Starting phenix.real_space_refine on Sat Jun 21 15:33:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnu_41426/06_2025/8tnu_41426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnu_41426/06_2025/8tnu_41426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tnu_41426/06_2025/8tnu_41426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnu_41426/06_2025/8tnu_41426.map" model { file = "/net/cci-nas-00/data/ceres_data/8tnu_41426/06_2025/8tnu_41426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnu_41426/06_2025/8tnu_41426.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 15563 2.51 5 N 4171 2.21 5 O 5015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24893 Number of models: 1 Model: "" Number of chains: 41 Chain: "B" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1711 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "Z" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1008 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "J" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1734 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 212} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "H" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1734 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 212} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "G" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "E" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "F" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3500 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "X" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "Y" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1024 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 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: "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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "a" 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: "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: 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: "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: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "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: "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: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 16.01, per 1000 atoms: 0.64 Number of scatterers: 24893 At special positions: 0 Unit cell: (186.75, 204.18, 126.16, 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 144 16.00 O 5015 8.00 N 4171 7.00 C 15563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 207 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 605 " - pdb=" SG CYS G 501 " distance=1.82 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 98 " distance=2.03 Simple disulfide: pdb=" SG CYS J 151 " - pdb=" SG CYS J 207 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=1.87 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 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 E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS Y 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS X 605 " distance=2.03 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA R 3 " - " MAN R 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " NAG-ASN " NAG A 1 " - " ASN Z 637 " " NAG D 1 " - " ASN G 276 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 332 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 355 " " NAG E 609 " - " ASN E 363 " " NAG E 610 " - " ASN E 386 " " NAG E 611 " - " ASN E 392 " " NAG E 612 " - " ASN E 448 " " NAG F 601 " - " ASN F 133 " " NAG F 602 " - " ASN F 197 " " NAG F 603 " - " ASN F 301 " " NAG F 604 " - " ASN F 332 " " NAG F 605 " - " ASN F 339 " " NAG F 606 " - " ASN F 355 " " NAG F 607 " - " ASN F 363 " " NAG F 608 " - " ASN F 386 " " NAG F 609 " - " ASN F 392 " " NAG F 610 " - " ASN F 234 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 301 " " NAG G 603 " - " ASN G 332 " " NAG G 604 " - " ASN G 339 " " NAG G 605 " - " ASN G 355 " " NAG G 606 " - " ASN G 363 " " NAG G 607 " - " ASN G 392 " " NAG G 608 " - " ASN G 197 " " NAG G 609 " - " ASN G 386 " " NAG I 1 " - " ASN G 88 " " NAG M 1 " - " ASN G 156 " " NAG N 1 " - " ASN G 160 " " NAG O 1 " - " ASN G 295 " " NAG P 1 " - " ASN G 234 " " NAG Q 1 " - " ASN G 448 " " NAG S 1 " - " ASN E 88 " " NAG T 1 " - " ASN E 276 " " NAG U 1 " - " ASN E 156 " " NAG V 1 " - " ASN E 160 " " NAG W 1 " - " ASN E 262 " " NAG X 701 " - " ASN X 611 " " NAG X 702 " - " ASN X 618 " " NAG Y 701 " - " ASN Y 618 " " NAG Y 702 " - " ASN Y 611 " " NAG Z 701 " - " ASN Z 618 " " NAG Z 702 " - " ASN Z 611 " " NAG a 1 " - " ASN F 88 " " NAG b 1 " - " ASN F 448 " " NAG c 1 " - " ASN F 276 " " NAG d 1 " - " ASN F 262 " " NAG e 1 " - " ASN F 295 " " NAG f 1 " - " ASN F 160 " " NAG g 1 " - " ASN F 156 " " NAG h 1 " - " ASN X 637 " " NAG i 1 " - " ASN Y 637 " Time building additional restraints: 6.71 Conformation dependent library (CDL) restraints added in 3.1 seconds 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5684 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 57 sheets defined 18.2% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.695A pdb=" N THR B 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 removed outlier: 3.507A pdb=" N GLU B 144 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'Z' and resid 529 through 534 Processing helix chain 'Z' and resid 536 through 543 removed outlier: 4.293A pdb=" N GLN Z 540 " --> pdb=" O THR Z 536 " (cutoff:3.500A) Processing helix chain 'Z' and resid 569 through 596 removed outlier: 3.696A pdb=" N TRP Z 596 " --> pdb=" O LEU Z 592 " (cutoff:3.500A) Processing helix chain 'Z' and resid 618 through 625 Processing helix chain 'Z' and resid 627 through 636 removed outlier: 4.004A pdb=" N GLU Z 634 " --> pdb=" O GLN Z 630 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER Z 636 " --> pdb=" O ASP Z 632 " (cutoff:3.500A) Processing helix chain 'Z' and resid 638 through 664 removed outlier: 3.548A pdb=" N ILE Z 642 " --> pdb=" O TYR Z 638 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 removed outlier: 3.660A pdb=" N