " - " ASN O 295 " " NAG O 611 " - " ASN O 392 " " NAG O 612 " - " ASN O 301 " " NAG Q 601 " - " ASN Q 133 " " NAG Q 602 " - " ASN Q 156 " " NAG Q 603 " - " ASN Q 160 " " NAG Q 604 " - " ASN Q 197 " " NAG Q 605 " - " ASN Q 234 " " NAG Q 606 " - " ASN Q 276 " " NAG Q 607 " - " ASN Q 301 " " NAG Q 608 " - " ASN Q 332 " " NAG Q 609 " - " ASN Q 363 " " NAG Q 610 " - " ASN Q 386 " " NAG Q 611 " - " ASN Q 392 " " NAG Q 612 " - " ASN Q 448 " " NAG Q 613 " - " ASN Q 339 " " NAG Q 614 " - " ASN Q 295 " " NAG R 701 " - " ASN R 637 " " NAG R 702 " - " ASN R 618 " " NAG S 601 " - " ASN S 133 " " NAG S 602 " - " ASN S 160 " " NAG S 603 " - " ASN S 197 " " NAG S 604 " - " ASN S 234 " " NAG S 605 " - " ASN S 276 " " NAG S 606 " - " ASN S 301 " " NAG S 607 " - " ASN S 332 " " NAG S 608 " - " ASN S 386 " " NAG S 609 " - " ASN S 448 " " NAG S 610 " - " ASN S 295 " " NAG S 611 " - " ASN S 156 " " NAG S 612 " - " ASN S 363 " " NAG T 701 " - " ASN T 618 " " NAG a 1 " - " ASN O 88 " " NAG b 1 " - " ASN Q 262 " " NAG c 1 " - " ASN Q 88 " " NAG d 1 " - " ASN S 262 " " NAG e 1 " - " ASN S 88 " " NAG f 1 " - " ASN A 262 " " NAG g 1 " - " ASN A 88 " " NAG h 1 " - " ASN C 156 " " NAG i 1 " - " ASN C 262 " " NAG j 1 " - " ASN C 88 " " NAG k 1 " - " ASN E 234 " " NAG l 1 " - " ASN E 262 " " NAG m 1 " - " ASN E 88 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.4 microseconds 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8792 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 78 sheets defined 17.7% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'O' and resid 96 through 98 No H-bonds generated for 'chain 'O' and resid 96 through 98' Processing helix chain 'O' and resid 99 through 117 removed outlier: 3.519A pdb=" N GLN O 103 " --> pdb=" O ASN O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 353 removed outlier: 3.862A pdb=" N LYS O 351 " --> pdb=" O LYS O 347 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N HIS O 352 " --> pdb=" O GLN O 348 " (cutoff:3.500A) Processing helix chain 'O' and resid 368 through 373 Processing helix chain 'O' and resid 475 through 481 Processing helix chain 'P' and resid 529 through 534 Processing helix chain 'P' and resid 536 through 542 removed outlier: 3.943A pdb=" N GLN P 540 " --> pdb=" O THR P 536 " (cutoff:3.500A) Processing helix chain 'P' and resid 570 through 596 removed outlier: 3.623A pdb=" N TRP P 596 " --> pdb=" O LEU P 592 " (cutoff:3.500A) Processing helix chain 'P' and resid 619 through 624 removed outlier: 3.797A pdb=" N ASP P 624 " --> pdb=" O SER P 620 " (cutoff:3.500A) Processing helix chain 'P' and resid 627 through 635 Processing helix chain 'P' and resid 639 through 663 removed outlier: 3.813A pdb=" N LEU P 663 " --> pdb=" O ASP P 659 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 117 removed outlier: 4.447A pdb=" N GLU Q 102 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 354 removed outlier: 3.845A pdb=" N HIS Q 352 " --> pdb=" O GLN Q 348 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 425 through 429 removed outlier: 4.208A pdb=" N GLN Q 428 " --> pdb=" O ASN Q 425 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG Q 429 " --> pdb=" O MET Q 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 425 through 429' Processing helix chain 'Q' and resid 475 through 481 removed outlier: 3.504A pdb=" N TRP Q 479 " --> pdb=" O MET Q 475 " (cutoff:3.500A) Processing helix chain 'R' and resid 529 through 534 Processing helix chain 'R' and resid 535 through 537 No H-bonds generated for 'chain 'R' and resid 535 through 537' Processing helix chain 'R' and resid 541 through 545 removed outlier: 3.627A pdb=" N LEU R 544 " --> pdb=" O ALA R 541 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU R 545 " --> pdb=" O ARG R 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 541 through 545' Processing helix chain 'R' and resid 570 through 596 removed outlier: 3.554A pdb=" N TRP R 596 " --> pdb=" O LEU R 592 " (cutoff:3.500A) Processing helix chain 'R' and resid 618 through 623 Processing helix chain 'R' and resid 627 through 635 Processing helix chain 'R' and resid 639 through 663 removed outlier: 3.541A pdb=" N LEU R 663 " --> pdb=" O ASP R 659 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 97 Processing helix chain 'S' and resid 98 through 117 removed outlier: 4.130A pdb=" N GLU S 102 " --> pdb=" O ASN S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 335 through 353 removed outlier: 3.742A pdb=" N HIS S 352 " --> pdb=" O GLN S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 475 through 481 removed outlier: 3.577A pdb=" N TRP S 479 " --> pdb=" O MET S 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 529 through 534 Processing helix chain 'T' and resid 536 through 542 removed outlier: 4.097A pdb=" N GLN T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 570 through 596 Processing helix chain 'T' and resid 619 through 624 removed outlier: 3.812A pdb=" N ASP T 624 " --> pdb=" O SER T 620 " (cutoff:3.500A) Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 663 removed outlier: 3.716A pdb=" N LEU T 663 " --> pdb=" O ASP T 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.132A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 4.158A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 87 removed outlier: 4.147A pdb=" N THR U 87 " --> pdb=" O ALA U 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 61 through 64 removed outlier: 3.589A pdb=" N LYS W 64 " --> pdb=" O PRO W 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 61 through 64' Processing helix chain 'W' and resid 83 through 87 removed outlier: 3.610A pdb=" N THR W 87 " --> pdb=" O ALA W 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 87 removed outlier: 4.126A pdb=" N THR Y 87 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.283A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.776A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.964A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.832A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.504A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.015A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.631A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 619 through 624' Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 662 removed outlier: 3.975A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.286A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.643A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 354 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 381 removed outlier: 4.165A pdb=" N GLY E 380 " --> pdb=" O ASN E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.644A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.080A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 639 through 663 removed outlier: 3.523A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 495 through 499 removed outlier: 4.822A pdb=" N VAL P 608 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL O 38 " --> pdb=" O THR P 606 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR P 606 " --> pdb=" O VAL O 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 45 through 47 removed outlier: 4.101A pdb=" N ILE O 225 " --> pdb=" O VAL O 245 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL O 242 " --> pdb=" O LEU O 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'O' and resid 169 through 176 Processing sheet with id=AA5, first strand: chain 'O' and resid 201 through 203 removed outlier: 6.736A pdb=" N THR O 202 " --> pdb=" O TYR O 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 271 through 273 removed outlier: 5.516A pdb=" N ILE O 358 " --> pdb=" O GLU O 466 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE O 468 " --> pdb=" O ILE O 358 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG O 360 " --> pdb=" O PHE O 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 374 through 378 removed outlier: 4.581A pdb=" N PHE O 382 " --> pdb=" O LYS O 421 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS O 421 " --> pdb=" O PHE O 382 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA O 329 " --> pdb=" O CYS O 418 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER O 334 " --> pdb=" O GLN O 293 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLN O 293 " --> pdb=" O SER O 334 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE O 443 " --> pdb=" O ARG O 298 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASN O 300 " --> pdb=" O GLY O 441 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLY O 441 " --> pdb=" O ASN O 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 304 through 305 Processing sheet with id=AA9, first strand: chain 'Q' and resid 495 through 499 removed outlier: 5.093A pdb=" N VAL Q 36 " --> pdb=" O THR R 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 45 through 47 removed outlier: 4.075A pdb=" N ILE Q 225 " --> pdb=" O VAL Q 245 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL Q 242 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'Q' and resid 169 through 176 Processing sheet with id=AB4, first strand: chain 'Q' and resid 271 through 274 removed outlier: 11.218A pdb=" N VAL Q 286 " --> pdb=" O THR Q 455 " (cutoff:3.500A) removed outlier: 10.869A pdb=" N THR Q 455 " --> pdb=" O VAL Q 286 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N PHE Q 288 " --> pdb=" O ILE Q 