Starting phenix.real_space_refine on Sun Jun 22 21:08:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mxe_24072/06_2025/7mxe_24072.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mxe_24072/06_2025/7mxe_24072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mxe_24072/06_2025/7mxe_24072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mxe_24072/06_2025/7mxe_24072.map" model { file = "/net/cci-nas-00/data/ceres_data/7mxe_24072/06_2025/7mxe_24072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mxe_24072/06_2025/7mxe_24072.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5338 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 13833 2.51 5 N 3672 2.21 5 O 4520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22149 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "B" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 795 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "F" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "G" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3479 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "J" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3479 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "M" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "O" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "P" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3449 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 4 Chain: "R" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 989 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "W" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 840 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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: "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 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 12.71, per 1000 atoms: 0.57 Number of scatterers: 22149 At special positions: 0 Unit cell: (127.214, 156.637, 155.772, 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 124 16.00 O 4520 8.00 N 3672 7.00 C 13833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS J 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 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 O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.03 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.04 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.04 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.03 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " 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=2, symmetry=0 Links applied ALPHA1-2 " MAN X 4 " - " MAN X 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Y 10 " - " MAN Y 11 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN r 8 " - " MAN r 9 " ALPHA1-3 " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 8 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 10 " " BMA r 3 " - " MAN r 4 " " MAN r 7 " - " MAN r 10 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA X 3 " - " MAN X 6 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 10 " " BMA h 3 " - " MAN h 5 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 8 " " BMA r 3 " - " MAN r 7 " " MAN r 7 " - " MAN r 8 " " BMA s 3 " - " MAN s 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " NAG-ASN " NAG C 701 " - " ASN C 611 " " NAG E 1 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 295 " " NAG G 603 " - " ASN G 339 " " NAG G 604 " - " ASN G 355 " " NAG G 605 " - " ASN G 386 " " NAG G 606 " - " ASN G 392 " " NAG G 607 " - " ASN G 363 " " NAG G 608 " - " ASN G 448 " " NAG G 609 " - " ASN G 301 " " NAG I 1 " - " ASN D 637 " " NAG J 601 " - " ASN J 133 " " NAG J 602 " - " ASN J 301 " " NAG J 603 " - " ASN J 339 " " NAG J 604 " - " ASN J 355 " " NAG J 605 " - " ASN J 88 " " NAG K 1 " - " ASN F 637 " " NAG N 1 " - " ASN G 133 " " NAG P 601 " - " ASN P 88 " " NAG P 602 " - " ASN P 133 " " NAG P 603 " - " ASN P 197 " " NAG P 604 " - " ASN P 355 " " NAG P 605 " - " ASN P 392 " " NAG P 606 " - " ASN P 363 " " NAG P 607 " - " ASN P 301 " " NAG Q 1 " - " ASN G 156 " " NAG S 1 " - " ASN G 160 " " NAG T 1 " - " ASN G 197 " " NAG U 1 " - " ASN G 332 " " NAG V 1 " - " ASN G 262 " " NAG X 1 " - " ASN G 276 " " NAG Y 1 " - " ASN G 234 " " NAG Z 1 " - " ASN J 156 " " NAG a 1 " - " ASN J 160 " " NAG b 1 " - " ASN J 197 " " NAG c 1 " - " ASN J 295 " " NAG d 1 " - " ASN J 386 " " NAG e 1 " - " ASN J 392 " " NAG f 1 " - " ASN J 363 " " NAG g 1 " - " ASN J 332 " " NAG h 1 " - " ASN J 276 " " NAG i 1 " - " ASN J 234 " " NAG j 1 " - " ASN J 262 " " NAG k 1 " - " ASN J 448 " " NAG l 1 " - " ASN P 156 " " NAG m 1 " - " ASN P 160 " " NAG n 1 " - " ASN P 295 " " NAG o 1 " - " ASN P 448 " " NAG p 1 " - " ASN P 332 " " NAG q 1 " - " ASN P 262 " " NAG r 1 " - " ASN P 234 " " NAG s 1 " - " ASN P 276 " " NAG t 1 " - " ASN P 386 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.10 Conformation dependent library (CDL) restraints added in 2.7 seconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4842 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 44 sheets defined 13.6% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.776A pdb=" N ASP B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'C' and resid 536 through 541 removed outlier: 4.324A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 597 removed outlier: 3.749A pdb=" N ILE C 573 " --> pdb=" O THR C 569 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.651A pdb=" N ASP C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 658 removed outlier: 3.622A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.553A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 541 removed outlier: 4.161A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 595 removed outlier: 3.923A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 593 " --> pdb=" O ASP D 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 595 " --> pdb=" O GLN D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.670A pdb=" N ASP D 632 " --> pdb=" O TRP D 628 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.540A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.563A pdb=" N ASP D 659 " --> pdb=" O ASN D 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 595 removed outlier: 3.717A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.868A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.511A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) 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 662 removed