THR J 93 " --> pdb=" O ALA J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.971A pdb=" N SER J 143 " --> pdb=" O ARG J 140 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU J 144 " --> pdb=" O SER J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 200 No H-bonds generated for 'chain 'J' and resid 198 through 200' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.832A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 127 Processing helix chain 'K' and resid 183 through 188 Processing helix chain 'H' and resid 89 through 93 removed outlier: 3.581A pdb=" N THR H 93 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 144 removed outlier: 3.705A pdb=" N THR H 142 " --> pdb=" O SER H 139 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER H 143 " --> pdb=" O ARG H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.603A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.678A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.488A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.546A pdb=" N ARG G 151 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 481 removed outlier: 4.217A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.592A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.440A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 351 removed outlier: 3.950A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.744A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.866A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 460 through 464 removed outlier: 3.586A pdb=" N SER E 463 " --> pdb=" O SER E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.629A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 removed outlier: 4.029A pdb=" N ALA F 73 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS F 74 " --> pdb=" O THR F 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 70 through 74' Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.321A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.779A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 475 through 481 removed outlier: 4.100A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'X' and resid 529 through 534 Processing helix chain 'X' and resid 536 through 544 removed outlier: 4.031A pdb=" N GLN X 540 " --> pdb=" O THR X 536 " (cutoff:3.500A) Processing helix chain 'X' and resid 569 through 595 Processing helix chain 'X' and resid 611 through 615 Processing helix chain 'X' and resid 618 through 625 Processing helix chain 'X' and resid 627 through 635 Processing helix chain 'X' and resid 638 through 662 Processing helix chain 'Y' and resid 529 through 534 Processing helix chain 'Y' and resid 536 through 544 removed outlier: 4.094A pdb=" N GLN Y 540 " --> pdb=" O THR Y 536 " (cutoff:3.500A) Processing helix chain 'Y' and resid 569 through 596 removed outlier: 3.901A pdb=" N TRP Y 596 " --> pdb=" O LEU Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 618 through 623 removed outlier: 3.533A pdb=" N TRP Y 623 " --> pdb=" O LEU Y 619 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 635 Processing helix chain 'Y' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 4.234A pdb=" N PHE B 81 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 removed outlier: 4.234A pdb=" N PHE B 81 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.752A pdb=" N TRP B 36 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 52 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TRP B 38 " --> pdb=" O MET B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.772A pdb=" N SER B 100 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL B 113 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 104 removed outlier: 6.032A pdb=" N VAL B 103 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.969A pdb=" N GLY B 150 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 155 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR B 187 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.969A pdb=" N GLY B 150 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 155 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR B 187 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 161 through 165 removed outlier: 4.444A pdb=" N TYR B 205 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.703A pdb=" N ASP C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.577A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.046A pdb=" N TRP C 148 " --> pdb=" O LYS C 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Z' and resid 603 through 609 removed outlier: 3.599A pdb=" N CYS Z 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL G 36 " --> pdb=" O THR Z 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.606A pdb=" N PHE J 81 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER J 73 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.668A pdb=" N VAL J 113 " --> pdb=" O SER J 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 60 through 62 removed outlier: 5.558A pdb=" N TRP J 49 " --> pdb=" O ARG J 40 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG J 40 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY J 51 " --> pdb=" O TRP J 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 131 through 135 removed outlier: 6.233A pdb=" N TYR J 187 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 161 through 165 removed outlier: 4.339A pdb=" N TYR J 205 " --> pdb=" O VAL J 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.824A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.704A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.290A pdb=" N TRP K 148 " --> pdb=" O LYS K 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.670A pdb=" N PHE H 81 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.752A pdb=" N TRP H 36 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP H 38 " --> pdb=" O MET H 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.770A pdb=" N SER H 100 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL H 113 " --> pdb=" O SER H 100 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 30 through 32 removed outlier: 6.500A pdb=" N VAL