453 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N ILE Q 453 " --> pdb=" O PHE Q 288 " (cutoff:3.500A) removed outlier: 10.479A pdb=" N THR Q 290 " --> pdb=" O GLY Q 451 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY Q 451 " --> pdb=" O THR Q 290 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE Q 443 " --> pdb=" O ARG Q 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 271 through 274 removed outlier: 7.170A pdb=" N GLN Q 293 " --> pdb=" O SER Q 334 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER Q 334 " --> pdb=" O GLN Q 293 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA Q 329 " --> pdb=" O CYS Q 418 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 304 through 308 Processing sheet with id=AB7, first strand: chain 'Q' and resid 374 through 378 removed outlier: 4.813A pdb=" N PHE Q 382 " --> pdb=" O LYS Q 421 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS Q 421 " --> pdb=" O PHE Q 382 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 495 through 499 removed outlier: 5.242A pdb=" N VAL T 608 " --> pdb=" O VAL S 36 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL S 38 " --> pdb=" O THR T 606 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR T 606 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 45 through 47 removed outlier: 4.092A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL S 242 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 91 through 93 Processing sheet with id=AC2, first strand: chain 'S' and resid 170 through 176 Processing sheet with id=AC3, first strand: chain 'S' and resid 271 through 274 removed outlier: 6.333A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 294 through 297 Processing sheet with id=AC5, first strand: chain 'S' and resid 304 through 308 Processing sheet with id=AC6, first strand: chain 'S' and resid 374 through 377 removed outlier: 4.331A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS S 421 " --> pdb=" O PHE S 382 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 423 through 424 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AD1, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.715A pdb=" N VAL H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 58 through 59 removed outlier: 6.675A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP J 35A" --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA J 88 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL J 107 " --> pdb=" O TYR J 90 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'K' and resid 46 through 48 removed outlier: 6.603A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'L' and resid 44 through 49 removed outlier: 4.981A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'M' and resid 58 through 59 Processing sheet with id=AE1, first strand: chain 'M' and resid 45 through 46 removed outlier: 3.879A pdb=" N VAL M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.770A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'U' and resid 58 through 59 Processing sheet with id=AE6, first strand: chain 'U' and resid 45 through 46 removed outlier: 3.975A pdb=" N VAL U 107 " --> pdb=" O TYR U 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'V' and resid 45 through 46 Processing sheet with id=AE9, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'W' and resid 58 through 59 Processing sheet with id=AF2, first strand: chain 'W' and resid 45 through 46 removed outlier: 3.660A pdb=" N ALA W 88 " --> pdb=" O VAL W 109 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL W 107 " --> pdb=" O TYR W 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'X' and resid 53 through 54 removed outlier: 6.581A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'Y' and resid 58 through 59 Processing sheet with id=AF7, first strand: chain 'Y' and resid 45 through 46 Processing sheet with id=AF8, first strand: chain 'Z' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'Z' and resid 10 through 11 removed outlier: 3.858A pdb=" N LEU Z 11 " --> pdb=" O THR Z 103 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP Z 35 " --> pdb=" O LEU Z 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.003A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.098A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AG4, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AG5, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.358A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.423A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.851A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AG9, first strand: chain 'A' and resid 308 through 312 removed outlier: 6.675A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.816A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.947A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AH4, first strand: chain 'C' and resid 170 through 176 Processing sheet with id=AH5, first strand: chain 'C' and resid 271 through 274 removed outlier: 7.223A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 271 through 274 removed outlier: 11.208A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.367A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AH8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.264A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.043A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AI2, first strand: chain 'E' and resid 170 through 176 Processing sheet with id=AI3, first strand: chain 'E' and resid 201 through 202 removed outlier: 3.857A pdb=" N THR E 202 " --> pdb=" O CYS E 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'E' and resid 271 through 274 removed outlier: 7.230A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.668A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.384A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 301 through 312 removed outlier: 6.629A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3543 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: 8.16 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 12469 1.36 - 1.49: 10657 1.49 - 1.63: 16183 1.63 - 1.77: 1 1.77 - 1.91: 329 Bond restraints: 39639 Sorted by residual: bond pdb=" C1 NAG T 701 " pdb=" O5 NAG T 701 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " ideal model delta sigma weight residual 1.808 1.908 -0.100 3.30e-02 9.18e+02 9.19e+00 bond pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.81e+00 bond pdb=" C1 NAG j 2 " pdb=" O5 NAG j 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C1 NAG f 1 " pdb=" O5 NAG f 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.00e+00 ... (remaining 39634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 53415 3.30 - 6.59: 405 6.59 - 9.89: 6 9.89 - 13.18: 0 13.18 - 16.48: 1 Bond angle restraints: 53827 Sorted by residual: angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 130.88 -16.48 2.30e+00 1.89e-01 5.13e+01 angle pdb=" CB GLN V 90 " pdb=" CG GLN V 90 " pdb=" CD GLN V 90 " ideal model delta sigma weight residual 112.60 118.73 -6.13 1.70e+00 3.46e-01 1.30e+01 angle pdb=" C ASN C 295 " pdb=" N CYS C 296 " pdb=" CA CYS C 296 " ideal model delta sigma weight residual 121.62 115.52 6.10 1.83e+00 2.99e-01 1.11e+01 angle pdb=" CA GLU B 657 " pdb=" CB GLU B 657 " pdb=" CG GLU B 657 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CA GLU P 657 " pdb=" CB GLU P 657 " pdb=" CG GLU P 657 " ideal model delta sigma weight residual 114.10 120.54 -6.44 2.00e+00 2.50e-01 1.04e+01 ... (remaining 53822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.47: 23341 24.47 - 48.94: 1592 48.94 - 73.42: 329 73.42 - 97.89: 71 97.89 - 122.36: 39 Dihedral angle restraints: 25372 sinusoidal: 11733 harmonic: 13639 Sorted by residual: dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual 93.00 4.72 88.28 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -172.25 86.25 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS O 54 " pdb=" SG CYS O 54 " pdb=" SG CYS O 74 " pdb=" CB CYS O 74 " ideal model delta sinusoidal sigma weight residual 93.00 8.50 84.50 1 1.00e+01 1.00e-02 8.68e+01 ... (remaining 25369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5255 0.055 - 0.110: 892 0.110 - 0.165: 225 0.165 - 0.220: 15 0.220 - 0.275: 10 Chirality restraints: 6397 Sorted by residual: chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA i 3 " pdb=" C4 BMA i 3 " pdb=" C6 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA l 3 " pdb=" C4 BMA l 3 " pdb=" C6 BMA l 3 " pdb=" O5 BMA l 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 6394 not shown) Planarity restraints: 6816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN V 90 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLN V 90 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN V 90 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS V 91 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.045 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO H 14 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS M 13 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO M 14 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO M 14 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 14 " -0.037 5.00e-02 4.00e+02 ... (remaining 6813 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 664 2.66 - 3.22: 35499 3.22 - 3.78: 57192 3.78 - 4.34: 78867 4.34 - 4.90: 133646 Nonbonded interactions: 305868 