outlier: 3.552A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 113 removed outlier: 3.858A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.928A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.788A pdb=" N LYS G 344 " --> pdb=" O GLU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.910A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.153A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.686A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 98 No H-bonds generated for 'chain 'J' and resid 96 through 98' Processing helix chain 'J' and resid 99 through 113 removed outlier: 3.554A pdb=" N THR J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 179 No H-bonds generated for 'chain 'J' and resid 177 through 179' Processing helix chain 'J' and resid 335 through 350 removed outlier: 3.659A pdb=" N ASN J 339 " --> pdb=" O LYS J 335 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG J 350 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.546A pdb=" N THR J 372 " --> pdb=" O ASP J 368 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 368 through 373' Processing helix chain 'J' and resid 425 through 429 removed outlier: 3.997A pdb=" N GLN J 428 " --> pdb=" O ASN J 425 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG J 429 " --> pdb=" O MET J 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 425 through 429' Processing helix chain 'P' and resid 96 through 98 No H-bonds generated for 'chain 'P' and resid 96 through 98' Processing helix chain 'P' and resid 99 through 113 Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.894A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS P 126 " --> pdb=" O THR P 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 122 through 126' Processing helix chain 'P' and resid 335 through 350 removed outlier: 3.653A pdb=" N ASN P 339 " --> pdb=" O LYS P 335 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN P 348 " --> pdb=" O LYS P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 368 through 373 removed outlier: 3.583A pdb=" N THR P 373 " --> pdb=" O LEU P 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 481 removed outlier: 3.766A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER P 481 " --> pdb=" O ASP P 477 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 removed outlier: 3.996A pdb=" N GLU R 64 " --> pdb=" O PRO R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.665A pdb=" N GLU A 10 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 38 " --> pdb=" O TYR A 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100E through 100F Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.541A pdb=" N GLU B 105 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.676A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 605 through 609 removed outlier: 7.580A pdb=" N THR C 606 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL P 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL C 608 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL P 36 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ILE P 491 " --> pdb=" O PRO P 43 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TRP P 45 " --> pdb=" O VAL P 489 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL P 489 " --> pdb=" O TRP P 45 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N ASP P 47 " --> pdb=" O LYS P 487 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N LYS P 487 " --> pdb=" O ASP P 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 604 through 609 removed outlier: 3.550A pdb=" N CYS D 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL G 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N VAL G 38 " --> pdb=" O PRO G 498 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N TYR G 40 " --> pdb=" O VAL G 496 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N VAL G 496 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL G 42 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU G 494 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL G 44 " --> pdb=" O GLU G 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 605 through 609 removed outlier: 7.723A pdb=" N THR F 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N VAL J 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL F 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ILE J 491 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TRP J 45 " --> pdb=" O VAL J 489 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL J 489 " --> pdb=" O TRP J 45 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ASP J 47 " --> pdb=" O LYS J 487 " (cutoff:3.500A) removed outlier: 11.861A pdb=" N LYS J 487 " --> pdb=" O ASP J 47 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB2, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.622A pdb=" N CYS G 131 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 259 through 261 removed outlier: 5.887A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS G 378 " --> pdb=" O GLU G 381 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE G 383 " --> pdb=" O PHE G 376 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.980A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.540A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.763A pdb=" N GLU H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 100E through 100F Processing sheet with id=AB9, first strand: chain 'J' and resid 75 through 76 removed outlier: 7.342A pdb=" N CYS J 54 " --> pdb=" O VAL J 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 66 through 67 removed outlier: 7.765A pdb=" N HIS J 66 " --> pdb=" O SER J 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'J' and resid 169 through 176 Processing sheet with id=AC4, first strand: chain 'J' and resid 271 through 274 removed outlier: 3.774A pdb=" N SER J 393 " --> pdb=" O PHE J 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 374 through 378 removed outlier: 3.608A pdb=" N CYS J 378 " --> pdb=" O GLU J 381 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU J 381 " --> pdb=" O CYS J 378 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA J 329 " --> pdb=" O CYS J 418 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER J 334 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL J 292 " --> pdb=" O ILE J 449 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE J 443 " --> pdb=" O ARG J 298 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 304 through 307 Processing sheet with