H 103 " --> pdb=" O VAL Y 518 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N LEU Y 520 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.835A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.835A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 161 through 165 removed outlier: 4.465A pdb=" N TYR H 205 " --> pdb=" O VAL H 222 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.828A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.788A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 116 through 118 removed outlier: 3.747A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.340A pdb=" N TRP L 148 " --> pdb=" O LYS L 155 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.529A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.835A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AE1, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.291A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 10.640A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.933A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.640A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.701A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AE5, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AE6, first strand: chain 'E' and resid 45 through 46 removed outlier: 4.041A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.665A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AE9, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.708A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.526A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.084A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.042A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AF5, first strand: chain 'F' and resid 495 through 499 removed outlier: 5.631A pdb=" N VAL F 36 " --> pdb=" O THR X 606 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR X 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL F 38 " --> pdb=" O CYS X 604 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS X 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.864A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AF8, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.589A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AG1, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.361A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLY F 441 " --> pdb=" O ASN F 300 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASN F 300 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.063A pdb=" N ILE F 453 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 12.374A pdb=" N PHE F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.216A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.374A pdb=" N PHE F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 12.063A pdb=" N ILE F 453 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASN F 300 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLY F 441 " --> pdb=" O ASN F 300 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 304 through 308 979 hydrogen bonds defined for protein. 2571 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: 10.96 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7810 1.34 - 1.47: 6475 1.47 - 1.60: 10918 1.60 - 1.73: 0 1.73 - 1.86: 189 Bond restraints: 25392 Sorted by residual: bond pdb=" N VAL E 245 " pdb=" CA VAL E 245 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N GLN F 432 " pdb=" CA GLN F 432 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.16e-02 7.43e+03 9.17e+00 bond pdb=" N CYS E 247 " pdb=" CA CYS E 247 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.20e-02 6.94e+03 8.37e+00 bond pdb=" N VAL G 127 " pdb=" CA VAL G 127 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.28e-02 6.10e+03 8.31e+00 bond pdb=" N GLU X 648 " pdb=" CA GLU X 648 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.23e+00 ... (remaining 25387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 33487 2.52 - 5.04: 891 5.04 - 7.56: 116 7.56 - 10.08: 16 10.08 - 12.60: 5 Bond angle restraints: 34515 Sorted by residual: angle pdb=" N GLU X 584 " pdb=" CA GLU X 584 " pdb=" CB GLU X 584 " ideal model delta sigma weight residual 110.28 119.22 -8.94 1.55e+00 4.16e-01 3.33e+01 angle pdb=" C ASN E 80 " pdb=" CA ASN E 80 " pdb=" CB ASN E 80 " ideal model delta sigma weight residual 111.14 119.12 -7.98 1.56e+00 4.11e-01 2.62e+01 angle pdb=" C ASN F 425 " pdb=" N MET F 426 " pdb=" CA MET F 426 " ideal model delta sigma weight residual 122.61 130.09 -7.48 1.56e+00 4.11e-01 2.30e+01 angle pdb=" N THR E 123 " pdb=" CA THR E 123 " pdb=" C THR E 123 " ideal model delta sigma weight residual 109.81 120.32 -10.51 2.21e+00 2.05e-01 2.26e+01 angle pdb=" CA ARG L 18 " pdb=" CB ARG L 18 " pdb=" CG ARG L 18 " ideal model delta sigma weight residual 114.10 123.51 -9.41 2.00e+00 2.50e-01 2.21e+01 ... (remaining 34510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 15414 21.68 - 43.36: 851 43.36 - 65.03: 134 65.03 - 86.71: 64 86.71 - 108.39: 24 Dihedral angle restraints: 16487 sinusoidal: 7693 harmonic: 8794 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.66 75.66 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -154.80 68.80 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual -86.00 -19.43 -66.57 1 1.00e+01 1.00e-02 5.78e+01 ... (remaining 16484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3563 0.082 - 0.165: 591 0.165 - 0.247: 35 0.247 - 0.329: 13 0.329 - 0.411: 5 Chirality restraints: 4207 Sorted by residual: chirality pdb=" CB ILE C 2 " pdb=" CA ILE C 2 " pdb=" CG1 ILE C 2 " pdb=" CG2 ILE C 2 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C1 NAG Z 702 " pdb=" ND2 ASN Z 611 " pdb=" C2 NAG Z 702 " pdb=" O5 NAG Z 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN F 448 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 4204 not shown) Planarity restraints: 4328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS G 239 " -0.082 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO G 240 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO G 240 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO G 240 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN Z 611 " 0.031 2.00e-02 2.50e+03 3.00e-02 1.13e+01 pdb=" CG ASN Z 611 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN Z 611 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN Z 611 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG Z 702 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN J 63 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO J 64 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO J 64 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO J 64 " -0.041 5.00e-02 4.00e+02 ... (remaining 4325 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 1 2.21 - 2.88: 8993 2.88 - 3.56: 32761 3.56 - 4.23: 56210 4.23 - 4.90: 95229 Nonbonded interactions: 193194 Sorted by model distance: nonbonded pdb=" NZ LYS Z 574 " pdb=" OD2 ASP G 107 " model vdw 1.539 3.120 nonbonded pdb=" OG1 THR Z 538 " pdb=" NH1 ARG Z 542 " model vdw 2.276 3.120 nonbonded pdb=" OE2 GLU E 370 " pdb=" OH TYR E 384 " model vdw 2.302 3.040 nonbonded pdb=" O VAL F 36 " pdb=" OG1 THR X 606 " model vdw 2.305 3.040 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.306 3.040 ... (remaining 193189 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 'D' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' } ncs_group { reference = chain 'B' selection = (chain 'H' and (resid 2 through 26 or resid 30 or (resid 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 through 227)) selection = (chain 'J' and (resid 2 through 26 or resid 30 or (resid 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 through 227)) } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'E' and (resid 32 through 58 or resid 66 through 185 or resid 189 through \ 398 or resid 412 through 506 or resid 601 through 609)) selection = (chain 'F' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 506 or resid 601 through 609)) selection = (chain 'G' and (resid 32 through 58 or resid 66 through 398 or resid 412 through \ 506 or resid 601 through 609)) } ncs_group { reference = chain 'R' selection = chain 'W' } ncs_group { reference = (chain 'X' and (resid 516 through 663 or resid 701 through 702)) selection = (chain 'Y' and (resid 516 through 663 or resid 701 through 702)) selection = (chain 'Z' and (resid 516 through 663 or resid 701 through 702)) } ncs_group { reference = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 59.900 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 25532 Z= 0.293 Angle : 1.043 45.037 34887 Z= 0.548 Chirality : 0.059 0.411 4207 Planarity : 0.006 0.123 4269 Dihedral : 14.066 108.389 10659 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 10.87 % 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: -1.28 (0.14), residues: 2989 helix: -1.31 (0.19), residues: 475 sheet: -0.31 (0.16), residues: 994 loop : -0.98 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 45 HIS 0.005 0.001 HIS E 216 PHE 0.041 0.002 PHE H 81 TYR 0.041 0.002 TYR E 486 ARG 0.017 0.001 ARG X 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 59) link_NAG-ASN : angle 2.24856 ( 177) link_ALPHA1-6 : bond 0.00371 ( 2) link_ALPHA1-6 : angle 1.61314 ( 6) link_BETA1-4 : bond 0.01421 ( 29) link_BETA1-4 : angle 4.11310 ( 87) link_ALPHA1-3 : bond 0.00513 ( 2) link_ALPHA1-3 : angle 1.67368 ( 6) hydrogen bonds : bond 0.13635 ( 911) hydrogen bonds : angle 6.77047 ( 2571) SS BOND : bond 0.03816 ( 48) SS BOND : angle 5.55191 ( 96) covalent geometry : bond 0.00520 (25392) covalent geometry : angle 0.97132 (34515) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.5261 (mtp) cc_final: 0.4701 (ptp) REVERT: K 189 HIS cc_start: 0.8872 (m90) cc_final: 0.8657 (m90) REVERT: L 62 PHE cc_start: 0.8730 (m-80) cc_final: 0.8471 (m-80) REVERT: L 189 HIS cc_start: 0.7222 (m-70) cc_final: 0.7006 (m-70) REVERT: E 430 ILE cc_start: 0.8703 (pt) cc_final: 0.8278 (mm) REVERT: F 161 MET cc_start: 0.8269 (tpp) cc_final: 0.7999 (ttm) REVERT: X 626 MET cc_start: 0.8634 (ttm) cc_final: 0.8372 (ttm) REVERT: Y 543 ASN cc_start: 0.7509 (m-40) cc_final: 0.7226 (m-40) REVERT: Y 616 ASN cc_start: 0.8852 (p0) cc_final: 0.8620 (p0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3477 time to fit residues: 128.0212 Evaluate side-chains 169 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 121 optimal weight: 30.0000 chunk 234 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 142 optimal weight: 1.9990 chunk 174 optimal weight: 0.0870 chunk 271 optimal weight: 3.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 208 ASN J 59 ASN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS E 246 GLN ** F 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN X 653 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.093366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.056222 restraints weight = 94296.125| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.93 r_work: 0.2893 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 25532 Z= 0.216 Angle : 0.684 12.540 34887 Z= 0.337 Chirality : 0.046 0.300 4207 Planarity : 0.005 0.070 4269 Dihedral : 8.512 74.728 5172 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.08 % Allowed : 6.63 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 2989 helix: 0.44 (0.24), residues: 472 sheet: -0.11 (0.16), residues: 1007 loop : -0.51 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Z 610 HIS 0.007 0.001 HIS E 249 PHE 0.022 0.002 PHE H 81 TYR 0.017 0.002 TYR H 187 ARG 0.008 0.001 ARG X 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 59) link_NAG-ASN : angle 1.81273 ( 177) link_ALPHA1-6 : bond 0.00099 ( 2) link_ALPHA1-6 : angle 1.96206 ( 6) link_BETA1-4 : bond 0.00635 ( 29) link_BETA1-4 : angle 2.82821 ( 87) link_ALPHA1-3 : bond 0.00639 ( 2) link_ALPHA1-3 : angle 3.27989 ( 6) hydrogen bonds : bond 0.03618 ( 911) hydrogen bonds : angle 5.31867 ( 2571) SS BOND : bond 0.00364 ( 48) SS BOND : angle 1.21146 ( 96) covalent geometry : bond 0.00494 (25392) covalent geometry : angle 0.65487 (34515) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.5121 (mtp) cc_final: 0.4606 (ptp) REVERT: H 75 ASP cc_start: 0.9150 (p0) cc_final: 