Sorted by model distance: nonbonded pdb=" O SER S 365 " pdb=" O6 NAG S 612 " model vdw 2.098 3.040 nonbonded pdb=" OD1 ASN E 276 " pdb=" OG1 THR E 278 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASN O 276 " pdb=" OG1 THR O 278 " model vdw 2.171 3.040 nonbonded pdb=" OG SER C 481 " pdb=" OE1 GLU C 482 " model vdw 2.182 3.040 nonbonded pdb=" OD1 ASN D 625 " pdb=" O4 NAG j 2 " model vdw 2.204 3.040 ... (remaining 305863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 84 or resid 86 through 612)) selection = (chain 'C' and (resid 33 through 84 or resid 86 through 612)) selection = (chain 'E' and (resid 33 through 84 or resid 86 through 612)) selection = (chain 'O' and (resid 33 through 84 or resid 86 through 397 or resid 410 through \ 612)) selection = (chain 'Q' and (resid 33 through 84 or resid 86 through 612)) selection = (chain 'S' and (resid 33 through 84 or resid 86 through 397 or resid 410 through \ 612)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 517 through 663) selection = (chain 'F' and resid 517 through 663) selection = chain 'P' selection = (chain 'R' and resid 517 through 663) selection = (chain 'T' and resid 517 through 663) } ncs_group { reference = chain 'G' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'm' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'I' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'i' selection = chain 'l' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'V' selection = chain 'X' selection = (chain 'Z' and resid 1 through 104) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.140 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: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.020 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 39848 Z= 0.202 Angle : 0.707 16.479 54369 Z= 0.335 Chirality : 0.047 0.275 6397 Planarity : 0.004 0.067 6719 Dihedral : 17.003 122.361 16325 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 0.14 % Allowed : 20.86 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.12), residues: 4660 helix: 2.25 (0.20), residues: 756 sheet: -0.60 (0.15), residues: 1291 loop : -1.26 (0.12), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 588 TYR 0.015 0.001 TYR O 484 PHE 0.015 0.001 PHE A 317 TRP 0.014 0.001 TRP R 571 HIS 0.006 0.001 HIS Q 249 Details of bonding type rmsd covalent geometry : bond 0.00438 (39639) covalent geometry : angle 0.69031 (53827) SS BOND : bond 0.00407 ( 85) SS BOND : angle 1.51782 ( 170) hydrogen bonds : bond 0.12199 ( 1321) hydrogen bonds : angle 5.90547 ( 3543) link_ALPHA1-3 : bond 0.00466 ( 6) link_ALPHA1-3 : angle 1.69059 ( 18) link_BETA1-4 : bond 0.00730 ( 21) link_BETA1-4 : angle 1.73046 ( 63) link_NAG-ASN : bond 0.00375 ( 97) link_NAG-ASN : angle 1.75274 ( 291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 235 time to evaluate : 1.102 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 37 ILE cc_start: 0.8997 (mp) cc_final: 0.8766 (mt) outliers start: 6 outliers final: 1 residues processed: 241 average time/residue: 0.2292 time to fit residues: 87.9157 Evaluate side-chains 150 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 295 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 105 HIS ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 ASN A 195 ASN A 300 ASN C 432 GLN E 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.026317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.021205 restraints weight = 525335.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.021994 restraints weight = 274181.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.022564 restraints weight = 179265.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.022950 restraints weight = 132569.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.023265 restraints weight = 107055.228| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 39848 Z= 0.190 Angle : 0.642 10.665 54369 Z= 0.314 Chirality : 0.043 0.259 6397 Planarity : 0.004 0.063 6719 Dihedral : 10.111 102.662 7657 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 2.09 % Allowed : 20.11 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.12), residues: 4660 helix: 1.74 (0.19), residues: 816 sheet: -0.45 (0.15), residues: 1293 loop : -1.24 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 65 TYR 0.013 0.001 TYR J 25 PHE 0.017 0.001 PHE M 100F TRP 0.016 0.001 TRP R 571 HIS 0.004 0.001 HIS Q 85 Details of bonding type rmsd covalent geometry : bond 0.00410 (39639) covalent geometry : angle 0.61882 (53827) SS BOND : bond 0.00304 ( 85) SS BOND : angle 1.18159 ( 170) hydrogen bonds : bond 0.03617 ( 1321) hydrogen bonds : angle 4.87138 ( 3543) link_ALPHA1-3 : bond 0.00744 ( 6) link_ALPHA1-3 : angle 2.48947 ( 18) link_BETA1-4 : bond 0.00462 ( 21) link_BETA1-4 : angle 1.91856 ( 63) link_NAG-ASN : bond 0.00426 ( 97) link_NAG-ASN : angle 2.04601 ( 291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 162 time to evaluate : 1.313 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 104 MET cc_start: 0.9600 (ttt) cc_final: 0.9224 (tmm) REVERT: O 434 MET cc_start: 0.8223 (tmm) cc_final: 0.7846 (tmm) REVERT: P 530 MET cc_start: 0.9064 (mtm) cc_final: 0.7887 (mtm) REVERT: P 626 MET cc_start: 0.8745 (ttm) cc_final: 0.8311 (ttm) REVERT: Q 95 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8839 (ptm) REVERT: R 530 MET cc_start: 0.8936 (mtp) cc_final: 0.8558 (ttm) REVERT: R 584 GLU cc_start: 0.9340 (tt0) cc_final: 0.9058 (tt0) REVERT: R 626 MET cc_start: 0.8375 (ttm) cc_final: 0.7772 (ptm) REVERT: S 104 MET cc_start: 0.9600 (OUTLIER) cc_final: 0.9347 (ppp) REVERT: S 426 MET cc_start: 0.8725 (ptp) cc_final: 0.8493 (ptt) REVERT: S 447 SER cc_start: 0.9690 (OUTLIER) cc_final: 0.9425 (t) REVERT: T 544 LEU cc_start: 0.9892 (OUTLIER) cc_final: 0.9563 (mm) REVERT: T 584 GLU cc_start: 0.9382 (tt0) cc_final: 0.9024 (tm-30) REVERT: T 626 MET cc_start: 0.8324 (ttm) cc_final: 0.7972 (ttm) REVERT: J 69 ILE cc_start: 0.9610 (OUTLIER) cc_final: 0.9280 (tp) REVERT: K 4 MET cc_start: 0.8321 (mmm) cc_final: 0.8115 (mmm) REVERT: V 97 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8481 (p) REVERT: Z 4 MET cc_start: 0.8585 (mmm) cc_final: 0.8359 (mmm) REVERT: A 104 MET cc_start: 0.9196 (tmm) cc_final: 0.8949 (tmm) REVERT: A 434 MET cc_start: 0.8769 (tmm) cc_final: 0.8226 (tmm) REVERT: B 530 MET cc_start: 0.8635 (mtp) cc_final: 0.8420 (mtm) REVERT: B 621 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.8985 (pm20) REVERT: C 104 MET cc_start: 0.9626 (ttt) cc_final: 0.9276 (tmm) REVERT: C 296 CYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6333 (t) REVERT: D 530 MET cc_start: 0.9019 (mmm) cc_final: 0.8714 (mmm) REVERT: D 589 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8657 (p0) REVERT: D 626 MET cc_start: 0.8743 (ttt) cc_final: 0.8519 (ttt) REVERT: E 95 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8856 (ptm) REVERT: E 271 MET cc_start: 0.9065 (mmm) cc_final: 0.8585 (tpp) outliers start: 87 outliers final: 16 residues processed: 241 average time/residue: 0.2107 time to fit residues: 83.3853 Evaluate side-chains 163 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain Q residue 95 MET Chi-restraints excluded: chain Q residue 295 ASN Chi-restraints excluded: chain Q residue 333 VAL Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 433 CYS Chi-restraints excluded: chain S residue 447 SER Chi-restraints excluded: chain T residue 544 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Z residue 23 CYS Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 442 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 373 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 424 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 435 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 540 GLN Q 105 HIS Q 258 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 425 ASN H 1 GLN ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN K 37 GLN L 3 GLN M 81 ASN ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 81 ASN C 105 HIS D 625 ASN E 105 HIS E 216 HIS E 432 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.024761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.019850 restraints weight = 493518.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.020560 restraints weight = 270286.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.021078 restraints weight = 181675.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.021437 restraints weight = 136765.