id=AC7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AC9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.817A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.688A pdb=" N GLU M 10 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER M 110 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS M 12 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG M 38 " --> pdb=" O TYR M 47 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.688A pdb=" N GLU M 10 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER M 110 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS M 12 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 100E through 100F removed outlier: 3.590A pdb=" N VAL M 100I" --> pdb=" O HIS M 100F" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 13 removed outlier: 7.373A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR O 49 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 91 through 94 removed outlier: 3.522A pdb=" N GLU P 91 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'P' and resid 271 through 274 Processing sheet with id=AE1, first strand: chain 'P' and resid 374 through 378 removed outlier: 4.290A pdb=" N ALA P 329 " --> pdb=" O CYS P 418 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE P 443 " --> pdb=" O ARG P 298 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 304 through 312 removed outlier: 6.660A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.629A pdb=" N SER R 7 " --> pdb=" O THR R 21 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR R 21 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS R 22 " --> pdb=" O PHE R 78 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE R 78 " --> pdb=" O CYS R 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG R 50 " --> pdb=" O TRP R 35 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP R 35 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG R 50 " --> pdb=" O TRP R 35 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP R 35 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'W' and resid 45 through 50 removed outlier: 5.850A pdb=" N PHE W 46 " --> pdb=" O GLN W 37 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN W 37 " --> pdb=" O PHE W 46 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET W 48 " --> pdb=" O TRP W 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 89 through 92 663 hydrogen bonds defined for protein. 1740 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: 7.80 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6833 1.34 - 1.47: 5867 1.47 - 1.59: 9723 1.59 - 1.72: 0 1.72 - 1.84: 166 Bond restraints: 22589 Sorted by residual: bond pdb=" C THR P 123 " pdb=" N PRO P 124 " ideal model delta sigma weight residual 1.331 1.395 -0.063 7.90e-03 1.60e+04 6.42e+01 bond pdb=" C PRO A 75 " pdb=" N PRO A 76 " ideal model delta sigma weight residual 1.332 1.389 -0.058 1.30e-02 5.92e+03 1.97e+01 bond pdb=" N PRO A 76 " pdb=" CD PRO A 76 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" N PRO J 313 " pdb=" CD PRO J 313 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" N ASN D 656 " pdb=" CA ASN D 656 " ideal model delta sigma weight residual 1.460 1.485 -0.024 8.20e-03 1.49e+04 8.78e+00 ... (remaining 22584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 30190 2.70 - 5.40: 406 5.40 - 8.10: 75 8.10 - 10.80: 10 10.80 - 13.50: 1 Bond angle restraints: 30682 Sorted by residual: angle pdb=" C PRO A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta sigma weight residual 119.76 113.91 5.85 1.03e+00 9.43e-01 3.23e+01 angle pdb=" C ASP P 140 " pdb=" N ASP P 141 " pdb=" CA ASP P 141 " ideal model delta sigma weight residual 122.61 130.89 -8.28 1.56e+00 4.11e-01 2.82e+01 angle pdb=" C SER P 460 " pdb=" N THR P 461 " pdb=" CA THR P 461 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" CA PRO J 313 " pdb=" N PRO J 313 " pdb=" CD PRO J 313 " ideal model delta sigma weight residual 112.00 106.12 5.88 1.40e+00 5.10e-01 1.76e+01 angle pdb=" C ASN D 656 " pdb=" CA ASN D 656 " pdb=" CB ASN D 656 " ideal model delta sigma weight residual 116.53 110.50 6.03 1.47e+00 4.63e-01 1.68e+01 ... (remaining 30677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.30: 14267 23.30 - 46.60: 580 46.60 - 69.89: 109 69.89 - 93.19: 75 93.19 - 116.49: 47 Dihedral angle restraints: 15078 sinusoidal: 7546 harmonic: 7532 Sorted by residual: dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 169.55 -76.55 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS P 119 " pdb=" SG CYS P 119 " pdb=" SG CYS P 205 " pdb=" CB CYS P 205 " ideal model delta sinusoidal sigma weight residual -86.00 -159.61 73.61 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -146.09 60.09 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 15075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3288 0.075 - 0.150: 507 0.150 - 0.225: 23 0.225 - 0.300: 15 0.300 - 0.375: 2 Chirality restraints: 3835 Sorted by residual: chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C5 BMA h 3 " pdb=" C4 BMA h 3 " pdb=" C6 BMA h 3 " pdb=" O5 BMA h 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C5 BMA Y 3 " pdb=" C4 BMA Y 3 " pdb=" C6 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3832 not shown) Planarity restraints: 3769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 701 " 0.075 2.00e-02 2.50e+03 6.15e-02 4.73e+01 pdb=" C7 NAG F 701 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG F 701 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG F 701 " -0.097 2.00e-02 2.50e+03 pdb=" O7 NAG F 701 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.033 2.00e-02 2.50e+03 3.65e-02 1.67e+01 pdb=" CG ASN F 611 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.058 2.00e-02 2.50e+03 pdb=" C1 NAG F 701 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 701 " -0.044 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" C7 NAG C 701 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 701 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 701 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 701 " 0.008 2.00e-02 2.50e+03 ... (remaining 3766 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 333 2.67 - 3.23: 17582 3.23 - 3.79: 30500 3.79 - 4.34: 41400 4.34 - 4.90: 70316 Nonbonded interactions: 160131 Sorted by model distance: nonbonded pdb=" O GLU D 657 " pdb=" N ASP D 659 " model vdw 2.116 3.120 nonbonded pdb=" CA GLY D 597 " pdb=" OE1 GLN D 650 " model vdw 2.211 3.440 nonbonded pdb=" O LEU W 4 " pdb=" OG1 THR W 24 " model vdw 2.266 3.040 nonbonded pdb=" O ILE A 2 " pdb=" ND1 HIS A 3 " model vdw 2.285 3.120 nonbonded pdb=" O ASN D 656 " pdb=" OD2 ASP D 659 " model vdw 2.313 3.040 ... (remaining 160126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = (chain 'L' and (resid 1 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 41 or (resid 42 through 43 and (nam \ e N or name CA or name C or name O or name CB )) or resid 44 through 62 or (resi \ d 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throug \ h 99 or (resid 100 and (name N or name CA or name C or name O or name CB )) or r \ esid 101 through 102 or (resid 103 and (name N or name CA or name C or name O or \ name CB )) or resid 104 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'O' and (resid 1 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )))) } ncs_group { reference = (chain 'C' and resid 520 through 660) selection = (chain 'D' and (resid 520 through 546 or resid 567 through 660)) } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 't' } ncs_group { reference = (chain 'G' and (resid 33 through 77 or resid 82 through 504 or resid 601 through \ 605)) selection = (chain 'J' and (resid 33 through 77 or resid 82 through 504 or resid 601 through \ 605)) selection = (chain 'P' and (resid 33 through 504 or resid 601 through 605)) } ncs_group { reference = (chain 'Y' and (resid 2 or resid 5 through 11)) selection = (chain 'i' and (resid 1 or resid 4 through 10)) selection = (chain 'r' and (resid 1 or resid 4 through 10)) } ncs_group { reference = chain 'h' selection = chain 's' } ncs_group { reference = chain 'j' selection = chain 'k' selection = chain 'p' selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 52.140 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 : 0.006 0.268 22759 Z= 0.330 Angle : 0.790 13.501 31146 Z= 0.373 Chirality : 0.053 0.375 3835 Planarity : 0.004 0.062 3714 Dihedral : 14.971 116.490 10116 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 0.35 % Allowed : 4.37 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.14), residues: 2580 helix: -3.38 (0.18), residues: 307 sheet: -1.02 (0.17), residues: 868 loop : -2.87 (0.13), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP M 53 HIS 0.003 0.000 HIS P 105 PHE 0.016 0.001 PHE R 78 TYR 0.010 0.001 TYR O 36 ARG 0.003 0.000 ARG L 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 55) link_NAG-ASN : angle 1.51839 ( 165) link_ALPHA1-6 : bond 0.00518 ( 9) link_ALPHA1-6 : angle 1.18383 ( 27) link_BETA1-4 : bond 0.00875 ( 43) link_BETA1-4 : angle 1.98581 ( 129) link_ALPHA1-2 : bond 0.00389 ( 11) link_ALPHA1-2 : angle 1.47157 ( 33) link_ALPHA1-3 : bond 0.00589 ( 10) link_ALPHA1-3 : angle 1.42960 ( 30) hydrogen bonds : bond 0.13478 ( 644) hydrogen bonds : angle 5.90524 ( 1740) SS BOND : bond 0.00270 ( 40) SS BOND : angle 0.99255 ( 80) covalent geometry : bond 0.00533 (22589) covalent geometry : angle 0.77267 (30682) Misc. bond : bond 0.18984 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 463 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 568 LEU cc_start: 0.7074 (mt) cc_final: 0.6721 (pp) REVERT: C 607 ASN cc_start: 0.9034 (t0) cc_final: 0.8786 (t0) REVERT: C 660 LEU cc_start: 0.8345 (tp) cc_final: 0.8107 (tt) REVERT: D 601 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8572 (mtmm) REVERT: D 618 ASN cc_start: 0.7660 (m-40) cc_final: 0.7442 (m-40) REVERT: D 648 GLU cc_start: 0.7083 (pp20) cc_final: 0.6773 (pp20) REVERT: D 652 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7508 (mp-120) REVERT: D 655 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.6877 (mptt) REVERT: G 78 ASP cc_start: 0.8474 (t0) cc_final: 0.7918 (t0) REVERT: G 478 ASN cc_start: 0.8758 (m110) cc_final: 0.8541 (t0) REVERT: J 326 ILE cc_start: 0.8981 (mm) cc_final: 0.8768 (mm) REVERT: L 63 ARG cc_start: 0.7212 (mmm-85) cc_final: 0.6582 (mmm-85) REVERT: L 77 ASN cc_start: 0.7723 (t0) cc_final: 0.7267 (t0) REVERT: L 88 CYS cc_start: 0.6802 (p) cc_final: 0.6196 (p) REVERT: P 161 MET cc_start: 0.8456 (tpp) cc_final: 0.8136 (tpt) REVERT: P 359 ILE cc_start: 0.9196 (mm) cc_final: 0.8891 (mm) REVERT: P 395 TRP cc_start: 0.7786 (m100) cc_final: 0.7559 (m100) REVERT: P 430 ILE cc_start: 0.8754 (mt) cc_final: 0.8491 (tp) REVERT: R 16 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7606 (mt-10) REVERT: R 50 ARG cc_start: 0.8672 (ttp-170) cc_final: 0.8296 (ttp-170) REVERT: R 91 TYR cc_start: 0.8042 (m-80) cc_final: 0.7802 (m-80) outliers start: 8 outliers final: 1 residues processed: 470 average time/residue: 0.3609 time to fit residues: 254.9733 Evaluate side-chains 301 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 298 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain P residue 247 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN C 577 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN F 575 GLN F 591 GLN F 607 ASN G 82 GLN G 302 ASN G 411 ASN J 103 GLN J 183 GLN J 203 GLN M 35AASN M 43 GLN O 3 GLN O 38 GLN P 33 ASN P 103 GLN P 315 GLN P 356 ASN P 428 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.084964 restraints weight = 37803.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.086801 restraints weight = 25524.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.087701 restraints weight = 20040.745| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22759 Z= 0.216 Angle : 0.711 12.540 31146 Z= 0.339 Chirality : 0.047 0.261 3835 Planarity : 0.004 0.048 3714 Dihedral : 10.880 86.023 5423 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.51 % Allowed : 11.38 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.15), residues: 2580 helix: -1.73 (0.26), residues: 342 sheet: -0.58 (0.18), residues: 845 loop : -2.34 (0.14), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 45 HIS 0.006 0.001 HIS J 374 PHE 0.032 0.002 PHE R 78 TYR 0.020 0.002 TYR B 91 ARG 0.005 0.001 ARG J 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 55) link_NAG-ASN : angle 1.93230 ( 165) link_ALPHA1-6 : bond 0.00632 ( 9) link_ALPHA1-6 : angle 2.21768 ( 27) link_BETA1-4 : bond 0.00519 ( 43) link_BETA1-4 : angle 2.16155 ( 129) link_ALPHA1-2 : bond 0.00209 ( 11) link_ALPHA1-2 : angle 2.14097 ( 33) link_ALPHA1-3 : bond 0.01055 ( 10) link_ALPHA1-3 : angle 2.39098 ( 30) hydrogen bonds : bond 0.04878 ( 644) hydrogen bonds : angle 4.89563 ( 1740) SS BOND : bond 0.00478 ( 40) SS BOND : angle 1.26543 ( 80) covalent geometry : bond 0.00511 (22589) covalent geometry : angle 0.67390 (30682) Misc. bond : bond 0.00438 