0.8841 (p0) REVERT: H 78 LYS cc_start: 0.9197 (tptp) cc_final: 0.8944 (pttm) REVERT: L 62 PHE cc_start: 0.8848 (m-80) cc_final: 0.8607 (m-80) REVERT: X 626 MET cc_start: 0.8556 (ttm) cc_final: 0.8334 (ttm) REVERT: Y 634 GLU cc_start: 0.9161 (tt0) cc_final: 0.8884 (tt0) outliers start: 29 outliers final: 14 residues processed: 180 average time/residue: 0.3604 time to fit residues: 104.2588 Evaluate side-chains 156 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain Y residue 615 SER Chi-restraints excluded: chain Y residue 659 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 223 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 232 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 11 optimal weight: 50.0000 chunk 112 optimal weight: 40.0000 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 40.0000 chunk 136 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 59 ASN J 119 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN G 356 ASN E 428 GLN F 185 ASN ** F 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 543 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.089890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051664 restraints weight = 93772.936| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.84 r_work: 0.2752 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 25532 Z= 0.343 Angle : 0.754 9.635 34887 Z= 0.375 Chirality : 0.048 0.349 4207 Planarity : 0.005 0.062 4269 Dihedral : 7.787 65.784 5172 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 2.20 % Allowed : 8.68 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2989 helix: 0.61 (0.24), residues: 482 sheet: -0.16 (0.16), residues: 1065 loop : -0.56 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP X 623 HIS 0.010 0.002 HIS E 330 PHE 0.022 0.002 PHE H 81 TYR 0.017 0.002 TYR Z 638 ARG 0.008 0.001 ARG Z 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 59) link_NAG-ASN : angle 1.99512 ( 177) link_ALPHA1-6 : bond 0.00470 ( 2) link_ALPHA1-6 : angle 1.96368 ( 6) link_BETA1-4 : bond 0.00804 ( 29) link_BETA1-4 : angle 2.77945 ( 87) link_ALPHA1-3 : bond 0.00855 ( 2) link_ALPHA1-3 : angle 2.11974 ( 6) hydrogen bonds : bond 0.03878 ( 911) hydrogen bonds : angle 5.38157 ( 2571) SS BOND : bond 0.00507 ( 48) SS BOND : angle 1.24525 ( 96) covalent geometry : bond 0.00778 (25392) covalent geometry : angle 0.72782 (34515) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.5055 (mtp) cc_final: 0.4692 (ptp) REVERT: Z 626 MET cc_start: 0.7788 (ttt) cc_final: 0.7409 (ttt) REVERT: Z 633 LYS cc_start: 0.9349 (mmmt) cc_final: 0.8862 (mmmt) REVERT: J 27 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.8130 (m-70) REVERT: H 75 ASP cc_start: 0.9320 (p0) cc_final: 0.8590 (p0) REVERT: H 78 LYS cc_start: 0.9399 (tptp) cc_final: 0.8986 (pttm) REVERT: H 82 PHE cc_start: 0.9558 (m-10) cc_final: 0.9355 (m-80) REVERT: E 104 MET cc_start: 0.9280 (ttm) cc_final: 0.8799 (tpp) REVERT: E 288 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7774 (p90) REVERT: F 426 MET cc_start: 0.7808 (ptt) cc_final: 0.7525 (ptt) REVERT: X 530 MET cc_start: 0.8529 (mmm) cc_final: 0.8322 (mtt) REVERT: Y 530 MET cc_start: 0.9089 (mmm) cc_final: 0.8810 (mmt) outliers start: 59 outliers final: 34 residues processed: 178 average time/residue: 0.3441 time to fit residues: 101.1067 Evaluate side-chains 158 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 536 THR Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 636 SER Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 515 ILE Chi-restraints excluded: chain Y residue 608 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 72 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 162 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 281 optimal weight: 0.3980 chunk 93 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN J 59 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Y 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.091756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.053742 restraints weight = 94272.591| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 4.96 r_work: 0.2813 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25532 Z= 0.132 Angle : 0.587 10.839 34887 Z= 0.288 Chirality : 0.044 0.329 4207 Planarity : 0.004 0.056 4269 Dihedral : 6.966 57.298 5172 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 10.47 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2989 helix: 1.14 (0.25), residues: 471 sheet: 0.13 (0.16), residues: 1040 loop : -0.41 (0.17), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.004 0.001 HIS J 27 PHE 0.022 0.001 PHE H 81 TYR 0.015 0.001 TYR K 49 ARG 0.005 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 59) link_NAG-ASN : angle 1.71846 ( 177) link_ALPHA1-6 : bond 0.00541 ( 2) link_ALPHA1-6 : angle 1.77502 ( 6) link_BETA1-4 : bond 0.00785 ( 29) link_BETA1-4 : angle 2.55169 ( 87) link_ALPHA1-3 : bond 0.00942 ( 2) link_ALPHA1-3 : angle 2.19815 ( 6) hydrogen bonds : bond 0.03103 ( 911) hydrogen bonds : angle 5.00059 ( 2571) SS BOND : bond 0.00267 ( 48) SS BOND : angle 0.85149 ( 96) covalent geometry : bond 0.00300 (25392) covalent geometry : angle 0.55981 (34515) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 626 MET cc_start: 0.7731 (ttt) cc_final: 0.7292 (ttt) REVERT: J 27 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.7852 (m-70) REVERT: H 75 ASP cc_start: 0.9283 (p0) cc_final: 0.8468 (p0) REVERT: H 78 LYS cc_start: 0.9387 (tptp) cc_final: 0.9022 (pttm) REVERT: E 104 MET cc_start: 0.9192 (ttm) cc_final: 0.8626 (tpp) REVERT: E 217 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: F 426 MET cc_start: 0.7466 (ptt) cc_final: 0.7203 (ptt) REVERT: Y 634 GLU cc_start: 0.9128 (tt0) cc_final: 0.8769 (tt0) outliers start: 45 outliers final: 25 residues processed: 176 average time/residue: 0.3497 time to fit residues: 100.7011 Evaluate side-chains 162 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain X residue 587 LEU Chi-restraints excluded: chain Y residue 515 ILE Chi-restraints excluded: chain Y residue 608 VAL Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 654 