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.021714 restraints weight = 112140.263| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 39848 Z= 0.366 Angle : 0.797 10.973 54369 Z= 0.385 Chirality : 0.044 0.331 6397 Planarity : 0.005 0.080 6719 Dihedral : 8.520 103.963 7657 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 3.03 % Allowed : 19.63 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.12), residues: 4660 helix: 1.24 (0.18), residues: 840 sheet: -0.47 (0.15), residues: 1296 loop : -1.43 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 65 TYR 0.017 0.002 TYR D 638 PHE 0.018 0.002 PHE O 317 TRP 0.024 0.002 TRP R 571 HIS 0.007 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00763 (39639) covalent geometry : angle 0.77118 (53827) SS BOND : bond 0.00401 ( 85) SS BOND : angle 1.79890 ( 170) hydrogen bonds : bond 0.04039 ( 1321) hydrogen bonds : angle 5.02174 ( 3543) link_ALPHA1-3 : bond 0.00637 ( 6) link_ALPHA1-3 : angle 2.47605 ( 18) link_BETA1-4 : bond 0.00464 ( 21) link_BETA1-4 : angle 2.02822 ( 63) link_NAG-ASN : bond 0.00789 ( 97) link_NAG-ASN : angle 2.35217 ( 291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 137 time to evaluate : 1.513 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: 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: 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: symmetry clash revert: symmetry clash REVERT: O 104 MET cc_start: 0.9598 (ttt) cc_final: 0.9252 (tmm) REVERT: O 161 MET cc_start: 0.9339 (tpp) cc_final: 0.9055 (tpp) REVERT: O 261 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9483 (mp) REVERT: O 434 MET cc_start: 0.8742 (tmm) cc_final: 0.8005 (tmm) REVERT: P 530 MET cc_start: 0.8926 (mtm) cc_final: 0.8290 (mtm) REVERT: P 544 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9581 (mm) REVERT: P 626 MET cc_start: 0.8471 (ttm) cc_final: 0.8190 (ttm) REVERT: Q 265 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9058 (mt) REVERT: Q 434 MET cc_start: 0.8756 (ttp) cc_final: 0.8099 (tmm) REVERT: R 530 MET cc_start: 0.8735 (mtp) cc_final: 0.8404 (ttm) REVERT: R 626 MET cc_start: 0.8239 (ttm) cc_final: 0.8009 (ttm) REVERT: S 95 MET cc_start: 0.9365 (ppp) cc_final: 0.8674 (ppp) REVERT: S 104 MET cc_start: 0.9571 (tmm) cc_final: 0.9362 (ppp) REVERT: S 447 SER cc_start: 0.9727 (OUTLIER) cc_final: 0.9483 (t) REVERT: T 584 GLU cc_start: 0.9357 (tt0) cc_final: 0.9012 (tm-30) REVERT: J 69 ILE cc_start: 0.9663 (OUTLIER) cc_final: 0.9350 (tp) REVERT: M 25 TYR cc_start: 0.8583 (m-10) cc_final: 0.8229 (m-80) REVERT: N 4 MET cc_start: 0.8460 (mmm) cc_final: 0.8069 (mmm) REVERT: A 104 MET cc_start: 0.9363 (tmm) cc_final: 0.9032 (tmm) REVERT: A 150 MET cc_start: 0.8459 (mmm) cc_final: 0.8150 (mmm) REVERT: A 161 MET cc_start: 0.9163 (tpp) cc_final: 0.8907 (tpp) REVERT: A 271 MET cc_start: 0.9083 (mmm) cc_final: 0.8830 (mmm) REVERT: B 621 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8835 (pm20) REVERT: C 104 MET cc_start: 0.9614 (ttt) cc_final: 0.9285 (tmm) REVERT: D 530 MET cc_start: 0.8973 (mmm) cc_final: 0.8754 (mmm) REVERT: D 626 MET cc_start: 0.8469 (ttt) cc_final: 0.8236 (ttt) REVERT: E 104 MET cc_start: 0.9315 (ppp) cc_final: 0.9042 (ppp) REVERT: E 271 MET cc_start: 0.8944 (mmm) cc_final: 0.8643 (tpp) REVERT: E 434 MET cc_start: 0.8304 (tpp) cc_final: 0.8101 (tpp) REVERT: F 530 MET cc_start: 0.9083 (mpp) cc_final: 0.8755 (mpp) outliers start: 126 outliers final: 50 residues processed: 257 average time/residue: 0.2014 time to fit residues: 86.4982 Evaluate side-chains 185 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 129 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 261 LEU Chi-restraints excluded: chain O residue 297 THR Chi-restraints excluded: chain O residue 373 THR Chi-restraints excluded: chain O residue 469 ARG Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain Q residue 196 CYS Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 295 ASN Chi-restraints excluded: chain Q residue 333 VAL Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain R residue 544 LEU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 433 CYS Chi-restraints excluded: chain S residue 447 SER Chi-restraints excluded: chain T residue 589 ASP Chi-restraints excluded: chain T residue 624 ASP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 589 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 255 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 353 optimal weight: 5.9990 chunk 349 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 392 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 288 optimal weight: 0.9980 chunk 441 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 258 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN M 81 ASN ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 170 GLN D 540 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.025380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.020364 restraints weight = 496461.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.021117 restraints weight = 268533.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.021659 restraints weight = 178901.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.022052 restraints weight = 134057.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.022320 restraints weight = 108370.818| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39848 Z= 0.127 Angle : 0.611 11.858 54369 Z= 0.295 Chirality : 0.043 0.256 6397 Planarity : 0.004 0.067 6719 Dihedral : 7.428 99.379 7657 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.17 % Favored : 94.78 % Rotamer: Outliers : 2.36 % Allowed : 20.30 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.12), residues: 4660 helix: 1.65 (0.19), residues: 825 sheet: -0.24 (0.15), residues: 1328 loop : -1.28 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 469 TYR 0.013 0.001 TYR E 435 PHE 0.016 0.001 PHE O 317 TRP 0.016 0.001 TRP R 571 HIS 0.004 0.001 HIS Q 85 Details of bonding type rmsd covalent geometry : bond 0.00280 (39639) covalent geometry : angle 0.58454 (53827) SS BOND : bond 0.00329 ( 85) SS BOND : angle 1.60793 ( 170) hydrogen bonds : bond 0.03384 ( 1321) hydrogen bonds : angle 4.63450 ( 3543) link_ALPHA1-3 : bond 0.00800 ( 6) link_ALPHA1-3 : angle 2.38044 ( 18) link_BETA1-4 : bond 0.00480 ( 21) link_BETA1-4 : angle 1.76528 ( 63) link_NAG-ASN : bond 0.00400 ( 97) link_NAG-ASN : angle 2.01279 ( 291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 147 time to evaluate : 0.942 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: 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: 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: O 104 MET cc_start: 0.9573 (ttt) cc_final: 0.9252 (tmm) REVERT: O 161 MET cc_start: 0.9253 (tpp) cc_final: 0.8941 (tpp) REVERT: O 271 MET cc_start: 0.9248 (tpp) cc_final: 0.8645 (tpp) REVERT: O 434 MET cc_start: 0.8812 (tmm) cc_final: 0.8203 (tmm) REVERT: O 499 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8798 (p) REVERT: P 530 MET cc_start: 0.8860 (mtm) cc_final: 0.8354 (mtm) REVERT: P 626 MET cc_start: 0.8492 (ttm) cc_final: 0.8234 (ttm) REVERT: Q 104 MET cc_start: 0.9517 (ttt) cc_final: 0.9203 (ttm) REVERT: Q 265 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9039 (mt) REVERT: R 530 MET cc_start: 0.8752 (mtp) cc_final: 0.8435 (ttm) REVERT: R 626 MET cc_start: 0.8259 (ttm) cc_final: 0.8016 (ttm) REVERT: S 95 MET cc_start: 0.9332 (ppp) cc_final: 0.8665 (ppp) REVERT: S 104 MET cc_start: 0.9574 (tmm) cc_final: 0.9290 (tmm) REVERT: S 155 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9068 (mmmt) REVERT: S 271 MET cc_start: 0.8834 (tpp) cc_final: 0.8560 (tpp) REVERT: T 584 GLU cc_start: 0.9326 (tt0) cc_final: 0.8950 (tm-30) REVERT: H 38 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8688 (tmm-80) REVERT: J 69 ILE cc_start: 0.9632 (OUTLIER) cc_final: 0.9318 (tp) REVERT: M 25 TYR cc_start: 0.8590 (m-10) cc_final: 0.8306 (m-10) REVERT: V 4 MET cc_start: 0.8569 (mmm) cc_final: 0.8026 (mmm) REVERT: V 69 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9265 (p) REVERT: A 104 MET cc_start: 0.9411 (tmm) cc_final: 0.9122 (ppp) REVERT: A 161 MET cc_start: 0.9122 (tpp) cc_final: 0.8873 (tpp) REVERT: A 271 MET cc_start: 0.9048 (mmm) cc_final: 0.8846 (mmm) REVERT: A 434 MET cc_start: 0.8906 (tmm) cc_final: 0.7946 (tmm) REVERT: B 621 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8764 (pm20) REVERT: C 104 MET cc_start: 0.9587 (ttt) cc_final: 0.9278 (tmm) REVERT: C 161 MET cc_start: 0.9084 (tpp) cc_final: 0.8871 (tpp) REVERT: D 530 MET cc_start: 0.9099 (mmm) cc_final: 0.8806 (mmm) REVERT: D 540 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8917 (mt0) REVERT: E 69 TRP cc_start: 0.9319 (OUTLIER) cc_final: 0.9020 (m100) REVERT: E 104 MET cc_start: 0.9389 (ppp) cc_final: 0.9055 (ppp) REVERT: E 271 MET cc_start: 0.8878 (mmm) cc_final: 0.8631 (tpp) REVERT: E 426 MET cc_start: 0.8550 (ptt) cc_final: 0.8321 (ptt) REVERT: F 530 MET cc_start: 0.9029 (mpp) cc_final: 0.8783 (mpp) REVERT: F 584 GLU cc_start: 0.8708 (pp20) cc_final: 0.8304 (tm-30) outliers start: 98 outliers final: 47 residues processed: 242 average time/residue: 0.2053 time to fit residues: 81.2778 Evaluate side-chains 188 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 132 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 297 THR Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 499 THR Chi-restraints excluded: chain P residue 620 SER Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 196 CYS Chi-restraints excluded: chain Q residue 201 CYS Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 295 ASN Chi-restraints excluded: chain Q residue 333 VAL Chi-restraints excluded: chain Q residue 446 VAL Chi-restraints excluded: chain R residue 544 LEU Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain S residue 100 MET Chi-restraints excluded: chain S residue 155 LYS Chi-restraints excluded: chain S residue 433 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Z residue 20 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 181 optimal weight: 4.9990 chunk 400 optimal weight: 6.9990 chunk 372 optimal weight: 0.0070 chunk 66 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 363 optimal weight: 0.9980 chunk 458 optimal weight: 0.0980 chunk 456 optimal weight: 6.9990 chunk 453 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 258 GLN Q 377 ASN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN D 540 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.025663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.020624 restraints weight = 528957.