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 304 time to evaluate : 2.644 Fit side-chains revert: symmetry clash REVERT: F 590 GLN cc_start: 0.9053 (mm110) cc_final: 0.8811 (mm-40) REVERT: F 652 GLN cc_start: 0.8240 (tm-30) cc_final: 0.8011 (tm-30) REVERT: F 655 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7630 (mttp) REVERT: H 62 HIS cc_start: 0.8200 (m90) cc_final: 0.8000 (m-70) REVERT: J 104 MET cc_start: 0.8706 (ttt) cc_final: 0.8414 (ttt) REVERT: L 77 ASN cc_start: 0.7928 (t0) cc_final: 0.7539 (t0) REVERT: M 56 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7864 (mttm) REVERT: P 205 CYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5677 (m) REVERT: P 359 ILE cc_start: 0.9251 (mm) cc_final: 0.8951 (mm) REVERT: R 50 ARG cc_start: 0.8909 (ttp-170) cc_final: 0.8609 (ttp-170) outliers start: 57 outliers final: 32 residues processed: 349 average time/residue: 0.3330 time to fit residues: 182.2951 Evaluate side-chains 293 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 377 ASN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain R residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 232 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN C 650 GLN D 653 GLN F 607 ASN G 103 GLN G 411 ASN P 183 GLN W 1 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.085434 restraints weight = 37631.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.087594 restraints weight = 25501.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.088562 restraints weight = 18599.160| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22759 Z= 0.133 Angle : 0.588 10.393 31146 Z= 0.279 Chirality : 0.044 0.276 3835 Planarity : 0.003 0.036 3714 Dihedral : 9.589 79.477 5419 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.43 % Allowed : 14.56 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.16), residues: 2580 helix: -1.10 (0.29), residues: 344 sheet: -0.30 (0.18), residues: 826 loop : -2.09 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 45 HIS 0.006 0.001 HIS H 61 PHE 0.016 0.001 PHE R 78 TYR 0.015 0.001 TYR M 47 ARG 0.002 0.000 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 55) link_NAG-ASN : angle 1.85064 ( 165) link_ALPHA1-6 : bond 0.00643 ( 9) link_ALPHA1-6 : angle 1.64211 ( 27) link_BETA1-4 : bond 0.00508 ( 43) link_BETA1-4 : angle 1.81224 ( 129) link_ALPHA1-2 : bond 0.00387 ( 11) link_ALPHA1-2 : angle 1.52891 ( 33) link_ALPHA1-3 : bond 0.01326 ( 10) link_ALPHA1-3 : angle 1.81684 ( 30) hydrogen bonds : bond 0.03795 ( 644) hydrogen bonds : angle 4.62359 ( 1740) SS BOND : bond 0.00382 ( 40) SS BOND : angle 1.49147 ( 80) covalent geometry : bond 0.00309 (22589) covalent geometry : angle 0.55222 (30682) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 655 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7403 (mptt) REVERT: F 590 GLN cc_start: 0.8955 (mm110) cc_final: 0.8646 (mm-40) REVERT: F 591 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8631 (tt0) REVERT: F 652 GLN cc_start: 0.8218 (tm-30) cc_final: 0.8008 (tm-30) REVERT: H 62 HIS cc_start: 0.8311 (m90) cc_final: 0.8035 (m-70) REVERT: J 104 MET cc_start: 0.8756 (ttt) cc_final: 0.8517 (ttt) REVERT: L 65 SER cc_start: 0.8774 (m) cc_final: 0.8537 (p) REVERT: L 77 ASN cc_start: 0.7934 (t0) cc_final: 0.7558 (t0) REVERT: M 56 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7820 (mttm) REVERT: P 199 SER cc_start: 0.8839 (t) cc_final: 0.8463 (m) REVERT: P 205 CYS cc_start: 0.5968 (OUTLIER) cc_final: 0.5749 (m) REVERT: P 359 ILE cc_start: 0.9249 (mm) cc_final: 0.8947 (mm) REVERT: R 16 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7538 (mt-10) REVERT: W 79 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8410 (mm110) outliers start: 55 outliers final: 27 residues processed: 305 average time/residue: 0.3412 time to fit residues: 162.9114 Evaluate side-chains 284 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 277 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 172 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 231 optimal weight: 0.0570 chunk 63 optimal weight: 0.7980 chunk 125 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.5706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN D 653 GLN R 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.102738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.082164 restraints weight = 38329.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.084441 restraints weight = 26104.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.085598 restraints weight = 18898.333| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22759 Z= 0.173 Angle : 0.653 16.271 31146 Z= 0.307 Chirality : 0.046 0.263 3835 Planarity : 0.003 0.040 3714 Dihedral : 9.089 75.153 5418 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.78 % Allowed : 15.84 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.16), residues: 2580 helix: -0.86 (0.29), residues: 344 sheet: -0.28 (0.18), residues: 867 loop : -1.91 (0.15), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 32 HIS 0.005 0.001 HIS P 105 PHE 0.020 0.002 PHE R 78 TYR 0.015 0.001 TYR P 217 ARG 0.005 0.000 ARG R 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 55) link_NAG-ASN : angle 2.34833 ( 165) link_ALPHA1-6 : bond 0.00545 ( 9) link_ALPHA1-6 : angle 1.67663 ( 27) link_BETA1-4 : bond 0.00483 ( 43) link_BETA1-4 : angle 1.82272 ( 129) link_ALPHA1-2 : bond 0.00247 ( 11) link_ALPHA1-2 : angle 1.66979 ( 33) link_ALPHA1-3 : bond 0.01304 ( 10) link_ALPHA1-3 : angle 1.88094 ( 30) hydrogen bonds : bond 0.04203 ( 644) hydrogen bonds : angle 4.68368 ( 1740) SS BOND : bond 0.00455 ( 40) SS BOND : angle 2.29047 ( 80) covalent geometry : bond 0.00413 (22589) covalent geometry : angle 0.60562 (30682) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 655 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7656 (mptt) REVERT: F 590 GLN cc_start: 0.9000 (mm110) cc_final: 0.8685 (mm-40) REVERT: F 652 GLN cc_start: 0.8216 (tm-30) cc_final: 0.8015 (tm-30) REVERT: F 655 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7747 (mttm) REVERT: J 95 MET cc_start: 0.9257 (ptm) cc_final: 0.8957 (ttp) REVERT: J 104 MET cc_start: 0.8762 (ttt) cc_final: 0.8531 (ttt) REVERT: L 65 SER cc_start: 0.8716 (m) cc_final: 0.8457 (p) REVERT: L 77 ASN cc_start: 0.7927 (t0) cc_final: 0.7557 (t0) REVERT: P 116 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8863 (mp) REVERT: P 199 SER cc_start: 0.8940 (t) cc_final: 0.8620 (m) REVERT: P 359 ILE cc_start: 0.9270 (mm) cc_final: 0.8976 (mm) REVERT: R 16 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7547 (mt-10) outliers start: 63 outliers final: 49 residues processed: 304 average time/residue: 0.3452 time to fit residues: 163.7418 Evaluate side-chains 296 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain W residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 173 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.083573 restraints weight = 38004.