GLU Chi-restraints excluded: chain Y residue 659 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 37 optimal weight: 6.9990 chunk 97 optimal weight: 40.0000 chunk 265 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 34 optimal weight: 0.1980 chunk 129 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 117 optimal weight: 50.0000 chunk 230 optimal weight: 0.6980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS F 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.090272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052178 restraints weight = 95170.882| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.93 r_work: 0.2776 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 25532 Z= 0.281 Angle : 0.683 10.519 34887 Z= 0.336 Chirality : 0.046 0.331 4207 Planarity : 0.004 0.053 4269 Dihedral : 7.015 58.452 5172 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 2.38 % Allowed : 10.69 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2989 helix: 1.03 (0.25), residues: 473 sheet: 0.00 (0.16), residues: 1070 loop : -0.48 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 112 HIS 0.008 0.001 HIS E 330 PHE 0.021 0.002 PHE H 81 TYR 0.029 0.001 TYR L 49 ARG 0.007 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 59) link_NAG-ASN : angle 1.88217 ( 177) link_ALPHA1-6 : bond 0.00370 ( 2) link_ALPHA1-6 : angle 1.76984 ( 6) link_BETA1-4 : bond 0.00731 ( 29) link_BETA1-4 : angle 2.59176 ( 87) link_ALPHA1-3 : bond 0.00834 ( 2) link_ALPHA1-3 : angle 2.19327 ( 6) hydrogen bonds : bond 0.03435 ( 911) hydrogen bonds : angle 5.06871 ( 2571) SS BOND : bond 0.00421 ( 48) SS BOND : angle 1.01417 ( 96) covalent geometry : bond 0.00646 (25392) covalent geometry : angle 0.65764 (34515) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 131 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 626 MET cc_start: 0.7923 (ttt) cc_final: 0.7480 (ttt) REVERT: Z 633 LYS cc_start: 0.9378 (mmmt) cc_final: 0.9030 (mmmm) REVERT: J 27 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.8158 (m-70) REVERT: H 75 ASP cc_start: 0.9276 (p0) cc_final: 0.8648 (p0) REVERT: H 78 LYS cc_start: 0.9430 (tptp) cc_final: 0.9088 (pttp) REVERT: E 104 MET cc_start: 0.9272 (ttm) cc_final: 0.8678 (tpp) REVERT: E 217 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: F 426 MET cc_start: 0.7809 (ptt) cc_final: 0.7559 (ptt) REVERT: X 626 MET cc_start: 0.8645 (ttm) cc_final: 0.7906 (ttm) REVERT: Y 616 ASN cc_start: 0.9250 (p0) cc_final: 0.9023 (p0) outliers start: 64 outliers final: 40 residues processed: 181 average time/residue: 0.3607 time to fit residues: 107.5499 Evaluate side-chains 170 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 536 THR Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 636 SER Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain K residue 189 HIS Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain Y residue 515 ILE Chi-restraints excluded: chain Y residue 520 LEU Chi-restraints excluded: chain Y residue 608 VAL Chi-restraints excluded: chain Y residue 659 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 20 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 282 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 294 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.091335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053343 restraints weight = 94091.600| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.84 r_work: 0.2806 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25532 Z= 0.126 Angle : 0.588 11.353 34887 Z= 0.289 Chirality : 0.044 0.320 4207 Planarity : 0.004 0.051 4269 Dihedral : 6.587 57.090 5172 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 1.64 % Allowed : 12.37 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2989 helix: 1.29 (0.25), residues: 472 sheet: 0.20 (0.17), residues: 1035 loop : -0.40 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.013 0.001 HIS K 189 PHE 0.022 0.001 PHE H 81 TYR 0.026 0.001 TYR L 49 ARG 0.006 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 59) link_NAG-ASN : angle 1.70748 ( 177) link_ALPHA1-6 : bond 0.00390 ( 2) link_ALPHA1-6 : angle 1.54425 ( 6) link_BETA1-4 : bond 0.00799 ( 29) link_BETA1-4 : angle 2.46918 ( 87) link_ALPHA1-3 : bond 0.01006 ( 2) link_ALPHA1-3 : angle 1.94599 ( 6) hydrogen bonds : bond 0.03010 ( 911) hydrogen bonds : angle 4.85742 ( 2571) SS BOND : bond 0.00428 ( 48) SS BOND : angle 0.88851 ( 96) covalent geometry : bond 0.00286 (25392) covalent geometry : angle 0.56222 (34515) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 543 ASN cc_start: 0.8826 (m-40) cc_final: 0.8095 (t0) REVERT: J 27 HIS cc_start: 0.8544 (OUTLIER) cc_final: 0.7993 (m-70) REVERT: H 78 LYS cc_start: 0.9407 (tptp) cc_final: 0.9150 (tptp) REVERT: E 104 MET cc_start: 0.9193 (ttm) cc_final: 0.8631 (tpp) REVERT: E 217 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: F 426 MET cc_start: 0.7503 (ptt) cc_final: 0.7235 (ptt) REVERT: X 626 MET cc_start: 0.8618 (ttm) cc_final: 0.8147 (ttm) REVERT: Y 530 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8755 (mtp) REVERT: Y 616 ASN cc_start: 0.9172 (p0) cc_final: 0.8962 (p0) outliers start: 44 outliers final: 32 residues processed: 173 average time/residue: 0.3494 time to fit residues: 100.0431 Evaluate side-chains 167 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain X residue 657 GLU Chi-restraints excluded: chain Y residue 515 ILE Chi-restraints excluded: chain Y residue 530 MET Chi-restraints excluded: chain Y residue 608 VAL Chi-restraints excluded: chain Y residue 659 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 103 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 296 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 HIS ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS F 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.089924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051940 restraints weight = 95150.636| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.91 r_work: 0.2769 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25532 Z= 0.271 Angle : 0.679 12.304 34887 Z= 0.334 Chirality : 0.046 0.329 4207 Planarity : 0.004 0.050 4269 Dihedral : 6.767 58.345 5172 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 2.16 % Allowed : 12.70 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2989 helix: 0.96 (0.25), residues: 479 sheet: 0.02 (0.16), residues: 1073 loop : -0.44 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 479 HIS 0.006 0.001 HIS E 330 PHE 0.019 0.002 PHE H 81 TYR 0.021 0.001 TYR L 49 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 59) link_NAG-ASN : angle 1.90692 ( 177) link_ALPHA1-6 : bond 0.00112 ( 2) link_ALPHA1-6 : angle 1.66960 ( 6) link_BETA1-4 : bond 0.00748 ( 29) link_BETA1-4 : angle 2.55724 ( 87) link_ALPHA1-3 : bond 0.00830 ( 2) link_ALPHA1-3 : angle 1.98297 ( 6) hydrogen bonds : bond 0.03392 ( 911) hydrogen bonds : angle 4.98306 ( 2571) SS BOND : bond 0.00429 ( 48) SS BOND : angle 1.05370 ( 96) covalent geometry : bond 0.00623 (25392) covalent geometry : angle 0.65368 (34515) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 626 MET cc_start: 0.8006 (ttt) cc_final: 0.7780 (ttt) REVERT: H 78 LYS cc_start: 0.9459 (tptp) cc_final: 0.9181 (tptp) REVERT: E 104 MET cc_start: 0.9269 (ttm) cc_final: 0.8658 (tpp) REVERT: E 217 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: X 626 MET cc_start: 0.8669 (ttm) cc_final: 0.8109 (ttm) REVERT: Y 530 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8816 (mtp) REVERT: Y 616 ASN cc_start: 0.9258 (p0) cc_final: 0.9046 (p0) outliers start: 58 outliers final: 45 residues processed: 181 average time/residue: 0.3392 time to fit residues: 101.0015 Evaluate side-chains 176 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 636 SER Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain X residue 657 GLU Chi-restraints excluded: chain Y residue 515 ILE Chi-restraints excluded: chain Y residue 530 MET Chi-restraints excluded: chain Y residue 608 VAL Chi-restraints excluded: chain Y residue 659 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 269 optimal weight: 0.0170 chunk 258 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 1 optimal weight: 50.0000 chunk 127 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN E 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.091440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053592 restraints weight = 94777.133| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.84 r_work: 0.2827 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25532 Z= 0.126 Angle : 0.595 12.597 34887 Z= 0.291 Chirality : 0.044 0.318 4207 Planarity : 0.003 0.049 4269 Dihedral : 6.358 59.480 5172 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 1.79 % Allowed : 13.23 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2989 helix: 1.21 (0.25), residues: 478 sheet: 0.20 (0.17), residues: 1041 loop : -0.41 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.018 0.001 HIS J 27 PHE 0.021 0.001 PHE H 81 TYR 0.022 0.001 TYR L 49 ARG 0.003 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 59) link_NAG-ASN : angle 1.72282 ( 177) link_ALPHA1-6 : bond 0.00174 ( 2) link_ALPHA1-6 : angle 1.64221 ( 6) link_BETA1-4 : bond 0.00791 ( 29) link_BETA1-4 : angle 2.42400 ( 87) link_ALPHA1-3 : bond 0.00943 ( 2) link_ALPHA1-3 : angle 1.68186 ( 6) hydrogen bonds : bond 0.02980 ( 911) hydrogen bonds : angle 4.77647 ( 2571) SS BOND : bond 0.00275 ( 48) SS BOND : angle 0.88832 ( 96) covalent geometry : bond 0.00286 (25392) covalent geometry : angle 0.57020 (34515) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 543 ASN cc_start: 0.8815 (m-40) cc_final: 0.8088 (t0) REVERT: H 78 LYS cc_start: 0.9439 (tptp) cc_final: 0.9168 (tptp) REVERT: E 104 MET cc_start: 0.9203 (ttm) cc_final: 0.8674 (tpp) REVERT: E 161 MET cc_start: 0.9334 (tpt) cc_final: 0.9127 (tpt) REVERT: E 217 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: F 426 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7321 (ptt) REVERT: X 626 MET cc_start: 0.8657 (ttm) cc_final: 0.8057 (ttm) REVERT: X 629 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8857 (mm) REVERT: Y 616 ASN cc_start: 0.9204 (p0) cc_final: 0.8981 (p0) outliers start: 48 outliers final: 38 residues processed: 175 average time/residue: 0.3548 time to fit residues: 102.7218 Evaluate side-chains 175 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 636 SER Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain X residue 629 LEU Chi-restraints excluded: chain X residue 657 GLU Chi-restraints excluded: chain Y residue 515 ILE Chi-restraints excluded: chain Y residue 530 MET Chi-restraints excluded: chain Y residue 608 VAL Chi-restraints excluded: chain Y residue 659 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 296 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 206 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 1 optimal weight: 40.0000 chunk 279 optimal weight: 0.3980 chunk 166 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN X 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.090506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.052560 restraints weight = 94994.137| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.83 r_work: 0.2798 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25532 Z= 0.200 Angle : 0.631 12.569 34887 Z= 0.309 Chirality : 0.045 0.316 4207 Planarity : 0.004 0.049 4269 Dihedral : 6.391 58.333 5172 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 1.90 % Allowed : 13.26 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2989 helix: 1.16 (0.25), residues: 478 sheet: 0.12 (0.16), residues: 1075 loop : -0.44 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 571 HIS 0.005 0.001 HIS E 330 PHE 0.019 0.001 PHE H 81 TYR 0.025 0.001 TYR Y 638 ARG 0.005 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 59) link_NAG-ASN : angle 1.78039 ( 177) link_ALPHA1-6 : bond 0.00074 ( 2) link_ALPHA1-6 : angle 1.69066 ( 6) link_BETA1-4 : bond 0.00743 ( 29) link_BETA1-4 : angle 2.44841 ( 87) link_ALPHA1-3 : bond 0.00811 ( 2) link_ALPHA1-3 : angle 1.68945 ( 6) hydrogen bonds : bond 0.03121 ( 911) hydrogen bonds : angle 4.80854 ( 2571) SS BOND : bond 0.00321 ( 48) SS BOND : angle 