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.021405 restraints weight = 274811.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.021972 restraints weight = 178943.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.022362 restraints weight = 131908.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.022658 restraints weight = 106421.205| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 39848 Z= 0.104 Angle : 0.594 11.003 54369 Z= 0.285 Chirality : 0.043 0.255 6397 Planarity : 0.004 0.070 6719 Dihedral : 6.852 95.884 7657 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 1.97 % Allowed : 20.57 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.12), residues: 4660 helix: 1.75 (0.19), residues: 810 sheet: -0.15 (0.15), residues: 1336 loop : -1.25 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 65 TYR 0.011 0.001 TYR E 435 PHE 0.013 0.001 PHE Y 78 TRP 0.018 0.001 TRP T 628 HIS 0.003 0.001 HIS Q 249 Details of bonding type rmsd covalent geometry : bond 0.00235 (39639) covalent geometry : angle 0.56905 (53827) SS BOND : bond 0.00242 ( 85) SS BOND : angle 1.47493 ( 170) hydrogen bonds : bond 0.03224 ( 1321) hydrogen bonds : angle 4.53930 ( 3543) link_ALPHA1-3 : bond 0.00970 ( 6) link_ALPHA1-3 : angle 2.13515 ( 18) link_BETA1-4 : bond 0.00517 ( 21) link_BETA1-4 : angle 1.66522 ( 63) link_NAG-ASN : bond 0.00372 ( 97) link_NAG-ASN : angle 1.96824 ( 291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 146 time to evaluate : 1.070 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: 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: 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: O 104 MET cc_start: 0.9583 (ttt) cc_final: 0.9253 (tmm) REVERT: O 161 MET cc_start: 0.9248 (tpp) cc_final: 0.8922 (tpp) REVERT: O 271 MET cc_start: 0.9272 (tpp) cc_final: 0.8511 (mmm) REVERT: O 434 MET cc_start: 0.8892 (tmm) cc_final: 0.8337 (tmm) REVERT: O 499 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8782 (p) REVERT: P 530 MET cc_start: 0.8846 (mtm) cc_final: 0.8408 (mtm) REVERT: P 544 LEU cc_start: 0.9813 (OUTLIER) cc_final: 0.9579 (mm) REVERT: P 626 MET cc_start: 0.8494 (ttm) cc_final: 0.8237 (ttm) REVERT: Q 104 MET cc_start: 0.9528 (ttt) cc_final: 0.9212 (ttm) REVERT: Q 141 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8653 (p0) REVERT: Q 150 MET cc_start: 0.8589 (mmm) cc_final: 0.8323 (mmm) REVERT: R 530 MET cc_start: 0.8745 (mtp) cc_final: 0.8446 (ttm) REVERT: R 626 MET cc_start: 0.8218 (ttm) cc_final: 0.7967 (ttm) REVERT: S 95 MET cc_start: 0.9290 (ppp) cc_final: 0.8522 (ppp) REVERT: S 104 MET cc_start: 0.9555 (tmm) cc_final: 0.9278 (tmm) REVERT: S 155 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9025 (mmmt) REVERT: S 271 MET cc_start: 0.8831 (tpp) cc_final: 0.8564 (tpp) REVERT: S 434 MET cc_start: 0.8580 (mtm) cc_final: 0.8354 (ppp) REVERT: T 530 MET cc_start: 0.9136 (mmm) cc_final: 0.8764 (mmm) REVERT: T 584 GLU cc_start: 0.9319 (tt0) cc_final: 0.8956 (tm-30) REVERT: H 38 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8760 (tmm-80) REVERT: J 69 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9312 (tp) REVERT: K 104 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8707 (mm) REVERT: M 25 TYR cc_start: 0.8609 (m-10) cc_final: 0.8292 (m-80) REVERT: N 4 MET cc_start: 0.8435 (mmm) cc_final: 0.8092 (mmm) REVERT: V 4 MET cc_start: 0.8568 (mmm) cc_final: 0.8164 (mmm) REVERT: A 104 MET cc_start: 0.9406 (tmm) cc_final: 0.9111 (ppp) REVERT: A 161 MET cc_start: 0.9112 (tpp) cc_final: 0.8909 (tpp) REVERT: A 265 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9308 (mp) REVERT: A 271 MET cc_start: 0.9041 (mmm) cc_final: 0.8565 (tpp) REVERT: A 434 MET cc_start: 0.8924 (tmm) cc_final: 0.7918 (tmm) REVERT: B 621 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8739 (pm20) REVERT: C 104 MET cc_start: 0.9589 (ttt) cc_final: 0.9297 (tmm) REVERT: C 265 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9072 (mp) REVERT: D 530 MET cc_start: 0.9066 (mmm) cc_final: 0.8464 (mmm) REVERT: E 69 TRP cc_start: 0.9284 (OUTLIER) cc_final: 0.9004 (m100) REVERT: E 104 MET cc_start: 0.9403 (ppp) cc_final: 0.9051 (ppp) REVERT: E 271 MET cc_start: 0.8919 (mmm) cc_final: 0.8657 (tpp) REVERT: E 426 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8227 (pmm) REVERT: F 530 MET cc_start: 0.9074 (mpp) cc_final: 0.7343 (mpp) REVERT: F 584 GLU cc_start: 0.8726 (pp20) cc_final: 0.8341 (tm-30) outliers start: 82 outliers final: 43 residues processed: 225 average time/residue: 0.2235 time to fit residues: 82.7728 Evaluate side-chains 187 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 132 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 255 VAL Chi-restraints excluded: chain O residue 297 THR Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 469 ARG Chi-restraints excluded: chain O residue 494 LEU Chi-restraints excluded: chain O residue 499 THR Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 141 ASP Chi-restraints excluded: chain Q residue 196 CYS Chi-restraints excluded: chain Q residue 295 ASN Chi-restraints excluded: chain Q residue 333 VAL Chi-restraints excluded: chain S residue 155 LYS Chi-restraints excluded: chain S residue 433 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 291 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 413 optimal weight: 4.9990 chunk 351 optimal weight: 0.0870 chunk 158 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 423 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN M 81 ASN ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.025037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.020125 restraints weight = 487937.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.020849 restraints weight = 266360.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.021373 restraints weight = 178428.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.021753 restraints weight = 134058.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.022026 restraints weight = 108927.478| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 39848 Z= 0.211 Angle : 0.636 10.824 54369 Z= 0.306 Chirality : 0.042 0.275 6397 Planarity : 0.004 0.068 6719 Dihedral : 6.650 96.075 7657 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.56 % Favored : 94.38 % Rotamer: Outliers : 2.48 % Allowed : 20.42 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.12), residues: 4660 helix: 1.64 (0.19), residues: 834 sheet: -0.16 (0.15), residues: 1318 loop : -1.22 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 65 TYR 0.013 0.001 TYR S 39 PHE 0.015 0.001 PHE O 317 TRP 0.019 0.002 TRP C 96 HIS 0.004 0.001 HIS S 216 Details of bonding type rmsd covalent geometry : bond 0.00448 (39639) covalent geometry : angle 0.61095 (53827) SS BOND : bond 0.00283 ( 85) SS BOND : angle 1.52530 ( 170) hydrogen bonds : bond 0.03358 ( 1321) hydrogen bonds : angle 4.61672 ( 3543) link_ALPHA1-3 : bond 0.00787 ( 6) link_ALPHA1-3 : angle 2.25640 ( 18) link_BETA1-4 : bond 0.00393 ( 21) link_BETA1-4 : angle 1.71835 ( 63) link_NAG-ASN : bond 0.00454 ( 97) link_NAG-ASN : angle 2.03922 ( 291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 140 time to evaluate : 1.359 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 104 MET cc_start: 0.9589 (ttt) cc_final: 0.9267 (tmm) REVERT: O 161 MET cc_start: 0.9250 (tpp) cc_final: 0.9034 (tpp) REVERT: O 434 MET cc_start: 0.8968 (tmm) cc_final: 0.8383 (tmm) REVERT: P 530 MET cc_start: 0.8866 (mtm) cc_final: 0.8338 (mtm) REVERT: P 544 LEU cc_start: 0.9863 (OUTLIER) cc_final: 0.9577 (mm) REVERT: P 626 MET cc_start: 0.8527 (ttm) cc_final: 0.8252 (ttm) REVERT: Q 104 MET cc_start: 0.9547 (ttt) cc_final: 0.9227 (ttm) REVERT: Q 141 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8634 (p0) REVERT: Q 150 MET cc_start: 0.8579 (mmm) cc_final: 0.8311 (mmm) REVERT: Q 265 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9009 (mt) REVERT: R 530 MET cc_start: 0.8692 (mtp) cc_final: 0.8482 (ttm) REVERT: R 626 MET cc_start: 0.8233 (ttm) cc_final: 0.8003 (ttm) REVERT: S 95 MET cc_start: 0.9334 (ppp) cc_final: 0.8592 (ppp) REVERT: S 104 MET cc_start: 0.9570 (tmm) cc_final: 0.9283 (tmm) REVERT: S 155 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9031 (mmmt) REVERT: S 287 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8822 (tt0) REVERT: S 434 MET cc_start: 0.8562 (mtm) cc_final: 0.8352 (ppp) REVERT: T 530 MET cc_start: 0.9122 (mmm) cc_final: 0.8639 (mpp) REVERT: T 584 GLU cc_start: 0.9335 (tt0) cc_final: 0.8994 (tm-30) REVERT: T 654 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8773 (mt-10) REVERT: H 37 ILE cc_start: 0.9418 (mt) cc_final: 0.8918 (tp) REVERT: H 38 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8781 (tmm-80) REVERT: J 69 ILE cc_start: 0.9654 (OUTLIER) cc_final: 0.9342 (tp) REVERT: K 104 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8831 (mm) REVERT: M 25 TYR cc_start: 0.8671 (m-10) cc_final: 0.8388 (m-10) REVERT: N 4 MET cc_start: 0.8360 (mmm) cc_final: 0.8097 (mmm) REVERT: V 4 MET cc_start: 0.8512 (mmm) cc_final: 0.8151 (mmm) REVERT: A 104 MET cc_start: 0.9391 (tmm) cc_final: 0.9081 (ppp) REVERT: A 161 MET cc_start: 0.9167 (tpp) cc_final: 0.8934 (tpp) REVERT: A 271 MET cc_start: 0.9062 (mmm) cc_final: 0.8637 (tpp) REVERT: A 434 MET cc_start: 0.8958 (tmm) cc_final: 0.7948 (tmm) REVERT: B 530 MET cc_start: 0.9110 (mmm) cc_final: 0.8645 (tpp) REVERT: C 104 MET cc_start: 0.9604 (ttt) cc_final: 0.9301 (tmm) REVERT: C 161 MET cc_start: 0.9057 (tpp) cc_final: 0.8663 (tpp) REVERT: C 265 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9102 (mp) REVERT: E 69 TRP cc_start: 0.9264 (OUTLIER) cc_final: 0.8800 (m100) REVERT: E 104 MET cc_start: 0.9378 (ppp) cc_final: 0.9082 (ppp) REVERT: E 271 MET cc_start: 0.8946 (mmm) cc_final: 0.8690 (tpp) REVERT: E 426 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8423 (pmm) REVERT: E 490 LYS cc_start: 0.9622 (OUTLIER) cc_final: 0.9386 (ptmt) REVERT: F 530 MET cc_start: 0.8904 (mpp) cc_final: 0.8300 (mmp) outliers start: 103 outliers final: 62 residues processed: 239 average time/residue: 0.2250 time to fit residues: 88.8801 Evaluate side-chains 200 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 126 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 255 VAL Chi-restraints excluded: chain O residue 297 THR Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 469 ARG Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 141 ASP Chi-restraints excluded: chain Q residue 196 CYS Chi-restraints excluded: chain Q residue 201 CYS Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 295 ASN Chi-restraints excluded: chain Q residue 333 VAL Chi-restraints excluded: chain R residue 544 LEU Chi-restraints excluded: chain S residue 100 MET Chi-restraints excluded: chain S residue 155 LYS Chi-restraints excluded: chain S residue 202 THR Chi-restraints excluded: chain S residue 287 GLN Chi-restraints excluded: chain S residue 433 CYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 620 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 490 LYS Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 444 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 387 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 434 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 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 = 0.2973 r_free = 0.2973 target = 0.024437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.019324 restraints weight = 631623.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.020094 restraints weight = 314935.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.020652 restraints weight = 201977.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.021056 restraints weight = 148177.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.021342 restraints weight = 118180.110| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 39848 Z= 0.344 Angle : 0.751 10.658 54369 Z= 0.363 Chirality : 0.042 0.266 6397 Planarity : 0.005 0.079 6719 Dihedral : 6.798 97.180 7657 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 2.55 % Allowed : 20.81 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.12), residues: 4660 helix: 1.31 (0.18), residues: 840 sheet: -0.43 (0.15), residues: 1270 loop : -1.37 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 65 TYR 0.016 0.002 TYR V 86 PHE 0.021 0.002 PHE O 317 TRP 0.024 0.002 TRP C 96 HIS 0.005 0.001 HIS Q 374 Details of bonding type rmsd covalent geometry : bond 0.00718 (39639) covalent geometry : angle 0.72563 (53827) SS BOND : bond 0.00383 ( 85) SS BOND : angle 1.76897 ( 170) hydrogen bonds : bond 0.03757 ( 1321) hydrogen bonds : angle 4.88103 ( 3543) link_ALPHA1-3 : bond 0.00595 ( 6) link_ALPHA1-3 : angle 2.38384 ( 18) link_BETA1-4 : bond 0.00424 ( 21) link_BETA1-4 : angle 1.78127 ( 63) link_NAG-ASN : bond 0.00646 ( 97) link_NAG-ASN : angle 2.24603 ( 291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 129 time to evaluate : 1.407 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 104 MET cc_start: 0.9596 (ttt) cc_final: 0.9275 (tmm) REVERT: O 271 MET cc_start: 0.9261 (tpp) cc_final: 0.8612 (tpp) REVERT: O 434 MET cc_start: 0.9025 (tmm) cc_final: 0.8424 (tmm) REVERT: P 530 MET cc_start: 0.8875 (mtm) cc_final: 0.8310 (mtm) REVERT: P 544 LEU cc_start: 0.9872 (OUTLIER) cc_final: 0.9593 (mm) REVERT: P 626 MET cc_start: 0.8503 (ttm) cc_final: 0.8208 (ttm) REVERT: Q 104 MET cc_start: 0.9524 (ttt) cc_final: 0.9207 (ttm) REVERT: Q 141 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8545 (p0) REVERT: Q 150 MET cc_start: 0.8688 (mmm) cc_final: 0.8353 (mmm) REVERT: Q 265 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9264 (mp) REVERT: R 584 GLU cc_start: 0.9103 (tt0) cc_final: 0.8312 (tm-30) REVERT: R 626 MET cc_start: 0.8258 (ttm) cc_final: 0.8012 (ttm) REVERT: S 95 MET cc_start: 0.9380 (ppp) cc_final: 0.8717 (ppp) REVERT: S 104 MET cc_start: 0.9588 (tmm) cc_final: 0.9259 (tmm) REVERT: S 141 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8865 (p0) REVERT: S 287 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8781 (tt0) REVERT: S 447 SER cc_start: 0.9757 (OUTLIER) cc_final: 0.9467 (t) REVERT: T 584 GLU cc_start: 0.9327 (tt0) cc_final: 0.8988 (tm-30) REVERT: J 69 ILE cc_start: 0.9678 (OUTLIER) cc_final: 0.9356 (tp) REVERT: K 24 ARG cc_start: 0.9513 (OUTLIER) cc_final: 0.9067 (mtm-85) REVERT: M 25 TYR cc_start: 0.8734 (m-10) cc_final: 0.8402 (m-10) REVERT: N 4 MET cc_start: 0.8285 (mmm) cc_final: 0.7976 (mmm) REVERT: N 69 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9165 (p) REVERT: V 4 MET cc_start: 0.8361 (mmm) cc_final: 0.8022 (mmm) REVERT: A 104 MET cc_start: 0.9402 (tmm) cc_final: 0.8994 (tmm) REVERT: A 161 MET cc_start: 0.9155 (tpp) cc_final: 0.8934 (tpp) REVERT: A 271 MET cc_start: 0.9069 (mmm) cc_final: 0.8722 (tpp) REVERT: A 434 MET cc_start: 0.9066 (tmm) cc_final: 0.8078 (tmm) REVERT: B 530 MET cc_start: 0.9036 (mmm) cc_final: 0.8664 (tpp) REVERT: B 626 MET cc_start: 0.7792 (ppp) cc_final: 0.7540 (ppp) REVERT: C 104 MET cc_start: 0.9616 (ttt) cc_final: 0.9291 (tmm) REVERT: C 265 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9129 (mp) REVERT: D 584 GLU cc_start: 0.9336 (tt0) cc_final: 0.8973 (tm-30) REVERT: E 69 TRP cc_start: 0.9281 (OUTLIER) cc_final: 0.8849 (m100) REVERT: E 104 MET cc_start: 0.9400 (ppp) cc_final: 0.9100 (ppp) REVERT: E 490 LYS cc_start: 0.9621 (OUTLIER) cc_final: 0.9393 (ptmt) REVERT: F 530 MET cc_start: 0.8891 (mpp) cc_final: 0.8400 (mpp) outliers start: 106 outliers final: 73 residues processed: 231 average time/residue: 0.2228 time to fit residues: 85.3304 Evaluate side-chains 204 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 119 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 255 VAL Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain O residue 297 THR Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 469 ARG Chi-restraints excluded: chain P residue 534 SER Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain P residue 576 LEU Chi-restraints excluded: chain P residue 620 SER Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 141 ASP Chi-restraints excluded: chain Q residue 196 CYS Chi-restraints excluded: chain Q residue 201 CYS Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 295 ASN Chi-restraints excluded: chain Q residue 333 VAL Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain R residue 544 LEU Chi-restraints excluded: chain S residue 100 MET Chi-restraints excluded: chain S residue 141 ASP Chi-restraints excluded: chain S residue 287 GLN Chi-restraints excluded: chain S residue 433 CYS Chi-restraints excluded: chain S residue 447 SER Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Z residue 20 THR Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 490 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 223 optimal weight: 4.9990 chunk 270 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 461 optimal weight: 4.9990 chunk 109 optimal weight: 0.0070 chunk 140 optimal weight: 0.9990 chunk 247 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 chunk 341 optimal weight: 5.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.024788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.019784 restraints weight = 546591.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.020542 restraints weight = 286585.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.021081 restraints weight = 187662.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.021480 restraints weight = 139270.