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.085523 restraints weight = 27040.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.086064 restraints weight = 21029.419| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22759 Z= 0.130 Angle : 0.597 13.824 31146 Z= 0.281 Chirality : 0.044 0.314 3835 Planarity : 0.003 0.042 3714 Dihedral : 8.477 70.443 5418 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.82 % Allowed : 16.63 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2580 helix: -0.59 (0.30), residues: 344 sheet: -0.15 (0.18), residues: 838 loop : -1.73 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 571 HIS 0.003 0.001 HIS P 105 PHE 0.015 0.001 PHE J 383 TYR 0.013 0.001 TYR M 47 ARG 0.006 0.000 ARG R 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 55) link_NAG-ASN : angle 2.09149 ( 165) link_ALPHA1-6 : bond 0.00585 ( 9) link_ALPHA1-6 : angle 1.61214 ( 27) link_BETA1-4 : bond 0.00505 ( 43) link_BETA1-4 : angle 1.71730 ( 129) link_ALPHA1-2 : bond 0.00290 ( 11) link_ALPHA1-2 : angle 1.55405 ( 33) link_ALPHA1-3 : bond 0.01344 ( 10) link_ALPHA1-3 : angle 1.84740 ( 30) hydrogen bonds : bond 0.03702 ( 644) hydrogen bonds : angle 4.54024 ( 1740) SS BOND : bond 0.00402 ( 40) SS BOND : angle 1.99799 ( 80) covalent geometry : bond 0.00304 (22589) covalent geometry : angle 0.55389 (30682) Misc. bond : bond 0.00056 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 256 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 655 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7821 (mptt) REVERT: F 590 GLN cc_start: 0.8946 (mm110) cc_final: 0.8558 (mm-40) REVERT: F 652 GLN cc_start: 0.8239 (tm-30) cc_final: 0.8000 (tm-30) REVERT: F 655 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7781 (mttm) REVERT: J 95 MET cc_start: 0.9188 (ptm) cc_final: 0.8951 (ttp) REVERT: L 77 ASN cc_start: 0.7856 (t0) cc_final: 0.7491 (t0) REVERT: P 199 SER cc_start: 0.8959 (t) cc_final: 0.8623 (m) REVERT: P 359 ILE cc_start: 0.9281 (mm) cc_final: 0.8983 (mm) REVERT: R 16 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7544 (mt-10) REVERT: W 79 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8415 (mm110) outliers start: 64 outliers final: 45 residues processed: 308 average time/residue: 0.4625 time to fit residues: 221.8058 Evaluate side-chains 290 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 244 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain R residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 131 optimal weight: 0.0070 chunk 29 optimal weight: 0.4980 chunk 228 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN D 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.080609 restraints weight = 38068.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.082736 restraints weight = 26537.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.083370 restraints weight = 20717.858| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22759 Z= 0.170 Angle : 0.638 14.796 31146 Z= 0.302 Chirality : 0.045 0.264 3835 Planarity : 0.004 0.059 3714 Dihedral : 8.382 71.709 5418 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.48 % Allowed : 16.59 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2580 helix: -0.42 (0.30), residues: 339 sheet: -0.13 (0.18), residues: 863 loop : -1.72 (0.15), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 47 HIS 0.004 0.001 HIS P 105 PHE 0.020 0.002 PHE R 78 TYR 0.013 0.001 TYR B 91 ARG 0.005 0.000 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 55) link_NAG-ASN : angle 2.15740 ( 165) link_ALPHA1-6 : bond 0.00559 ( 9) link_ALPHA1-6 : angle 1.60306 ( 27) link_BETA1-4 : bond 0.00497 ( 43) link_BETA1-4 : angle 1.76556 ( 129) link_ALPHA1-2 : bond 0.00229 ( 11) link_ALPHA1-2 : angle 1.65718 ( 33) link_ALPHA1-3 : bond 0.01368 ( 10) link_ALPHA1-3 : angle 1.81929 ( 30) hydrogen bonds : bond 0.04184 ( 644) hydrogen bonds : angle 4.63222 ( 1740) SS BOND : bond 0.00438 ( 40) SS BOND : angle 2.13570 ( 80) covalent geometry : bond 0.00406 (22589) covalent geometry : angle 0.59564 (30682) Misc. bond : bond 0.00062 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 250 time to evaluate : 2.981 Fit side-chains revert: symmetry clash REVERT: D 534 SER cc_start: 0.9036 (p) cc_final: 0.8816 (p) REVERT: D 655 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7998 (mptt) REVERT: F 590 GLN cc_start: 0.8992 (mm110) cc_final: 0.8602 (mm-40) REVERT: F 603 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8489 (mm) REVERT: F 652 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7817 (tm-30) REVERT: F 655 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7754 (mttm) REVERT: F 656 ASN cc_start: 0.8073 (m-40) cc_final: 0.7702 (m-40) REVERT: L 77 ASN cc_start: 0.7873 (t0) cc_final: 0.7474 (t0) REVERT: P 116 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8928 (mp) REVERT: P 199 SER cc_start: 0.9046 (t) cc_final: 0.8721 (m) REVERT: P 359 ILE cc_start: 0.9262 (mm) cc_final: 0.8972 (mm) REVERT: W 79 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8516 (mm110) outliers start: 79 outliers final: 56 residues processed: 312 average time/residue: 0.4789 time to fit residues: 240.5635 Evaluate side-chains 303 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 88 CYS Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain W residue 78 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 163 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 229 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN D 653 GLN P 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.098273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.077862 restraints weight = 38479.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.079656 restraints weight = 26275.