0.91226 ( 96) covalent geometry : bond 0.00464 (25392) covalent geometry : angle 0.60673 (34515) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 530 MET cc_start: 0.5686 (OUTLIER) cc_final: 0.5052 (mmt) REVERT: J 27 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.7946 (m-70) REVERT: H 78 LYS cc_start: 0.9461 (tptp) cc_final: 0.9193 (tptp) REVERT: E 104 MET cc_start: 0.9253 (ttm) cc_final: 0.8695 (tpp) REVERT: E 217 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: F 426 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7560 (ptt) REVERT: X 626 MET cc_start: 0.8684 (ttm) cc_final: 0.8040 (ttm) REVERT: X 629 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8943 (mm) REVERT: Y 616 ASN cc_start: 0.9250 (p0) cc_final: 0.9039 (p0) outliers start: 51 outliers final: 43 residues processed: 174 average time/residue: 0.3652 time to fit residues: 104.4102 Evaluate side-chains 180 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain Z residue 530 MET Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 636 SER Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain X residue 543 ASN Chi-restraints excluded: chain X residue 629 LEU Chi-restraints excluded: chain X residue 657 GLU Chi-restraints excluded: chain Y residue 515 ILE Chi-restraints excluded: chain Y residue 530 MET Chi-restraints excluded: chain Y residue 608 VAL Chi-restraints excluded: chain Y residue 659 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 153 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 253 optimal weight: 0.9980 chunk 252 optimal weight: 5.9990 chunk 17 optimal weight: 40.0000 chunk 184 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 209 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.091415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053609 restraints weight = 94757.324| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.84 r_work: 0.2829 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25532 Z= 0.128 Angle : 0.604 12.436 34887 Z= 0.294 Chirality : 0.044 0.314 4207 Planarity : 0.003 0.049 4269 Dihedral : 6.229 57.361 5172 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.75 % Allowed : 13.34 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2989 helix: 1.31 (0.25), residues: 474 sheet: 0.25 (0.17), residues: 1046 loop : -0.40 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 571 HIS 0.003 0.001 HIS E 374 PHE 0.020 0.001 PHE H 81 TYR 0.025 0.001 TYR Y 638 ARG 0.010 0.000 ARG X 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 59) link_NAG-ASN : angle 1.70751 ( 177) link_ALPHA1-6 : bond 0.00189 ( 2) link_ALPHA1-6 : angle 1.65874 ( 6) link_BETA1-4 : bond 0.00804 ( 29) link_BETA1-4 : angle 2.40658 ( 87) link_ALPHA1-3 : bond 0.00846 ( 2) link_ALPHA1-3 : angle 1.57005 ( 6) hydrogen bonds : bond 0.02940 ( 911) hydrogen bonds : angle 4.71887 ( 2571) SS BOND : bond 0.00259 ( 48) SS BOND : angle 0.83161 ( 96) covalent geometry : bond 0.00294 (25392) covalent geometry : angle 0.57987 (34515) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 530 MET cc_start: 0.5668 (OUTLIER) cc_final: 0.5049 (mmt) REVERT: Z 543 ASN cc_start: 0.8806 (m-40) cc_final: 0.8132 (t0) REVERT: J 155 ASP cc_start: 0.9382 (m-30) cc_final: 0.8943 (p0) REVERT: H 78 LYS cc_start: 0.9444 (tptp) cc_final: 0.9172 (tptp) REVERT: H 212 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8640 (mmtm) REVERT: E 104 MET cc_start: 0.9202 (ttm) cc_final: 0.8675 (tpp) REVERT: E 161 MET cc_start: 0.9331 (tpt) cc_final: 0.9123 (tpt) REVERT: E 217 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: F 426 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7435 (ptt) REVERT: X 626 MET cc_start: 0.8657 (ttm) cc_final: 0.8022 (ttm) REVERT: X 629 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8841 (mm) REVERT: Y 616 ASN cc_start: 0.9224 (p0) cc_final: 0.9002 (p0) outliers start: 47 outliers final: 39 residues processed: 176 average time/residue: 0.3311 time to fit residues: 96.2013 Evaluate side-chains 181 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain Z residue 530 MET Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain X residue 629 LEU Chi-restraints excluded: chain X residue 657 GLU Chi-restraints excluded: chain Y residue 515 ILE Chi-restraints excluded: chain Y residue 530 MET Chi-restraints excluded: chain Y residue 608 VAL Chi-restraints excluded: chain Y residue 659 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 269 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 254 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 17 optimal weight: 30.0000 chunk 231 optimal weight: 10.0000 chunk 222 optimal weight: 0.2980 chunk 128 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.090853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.053026 restraints weight = 94794.100| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.81 r_work: 0.2812 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25532 Z= 0.172 Angle : 0.622 12.533 34887 Z= 0.303 Chirality : 0.044 0.312 4207 Planarity : 0.004 0.049 4269 Dihedral : 6.224 57.465 5172 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.88 % Rotamer: Outliers : 1.68 % Allowed : 13.34 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2989 helix: 1.26 (0.25), residues: 477 sheet: 0.26 (0.17), residues: 1040 loop : -0.42 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 479 HIS 0.004 0.001 HIS E 330 PHE 0.019 0.001 PHE H 81 TYR 0.024 0.001 TYR Y 638 ARG 0.007 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 59) link_NAG-ASN : angle 1.72159 ( 177) link_ALPHA1-6 : bond 0.00130 ( 2) link_ALPHA1-6 : angle 1.67896 ( 6) link_BETA1-4 : bond 0.00771 ( 29) link_BETA1-4 : angle 2.41040 ( 87) link_ALPHA1-3 : bond 0.00764 ( 2) link_ALPHA1-3 : angle 1.55596 ( 6) hydrogen bonds : bond 0.03011 ( 911) hydrogen bonds : angle 4.71669 ( 2571) SS BOND : bond 0.00324 ( 48) SS BOND : angle 0.94041 ( 96) covalent geometry : bond 0.00397 (25392) covalent geometry : angle 0.59830 (34515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16088.88 seconds wall clock time: 275 minutes 19.64 seconds (16519.64 seconds total)