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.021768 restraints weight = 111808.560| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 39848 Z= 0.174 Angle : 0.628 10.445 54369 Z= 0.305 Chirality : 0.042 0.257 6397 Planarity : 0.004 0.100 6719 Dihedral : 6.494 95.397 7657 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 2.31 % Allowed : 21.02 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.12), residues: 4660 helix: 1.44 (0.18), residues: 840 sheet: -0.27 (0.15), residues: 1240 loop : -1.30 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG Y 65 TYR 0.012 0.001 TYR S 191 PHE 0.019 0.001 PHE O 317 TRP 0.020 0.001 TRP P 571 HIS 0.004 0.001 HIS Q 85 Details of bonding type rmsd covalent geometry : bond 0.00374 (39639) covalent geometry : angle 0.60276 (53827) SS BOND : bond 0.00284 ( 85) SS BOND : angle 1.57981 ( 170) hydrogen bonds : bond 0.03446 ( 1321) hydrogen bonds : angle 4.66245 ( 3543) link_ALPHA1-3 : bond 0.00677 ( 6) link_ALPHA1-3 : angle 1.96323 ( 18) link_BETA1-4 : bond 0.00377 ( 21) link_BETA1-4 : angle 1.64249 ( 63) link_NAG-ASN : bond 0.00387 ( 97) link_NAG-ASN : angle 2.02951 ( 291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 131 time to evaluate : 1.725 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: 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: symmetry clash revert: symmetry clash REVERT: O 104 MET cc_start: 0.9573 (ttt) cc_final: 0.9268 (tmm) REVERT: O 199 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8538 (p) REVERT: O 271 MET cc_start: 0.9261 (tpp) cc_final: 0.8638 (tpp) REVERT: O 434 MET cc_start: 0.8948 (tmm) cc_final: 0.8406 (tmm) REVERT: P 530 MET cc_start: 0.8788 (mtm) cc_final: 0.8179 (mtm) REVERT: P 544 LEU cc_start: 0.9844 (OUTLIER) cc_final: 0.9566 (mm) REVERT: P 626 MET cc_start: 0.8492 (ttm) cc_final: 0.8235 (ttm) REVERT: Q 104 MET cc_start: 0.9517 (ttt) cc_final: 0.9205 (ttm) REVERT: Q 141 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8602 (p0) REVERT: Q 150 MET cc_start: 0.8652 (mmm) cc_final: 0.8396 (mmm) REVERT: Q 265 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9241 (mp) REVERT: R 584 GLU cc_start: 0.9112 (tt0) cc_final: 0.8251 (tm-30) REVERT: S 95 MET cc_start: 0.9347 (ppp) cc_final: 0.8683 (ppp) REVERT: S 104 MET cc_start: 0.9563 (tmm) cc_final: 0.9252 (tmm) REVERT: S 141 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8894 (p0) REVERT: S 155 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9053 (mmmt) REVERT: S 271 MET cc_start: 0.8850 (tpp) cc_final: 0.8552 (tpp) REVERT: S 287 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8859 (tt0) REVERT: S 447 SER cc_start: 0.9744 (OUTLIER) cc_final: 0.9449 (t) REVERT: T 530 MET cc_start: 0.8912 (mmm) cc_final: 0.8058 (tpp) REVERT: T 584 GLU cc_start: 0.9303 (tt0) cc_final: 0.8966 (tm-30) REVERT: J 69 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9338 (tp) REVERT: K 24 ARG cc_start: 0.9506 (OUTLIER) cc_final: 0.9164 (mtm-85) REVERT: M 25 TYR cc_start: 0.8739 (m-10) cc_final: 0.8423 (m-10) REVERT: N 4 MET cc_start: 0.8306 (mmm) cc_final: 0.8077 (mmm) REVERT: V 4 MET cc_start: 0.8387 (mmm) cc_final: 0.8064 (mmm) REVERT: A 69 TRP cc_start: 0.9200 (OUTLIER) cc_final: 0.8966 (m100) REVERT: A 104 MET cc_start: 0.9413 (tmm) cc_final: 0.9104 (ppp) REVERT: A 161 MET cc_start: 0.9129 (tpp) cc_final: 0.8909 (tpp) REVERT: A 265 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9298 (mp) REVERT: A 271 MET cc_start: 0.9036 (mmm) cc_final: 0.8684 (tpp) REVERT: A 434 MET cc_start: 0.9024 (tmm) cc_final: 0.8014 (tmm) REVERT: B 530 MET cc_start: 0.9021 (mmm) cc_final: 0.8514 (mpp) REVERT: B 626 MET cc_start: 0.7912 (ppp) cc_final: 0.7449 (ppp) REVERT: C 104 MET cc_start: 0.9597 (ttt) cc_final: 0.9290 (tmm) REVERT: C 265 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9127 (mp) REVERT: C 271 MET cc_start: 0.8995 (tpp) cc_final: 0.8503 (tpp) REVERT: D 530 MET cc_start: 0.9167 (mmm) cc_final: 0.8505 (tpp) REVERT: E 66 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.5446 (t-170) REVERT: E 69 TRP cc_start: 0.9250 (OUTLIER) cc_final: 0.8726 (m100) REVERT: E 104 MET cc_start: 0.9405 (ppp) cc_final: 0.9094 (ppp) REVERT: E 271 MET cc_start: 0.9089 (tpp) cc_final: 0.8660 (tpp) REVERT: E 490 LYS cc_start: 0.9631 (OUTLIER) cc_final: 0.9393 (ptmt) outliers start: 96 outliers final: 66 residues processed: 222 average time/residue: 0.2329 time to fit residues: 86.3540 Evaluate side-chains 206 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 124 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 255 VAL Chi-restraints excluded: chain O residue 297 THR Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 494 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain P residue 620 SER Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 141 ASP Chi-restraints excluded: chain Q residue 196 CYS Chi-restraints excluded: chain Q residue 201 CYS Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 295 ASN Chi-restraints excluded: chain Q residue 333 VAL Chi-restraints excluded: chain R residue 544 LEU Chi-restraints excluded: chain S residue 100 MET Chi-restraints excluded: chain S residue 141 ASP Chi-restraints excluded: chain S residue 155 LYS Chi-restraints excluded: chain S residue 202 THR Chi-restraints excluded: chain S residue 287 GLN Chi-restraints excluded: chain S residue 433 CYS Chi-restraints excluded: chain S residue 447 SER Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Z residue 20 THR Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 490 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 404 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 432 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 59 optimal weight: 0.1980 chunk 180 optimal weight: 20.0000 chunk 381 optimal weight: 7.9990 chunk 448 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.024818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.019948 restraints weight = 488509.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.020669 restraints weight = 265991.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.021185 restraints weight = 178043.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.021562 restraints weight = 133783.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.021833 restraints weight = 108616.495| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39848 Z= 0.160 Angle : 0.621 11.230 54369 Z= 0.301 Chirality : 0.042 0.252 6397 Planarity : 0.004 0.094 6719 Dihedral : 6.283 94.376 7657 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 2.14 % Allowed : 21.22 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.12), residues: 4660 helix: 1.46 (0.19), residues: 840 sheet: -0.22 (0.15), residues: 1238 loop : -1.28 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG O 469 TYR 0.012 0.001 TYR Q 39 PHE 0.018 0.001 PHE O 317 TRP 0.017 0.001 TRP P 571 HIS 0.021 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00346 (39639) covalent geometry : angle 0.59783 (53827) SS BOND : bond 0.00296 ( 85) SS BOND : angle 1.48435 ( 170) hydrogen bonds : bond 0.03353 ( 1321) hydrogen bonds : angle 4.63810 ( 3543) link_ALPHA1-3 : bond 0.00656 ( 6) link_ALPHA1-3 : angle 1.77456 ( 18) link_BETA1-4 : bond 0.00406 ( 21) link_BETA1-4 : angle 1.58955 ( 63) link_NAG-ASN : bond 0.00361 ( 97) link_NAG-ASN : angle 1.99500 ( 291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 128 time to evaluate : 1.228 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: 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: symmetry clash revert: symmetry clash REVERT: O 104 MET cc_start: 0.9565 (ttt) cc_final: 0.9258 (tmm) REVERT: O 199 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8533 (p) REVERT: O 271 MET cc_start: 0.9266 (tpp) cc_final: 0.8608 (tpp) REVERT: O 434 MET cc_start: 0.8935 (tmm) cc_final: 0.8312 (tmm) REVERT: P 530 MET cc_start: 0.8783 (mtm) cc_final: 0.8099 (mtm) REVERT: P 544 LEU cc_start: 0.9846 (OUTLIER) cc_final: 0.9590 (mm) REVERT: P 626 MET cc_start: 0.8470 (ttm) cc_final: 0.8211 (ttm) REVERT: Q 104 MET cc_start: 0.9514 (ttt) cc_final: 0.9202 (ttm) REVERT: Q 141 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8505 (p0) REVERT: Q 150 MET cc_start: 0.8599 (mmm) cc_final: 0.8339 (mmm) REVERT: Q 265 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.8927 (mt) REVERT: R 530 MET cc_start: 0.8993 (mmm) cc_final: 0.8239 (mpp) REVERT: R 584 GLU cc_start: 0.9109 (tt0) cc_final: 0.8245 (tm-30) REVERT: S 95 MET cc_start: 0.9341 (ppp) cc_final: 0.8609 (ppp) REVERT: S 104 MET cc_start: 0.9558 (tmm) cc_final: 0.9249 (tmm) REVERT: S 141 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8888 (p0) REVERT: S 155 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9044 (mmmt) REVERT: S 271 MET cc_start: 0.8839 (tpp) cc_final: 0.8528 (tpp) REVERT: S 287 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: S 447 SER cc_start: 0.9744 (OUTLIER) cc_final: 0.9442 (t) REVERT: T 584 GLU cc_start: 0.9309 (tt0) cc_final: 0.8968 (tm-30) REVERT: J 69 ILE cc_start: 0.9663 (OUTLIER) cc_final: 0.9329 (tp) REVERT: K 104 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8944 (mm) REVERT: M 25 TYR cc_start: 0.8732 (m-10) cc_final: 0.8393 (m-10) REVERT: N 4 MET cc_start: 0.8352 (mmm) cc_final: 0.8125 (mmm) REVERT: V 4 MET cc_start: 0.8418 (mmm) cc_final: 0.8102 (mmm) REVERT: A 69 TRP cc_start: 0.9187 (OUTLIER) cc_final: 0.8958 (m100) REVERT: A 104 MET cc_start: 0.9406 (tmm) cc_final: 0.9092 (ppp) REVERT: A 161 MET cc_start: 0.9134 (tpp) cc_final: 0.8926 (tpp) REVERT: A 265 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9276 (mp) REVERT: A 271 MET cc_start: 0.9025 (mmm) cc_final: 0.8666 (tpp) REVERT: A 434 MET cc_start: 0.9015 (tmm) cc_final: 0.7966 (tmm) REVERT: B 626 MET cc_start: 0.7925 (ppp) cc_final: 0.7634 (ppp) REVERT: C 104 MET cc_start: 0.9599 (ttt) cc_final: 0.9282 (tmm) REVERT: C 141 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8748 (p0) REVERT: C 150 MET cc_start: 0.8536 (mmm) cc_final: 0.8149 (mmm) REVERT: C 265 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9122 (mp) REVERT: D 530 MET cc_start: 0.9162 (mmm) cc_final: 0.8745 (tpp) REVERT: E 66 HIS cc_start: 0.6233 (OUTLIER) cc_final: 0.5981 (t70) REVERT: E 69 TRP cc_start: 0.9100 (OUTLIER) cc_final: 0.8459 (m100) REVERT: E 104 MET cc_start: 0.9402 (ppp) cc_final: 0.9086 (ppp) REVERT: E 271 MET cc_start: 0.9096 (tpp) cc_final: 0.8728 (tpp) REVERT: E 490 LYS cc_start: 0.9638 (OUTLIER) cc_final: 0.9399 (ptmt) outliers start: 89 outliers final: 67 residues processed: 214 average time/residue: 0.2296 time to fit residues: 82.7052 Evaluate side-chains 209 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 125 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 255 VAL Chi-restraints excluded: chain O residue 297 THR Chi-restraints excluded: chain O residue 333 VAL Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 494 LEU Chi-restraints excluded: chain P residue 534 SER Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain P residue 620 SER Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 141 ASP Chi-restraints excluded: chain Q residue 196 CYS Chi-restraints excluded: chain Q residue 201 CYS Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 295 ASN Chi-restraints excluded: chain Q residue 333 VAL Chi-restraints excluded: chain R residue 544 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 100 MET Chi-restraints excluded: chain S residue 141 ASP Chi-restraints excluded: chain S residue 155 LYS Chi-restraints excluded: chain S residue 202 THR Chi-restraints excluded: chain S residue 287 GLN Chi-restraints excluded: chain S residue 433 CYS Chi-restraints excluded: chain S residue 447 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 490 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 337 optimal weight: 0.3980 chunk 442 optimal weight: 10.0000 chunk 355 optimal weight: 7.9990 chunk 354 optimal weight: 2.9990 chunk 435 optimal weight: 10.0000 chunk 333 optimal weight: 3.9990 chunk 451 optimal weight: 0.9980 chunk 281 optimal weight: 0.9980 chunk 454 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.024962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.019818 restraints weight = 617428.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.020614 restraints weight = 307195.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.021188 restraints weight = 196949.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.021602 restraints weight = 144303.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.021900 restraints weight = 114946.316| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39848 Z= 0.124 Angle : 0.618 15.600 54369 Z= 0.298 Chirality : 0.042 0.252 6397 Planarity : 0.004 0.072 6719 Dihedral : 6.096 93.288 7657 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 2.07 % Allowed : 21.27 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.12), residues: 4660 helix: 1.49 (0.19), residues: 840 sheet: -0.13 (0.15), residues: 1256 loop : -1.26 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 469 TYR 0.010 0.001 TYR S 191 PHE 0.015 0.001 PHE O 317 TRP 0.022 0.001 TRP B 623 HIS 0.015 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00275 (39639) covalent geometry : angle 0.59603 (53827) SS BOND : bond 0.00245 ( 85) SS BOND : angle 1.40336 ( 170) hydrogen bonds : bond 0.03223 ( 1321) hydrogen bonds : angle 4.57433 ( 3543) link_ALPHA1-3 : bond 0.00633 ( 6) link_ALPHA1-3 : angle 1.59308 ( 18) link_BETA1-4 : bond 0.00463 ( 21) link_BETA1-4 : angle 1.56014 ( 63) link_NAG-ASN : bond 0.00344 ( 97) link_NAG-ASN : angle 1.93807 ( 291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 134 time to evaluate : 1.301 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 104 MET cc_start: 0.9579 (ttt) cc_final: 0.9236 (tmm) REVERT: O 271 MET cc_start: 0.9282 (tpp) cc_final: 0.8582 (tpp) REVERT: O 434 MET cc_start: 0.8939 (tmm) cc_final: 0.8321 (tmm) REVERT: P 530 MET cc_start: 0.8802 (mtm) cc_final: 0.8130 (mtm) REVERT: P 544 LEU cc_start: 0.9843 (OUTLIER) cc_final: 0.9578 (mm) REVERT: P 626 MET cc_start: 0.8492 (ttm) cc_final: 0.8240 (ttm) REVERT: Q 104 MET cc_start: 0.9531 (ttt) cc_final: 0.9194 (ttt) REVERT: Q 141 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8469 (p0) REVERT: Q 150 MET cc_start: 0.8591 (mmm) cc_final: 0.8359 (mmm) REVERT: Q 265 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8896 (mt) REVERT: R 584 GLU cc_start: 0.9121 (tt0) cc_final: 0.8229 (tm-30) REVERT: S 95 MET cc_start: 0.9343 (ppp) cc_final: 0.8601 (ppp) REVERT: S 104 MET cc_start: 0.9566 (tmm) cc_final: 0.9248 (tmm) REVERT: S 141 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8895 (p0) REVERT: S 155 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8992 (mmmt) REVERT: S 271 MET cc_start: 0.8871 (tpp) cc_final: 0.8551 (tpp) REVERT: S 287 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8890 (tt0) REVERT: T 584 GLU cc_start: 0.9340 (tt0) cc_final: 0.8971 (tm-30) REVERT: T 626 MET cc_start: 0.8026 (ppp) cc_final: 0.7774 (ppp) REVERT: J 69 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9314 (tp) REVERT: K 24 ARG cc_start: 0.9542 (OUTLIER) cc_final: 0.9168 (mtm-85) REVERT: K 104 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8914 (mm) REVERT: M 25 TYR cc_start: 0.8773 (m-10) cc_final: 0.8386 (m-10) REVERT: N 4 MET cc_start: 0.8368 (mmm) cc_final: 0.8134 (mmm) REVERT: V 4 MET cc_start: 0.8425 (mmm) cc_final: 0.8097 (mmm) REVERT: A 69 TRP cc_start: 0.9166 (OUTLIER) cc_final: 0.8600 (m-90) REVERT: A 104 MET cc_start: 0.9415 (tmm) cc_final: 0.9103 (ppp) REVERT: A 161 MET cc_start: 0.9163 (tpp) cc_final: 0.8940 (tpp) REVERT: A 265 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9262 (mp) REVERT: A 271 MET cc_start: 0.9031 (mmm) cc_final: 0.8643 (tpp) REVERT: A 434 MET cc_start: 0.9008 (tmm) cc_final: 0.7938 (tmm) REVERT: B 626 MET cc_start: 0.7816 (ppp) cc_final: 0.7523 (ppp) REVERT: C 104 MET cc_start: 0.9613 (ttt) cc_final: 0.9310 (tmm) REVERT: C 141 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8704 (p0) REVERT: C 265 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9086 (mp) REVERT: C 271 MET cc_start: 0.8959 (tpp) cc_final: 0.8654 (tpp) REVERT: D 530 MET cc_start: 0.9163 (mmm) cc_final: 0.8747 (tpp) REVERT: E 69 TRP cc_start: 0.9237 (OUTLIER) cc_final: 0.8758 (m100) REVERT: E 104 MET cc_start: 0.9419 (ppp) cc_final: 0.9094 (ppp) REVERT: E 271 MET cc_start: 0.9104 (tpp) cc_final: 0.8708 (tpp) REVERT: E 490 LYS cc_start: 0.9644 (OUTLIER) cc_final: 0.9391 (ptmt) outliers start: 86 outliers final: 66 residues processed: 217 average time/residue: 0.2226 time to fit residues: 80.7956 Evaluate side-chains 206 residues out of total 4155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 125 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 255 VAL Chi-restraints excluded: chain O residue 297 THR Chi-restraints excluded: chain O residue 333 VAL Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 494 LEU Chi-restraints excluded: chain P residue 534 SER Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain P residue 620 SER Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 141 ASP Chi-restraints excluded: chain Q residue 196 CYS Chi-restraints excluded: chain Q residue 201 CYS Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 295 ASN Chi-restraints excluded: chain Q residue 333 VAL Chi-restraints excluded: chain R residue 544 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 100 MET Chi-restraints excluded: chain S residue 141 ASP Chi-restraints excluded: chain S residue 155 LYS Chi-restraints excluded: chain S residue 202 THR Chi-restraints excluded: chain S residue 287 GLN Chi-restraints excluded: chain S residue 433 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 490 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 389 optimal weight: 8.9990 chunk 375 optimal weight: 0.9990 chunk 227 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 455 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 351 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 653 GLN ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.024988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.019940 restraints weight = 561721.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.020713 restraints weight = 291266.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.021268 restraints weight = 189577.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.021642 restraints weight = 140004.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.021956 restraints weight = 113188.332| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39848 Z= 0.116 Angle : 0.603 11.310 54369 Z= 0.291 Chirality : 0.042 0.252 6397 Planarity : 0.004 0.072 6719 Dihedral : 5.905 91.683 7657 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.56 % Favored : 94.40 % Rotamer: Outliers : 2.00 % Allowed : 21.39 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.12), residues: 4660 helix: 1.56 (0.19), residues: 828 sheet: -0.09 (0.15), residues: 1260 loop : -1.20 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 469 TYR 0.022 0.001 TYR A 39 PHE 0.014 0.001 PHE O 317 TRP 0.023 0.001 TRP R 623 HIS 0.003 0.001 HIS Q 249 Details of bonding type rmsd covalent geometry : bond 0.00260 (39639) covalent geometry : angle 0.58116 (53827) SS BOND : bond 0.00244 ( 85) SS BOND : angle 1.35630 ( 170) hydrogen bonds : bond 0.03165 ( 1321) hydrogen bonds : angle 4.53312 ( 3543) link_ALPHA1-3 : bond 0.00581 ( 6) link_ALPHA1-3 : angle 1.50750 ( 18) link_BETA1-4 : bond 0.00482 ( 21) link_BETA1-4 : angle 1.53795 ( 63) link_NAG-ASN : bond 0.00334 ( 97) link_NAG-ASN : angle 1.90915 ( 291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6463.13 seconds wall clock time: 113 minutes 8.24 seconds (6788.24 seconds total)