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.080253 restraints weight = 21174.092| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 22759 Z= 0.260 Angle : 0.749 17.511 31146 Z= 0.356 Chirality : 0.049 0.276 3835 Planarity : 0.004 0.067 3714 Dihedral : 8.937 71.684 5418 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.71 % Favored : 93.26 % Rotamer: Outliers : 3.35 % Allowed : 17.12 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.16), residues: 2580 helix: -0.68 (0.29), residues: 346 sheet: -0.30 (0.18), residues: 903 loop : -1.76 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 47 HIS 0.005 0.001 HIS P 105 PHE 0.025 0.002 PHE R 78 TYR 0.017 0.002 TYR L 91 ARG 0.007 0.001 ARG J 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 55) link_NAG-ASN : angle 2.35761 ( 165) link_ALPHA1-6 : bond 0.00523 ( 9) link_ALPHA1-6 : angle 1.69035 ( 27) link_BETA1-4 : bond 0.00535 ( 43) link_BETA1-4 : angle 1.99715 ( 129) link_ALPHA1-2 : bond 0.00240 ( 11) link_ALPHA1-2 : angle 1.76257 ( 33) link_ALPHA1-3 : bond 0.01446 ( 10) link_ALPHA1-3 : angle 1.83100 ( 30) hydrogen bonds : bond 0.05124 ( 644) hydrogen bonds : angle 4.98923 ( 1740) SS BOND : bond 0.00673 ( 40) SS BOND : angle 2.49583 ( 80) covalent geometry : bond 0.00628 (22589) covalent geometry : angle 0.70536 (30682) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 238 time to evaluate : 2.347 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9085 (mttt) cc_final: 0.8645 (mtmm) REVERT: B 27 SER cc_start: 0.8995 (t) cc_final: 0.8538 (p) REVERT: F 590 GLN cc_start: 0.9009 (mm110) cc_final: 0.8723 (mm-40) REVERT: F 652 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7894 (tm-30) REVERT: F 656 ASN cc_start: 0.8124 (m-40) cc_final: 0.7759 (m-40) REVERT: G 355 ASN cc_start: 0.7240 (p0) cc_final: 0.7002 (t0) REVERT: J 207 LYS cc_start: 0.8280 (tptp) cc_final: 0.8063 (tptp) REVERT: L 77 ASN cc_start: 0.7879 (t0) cc_final: 0.7367 (t0) REVERT: L 79 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7808 (mt0) REVERT: P 116 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8905 (mp) REVERT: P 359 ILE cc_start: 0.9301 (mm) cc_final: 0.8999 (mm) REVERT: R 16 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7440 (mt-10) REVERT: W 79 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8500 (mm110) outliers start: 76 outliers final: 58 residues processed: 296 average time/residue: 0.3220 time to fit residues: 149.5962 Evaluate side-chains 289 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 430 ILE Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain W residue 78 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 189 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 173 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.096751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.075522 restraints weight = 38710.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.077940 restraints weight = 28605.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.078855 restraints weight = 20645.560| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22759 Z= 0.179 Angle : 0.667 16.648 31146 Z= 0.317 Chirality : 0.046 0.268 3835 Planarity : 0.004 0.056 3714 Dihedral : 8.631 71.018 5418 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.00 % Allowed : 17.73 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.16), residues: 2580 helix: -0.55 (0.29), residues: 344 sheet: -0.14 (0.17), residues: 904 loop : -1.76 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 571 HIS 0.004 0.001 HIS P 105 PHE 0.018 0.001 PHE R 78 TYR 0.013 0.001 TYR L 91 ARG 0.006 0.000 ARG J 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 55) link_NAG-ASN : angle 2.22812 ( 165) link_ALPHA1-6 : bond 0.00532 ( 9) link_ALPHA1-6 : angle 1.58665 ( 27) link_BETA1-4 : bond 0.00508 ( 43) link_BETA1-4 : angle 1.88256 ( 129) link_ALPHA1-2 : bond 0.00233 ( 11) link_ALPHA1-2 : angle 1.63176 ( 33) link_ALPHA1-3 : bond 0.01377 ( 10) link_ALPHA1-3 : angle 1.83159 ( 30) hydrogen bonds : bond 0.04384 ( 644) hydrogen bonds : angle 4.84530 ( 1740) SS BOND : bond 0.00600 ( 40) SS BOND : angle 2.30087 ( 80) covalent geometry : bond 0.00427 (22589) covalent geometry : angle 0.62322 (30682) Misc. bond : bond 0.00077 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 238 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9037 (mttt) cc_final: 0.8599 (mtmm) REVERT: B 27 SER cc_start: 0.8971 (t) cc_final: 0.8529 (p) REVERT: D 655 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8291 (mptt) REVERT: F 590 GLN cc_start: 0.8980 (mm110) cc_final: 0.8651 (mm-40) REVERT: F 652 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7879 (tm-30) REVERT: F 656 ASN cc_start: 0.8086 (m-40) cc_final: 0.7731 (m-40) REVERT: J 207 LYS cc_start: 0.8246 (tptp) cc_final: 0.8044 (tptp) REVERT: L 77 ASN cc_start: 0.7782 (t0) cc_final: 0.7311 (t0) REVERT: L 79 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7794 (mt0) REVERT: P 142 MET cc_start: 0.7342 (tpt) cc_final: 0.7118 (tpt) REVERT: P 199 SER cc_start: 0.9088 (t) cc_final: 0.8790 (m) REVERT: P 308 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7700 (mtm110) REVERT: P 359 ILE cc_start: 0.9290 (mm) cc_final: 0.8985 (mm) REVERT: R 16 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7508 (mt-10) REVERT: W 79 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8524 (mm110) outliers start: 68 outliers final: 57 residues processed: 290 average time/residue: 0.3438 time to fit residues: 155.3766 Evaluate side-chains 293 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 234 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 308 ARG Chi-restraints excluded: chain P residue 430 ILE Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 3 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN D 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.079682 restraints weight = 38492.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.081174 restraints weight = 28745.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.082010 restraints weight = 22971.460| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 22759 Z= 0.137 Angle : 0.637 15.856 31146 Z= 0.302 Chirality : 0.045 0.260 3835 Planarity : 0.003 0.047 3714 Dihedral : 8.517 78.024 5418 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.91 % Allowed : 18.22 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2580 helix: -0.37 (0.30), residues: 344 sheet: -0.05 (0.18), residues: 888 loop : -1.69 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 571 HIS 0.003 0.001 HIS P 105 PHE 0.014 0.001 PHE R 78 TYR 0.014 0.001 TYR M 47 ARG 0.006 0.000 ARG J 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 55) link_NAG-ASN : angle 1.86198 ( 165) link_ALPHA1-6 : bond 0.00532 ( 9) link_ALPHA1-6 : angle 1.55913 ( 27) link_BETA1-4 : bond 0.00517 ( 43) link_BETA1-4 : angle 1.81086 ( 129) link_ALPHA1-2 : bond 0.00239 ( 11) link_ALPHA1-2 : angle 1.59658 ( 33) link_ALPHA1-3 : bond 0.01357 ( 10) link_ALPHA1-3 : angle 1.81771 ( 30) hydrogen bonds : bond 0.03918 ( 644) hydrogen bonds : angle 4.69393 ( 1740) SS BOND : bond 0.00537 ( 40) SS BOND : angle 2.06623 ( 80) covalent geometry : bond 0.00323 (22589) covalent geometry : angle 0.59982 (30682) Misc. bond : bond 0.00128 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 243 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 SER cc_start: 0.8963 (t) cc_final: 0.8574 (p) REVERT: F 590 GLN cc_start: 0.8911 (mm110) cc_final: 0.8553 (mm-40) REVERT: F 652 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7834 (tm-30) REVERT: F 656 ASN cc_start: 0.8071 (m-40) cc_final: 0.7710 (m-40) REVERT: J 207 LYS cc_start: 0.8272 (tptp) cc_final: 0.8043 (tptp) REVERT: L 77 ASN cc_start: 0.7771 (t0) cc_final: 0.7306 (t0) REVERT: L 79 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7822 (mt0) REVERT: P 116 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8870 (mp) REVERT: P 199 SER cc_start: 0.9092 (t) cc_final: 0.8773 (m) REVERT: P 359 ILE cc_start: 0.9296 (mm) cc_final: 0.8988 (mm) REVERT: R 16 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7463 (mt-10) outliers start: 66 outliers final: 52 residues processed: 294 average time/residue: 0.3353 time to fit residues: 155.8077 Evaluate side-chains 290 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain W residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 191 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 237 optimal weight: 0.2980 chunk 153 optimal weight: 6.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN P 195 ASN W 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.098826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.079280 restraints weight = 38951.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.080421 restraints weight = 28266.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.081270 restraints weight = 23559.030| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22759 Z= 0.157 Angle : 0.646 15.643 31146 Z= 0.307 Chirality : 0.045 0.267 3835 Planarity : 0.003 0.045 3714 Dihedral : 8.448 86.156 5418 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.73 % Allowed : 18.53 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.16), residues: 2580 helix: -0.27 (0.30), residues: 344 sheet: -0.02 (0.18), residues: 876 loop : -1.65 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 571 HIS 0.003 0.001 HIS P 105 PHE 0.017 0.001 PHE R 78 TYR 0.013 0.001 TYR L 91 ARG 0.005 0.000 ARG J 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 55) link_NAG-ASN : angle 1.86466 ( 165) link_ALPHA1-6 : bond 0.00511 ( 9) link_ALPHA1-6 : angle 1.57240 ( 27) link_BETA1-4 : bond 0.00517 ( 43) link_BETA1-4 : angle 1.84688 ( 129) link_ALPHA1-2 : bond 0.00215 ( 11) link_ALPHA1-2 : angle 1.61697 ( 33) link_ALPHA1-3 : bond 0.01395 ( 10) link_ALPHA1-3 : angle 1.82676 ( 30) hydrogen bonds : bond 0.04048 ( 644) hydrogen bonds : angle 4.65788 ( 1740) SS BOND : bond 0.00533 ( 40) SS BOND : angle 2.06864 ( 80) covalent geometry : bond 0.00375 (22589) covalent geometry : angle 0.60969 (30682) Misc. bond : bond 0.00114 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 MET cc_start: 0.7580 (mtp) cc_final: 0.7122 (mtp) REVERT: B 27 SER cc_start: 0.9020 (t) cc_final: 0.8620 (p) REVERT: F 590 GLN cc_start: 0.8944 (mm110) cc_final: 0.8600 (mm-40) REVERT: F 652 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7845 (tm-30) REVERT: F 655 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7961 (mttt) REVERT: F 656 ASN cc_start: 0.8017 (m-40) cc_final: 0.7659 (m-40) REVERT: J 207 LYS cc_start: 0.8309 (tptp) cc_final: 0.8084 (tptp) REVERT: L 77 ASN cc_start: 0.7760 (t0) cc_final: 0.7289 (t0) REVERT: L 79 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7836 (mt0) REVERT: P 116 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8864 (mp) REVERT: P 142 MET cc_start: 0.7290 (tpt) cc_final: 0.7053 (tpt) REVERT: P 308 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7699 (mtm110) REVERT: P 359 ILE cc_start: 0.9294 (mm) cc_final: 0.8991 (mm) REVERT: R 16 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7466 (mt-10) REVERT: W 79 GLN cc_start: 0.8797 (mm110) cc_final: 0.8453 (mm110) outliers start: 62 outliers final: 56 residues processed: 289 average time/residue: 0.3492 time to fit residues: 158.6087 Evaluate side-chains 293 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 308 ARG Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain W residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 189 optimal weight: 6.9990 chunk 60 optimal weight: 0.0010 chunk 53 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.099027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.079500 restraints weight = 38804.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.081023 restraints weight = 27952.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.081842 restraints weight = 22633.640| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 22759 Z= 0.210 Angle : 0.792 59.199 31146 Z= 0.423 Chirality : 0.048 0.975 3835 Planarity : 0.003 0.045 3714 Dihedral : 8.451 86.115 5418 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 2.78 % Allowed : 18.53 % Favored : 78.69 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.16), residues: 2580 helix: -0.26 (0.30), residues: 344 sheet: -0.02 (0.18), residues: 876 loop : -1.66 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 571 HIS 0.003 0.001 HIS P 105 PHE 0.016 0.001 PHE R 78 TYR 0.013 0.001 TYR L 91 ARG 0.005 0.000 ARG J 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 55) link_NAG-ASN : angle 1.86428 ( 165) link_ALPHA1-6 : bond 0.00469 ( 9) link_ALPHA1-6 : angle 1.55133 ( 27) link_BETA1-4 : bond 0.00492 ( 43) link_BETA1-4 : angle 1.84700 ( 129) link_ALPHA1-2 : bond 0.00218 ( 11) link_ALPHA1-2 : angle 1.61289 ( 33) link_ALPHA1-3 : bond 0.01395 ( 10) link_ALPHA1-3 : angle 1.87241 ( 30) hydrogen bonds : bond 0.04033 ( 644) hydrogen bonds : angle 4.65744 ( 1740) SS BOND : bond 0.00525 ( 40) SS BOND : angle 2.02804 ( 80) covalent geometry : bond 0.00458 (22589) covalent geometry : angle 0.76434 (30682) Misc. bond : bond 0.00123 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7400.98 seconds wall clock time: 133 minutes 49.73 seconds (8029.73 seconds total)