Starting phenix.real_space_refine on Sat May 24 03:13:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnu_41426/05_2025/8tnu_41426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnu_41426/05_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_41426/05_2025/8tnu_41426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnu_41426/05_2025/8tnu_41426.map" model { file = "/net/cci-nas-00/data/ceres_data/8tnu_41426/05_2025/8tnu_41426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnu_41426/05_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-5687/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: 15.22, per 1000 atoms: 0.61 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: 6.10 Conformation dependent library (CDL) restraints added in 2.9 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: 4.05 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: 10.06 Time building geometry restraints manager: 7.12 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: 4.290 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: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.170 Set scattering table: 0.260 Process input model: 56.050 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.320 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:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.510 ------------------------------------------------------------------------------- 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 : 2.564 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: 0.3380 time to fit residues: 124.1497 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 = 94296.127| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.93 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 : 2.671 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: 0.5291 (mtp) cc_final: 0.4702 (ptp) REVERT: H 75 ASP cc_start: 0.9183 (p0) cc_final: 0.8894 (p0) REVERT: H 78 LYS cc_start: 0.9251 (tptp) cc_final: 0.8972 (pttm) REVERT: L 62 PHE cc_start: 0.8779 (m-80) cc_final: 0.8535 (m-80) REVERT: L 189 HIS cc_start: 0.7576 (m-70) cc_final: 0.7364 (m-70) REVERT: E 496 VAL cc_start: 0.9096 (m) cc_final: 0.8881 (m) REVERT: X 626 MET cc_start: 0.8500 (ttm) cc_final: 0.8281 (ttm) REVERT: Y 634 GLU cc_start: 0.8995 (tt0) cc_final: 0.8701 (tt0) outliers start: 29 outliers final: 14 residues processed: 180 average time/residue: 0.3535 time to fit residues: 102.4899 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 : 2.618 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 50.0000 chunk 112 optimal weight: 50.0000 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 40.0000 chunk 136 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 59 ASN J 80 GLN J 119 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS H 5 GLN H 27 HIS G 94 ASN G 425 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.089604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.051360 restraints weight = 93951.198| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.85 r_work: 0.2746 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 25532 Z= 0.366 Angle : 0.773 9.691 34887 Z= 0.384 Chirality : 0.049 0.353 4207 Planarity : 0.005 0.061 4269 Dihedral : 7.834 64.869 5172 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 2.31 % Allowed : 8.83 % Favored : 88.86 % 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: -0.45 (0.15), residues: 2989 helix: 0.55 (0.24), residues: 482 sheet: -0.17 (0.16), residues: 1063 loop : -0.59 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 623 HIS 0.010 0.002 HIS E 330 PHE 0.022 0.002 PHE H 81 TYR 0.018 0.002 TYR Z 638 ARG 0.008 0.001 ARG Z 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 59) link_NAG-ASN : angle 2.03557 ( 177) link_ALPHA1-6 : bond 0.00542 ( 2) link_ALPHA1-6 : angle 1.89873 ( 6) link_BETA1-4 : bond 0.00827 ( 29) link_BETA1-4 : angle 2.79434 ( 87) link_ALPHA1-3 : bond 0.00824 ( 2) link_ALPHA1-3 : angle 2.15695 ( 6) hydrogen bonds : bond 0.03941 ( 911) hydrogen bonds : angle 5.43767 ( 2571) SS BOND : bond 0.00587 ( 48) SS BOND : angle 1.26139 ( 96) covalent geometry : bond 0.00833 (25392) covalent geometry : angle 0.74604 (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 193 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 131 time to evaluate : 2.591 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: 0.4998 (mtp) cc_final: 0.4655 (ptp) REVERT: Z 626 MET cc_start: 0.7835 (ttt) cc_final: 0.7452 (ttt) REVERT: Z 633 LYS cc_start: 0.9369 (mmmt) cc_final: 0.8904 (mmmt) REVERT: J 27 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.8137 (m-70) REVERT: H 75 ASP cc_start: 0.9313 (p0) cc_final: 0.8700 (p0) REVERT: H 78 LYS cc_start: 0.9407 (tptp) cc_final: 0.9003 (pttm) REVERT: E 104 MET cc_start: 0.9293 (ttm) cc_final: 0.8818 (tpp) REVERT: E 288 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.7699 (p90) REVERT: F 426 MET cc_start: 0.7900 (ptt) cc_final: 0.7635 (ptt) REVERT: Y 530 MET cc_start: 0.9121 (mmm) cc_final: 0.8850 (mmt) outliers start: 62 outliers final: 38 residues processed: 179 average time/residue: 0.3325 time to fit residues: 97.9612 Evaluate side-chains 162 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 2.579 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain E residue 126 CYS 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 424 ILE 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 X residue 657 GLU 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: 40.0000 chunk 204 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 170 optimal weight: 0.6980 chunk 281 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** K 189 HIS L 166 GLN G 356 ASN F 352 HIS Y 616 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.091338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.053187 restraints weight = 94463.079| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 4.84 r_work: 0.2802 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25532 Z= 0.151 Angle : 0.598 11.057 34887 Z= 0.294 Chirality : 0.044 0.335 4207 Planarity : 0.004 0.055 4269 Dihedral : 7.031 57.629 5172 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.97 % Allowed : 10.36 % Favored : 87.67 % 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: 1.03 (0.25), residues: 472 sheet: 0.11 (0.16), residues: 1040 loop : -0.44 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 479 HIS 0.005 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 0.00249 ( 59) link_NAG-ASN : angle 1.75214 ( 177) link_ALPHA1-6 : bond 0.00593 ( 2) link_ALPHA1-6 : angle 1.87599 ( 6) link_BETA1-4 : bond 0.00819 ( 29) link_BETA1-4 : angle 2.56656 ( 87) link_ALPHA1-3 : bond 0.00931 ( 2) link_ALPHA1-3 : angle 2.26352 ( 6) hydrogen bonds : bond 0.03156 ( 911) hydrogen bonds : angle 5.04684 ( 2571) SS BOND : bond 0.00289 ( 48) SS BOND : angle 0.85832 ( 96) covalent geometry : bond 0.00343 (25392) covalent geometry : angle 0.57102 (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: 53 poor density : 136 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 626 MET cc_start: 0.7792 (ttt) cc_final: 0.7345 (ttt) REVERT: J 27 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.7960 (m-70) REVERT: H 75 ASP cc_start: 0.9263 (p0) cc_final: 0.8739 (p0) REVERT: H 78 LYS cc_start: 0.9399 (tptp) cc_final: 0.9061 (pttm) REVERT: E 104 MET cc_start: 0.9204 (ttm) cc_final: 0.8643 (tpp) REVERT: E 217 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: F 426 MET cc_start: 0.7497 (ptt) cc_final: 0.7258 (ptt) REVERT: X 626 MET cc_start: 0.8597 (ttm) cc_final: 0.8077 (ttm) REVERT: Y 634 GLU cc_start: 0.9122 (tt0) cc_final: 0.8749 (tt0) REVERT: Y 638 TYR cc_start: 0.9134 (m-10) cc_final: 0.8886 (m-10) outliers start: 53 outliers final: 29 residues processed: 177 average time/residue: 0.3309 time to fit residues: 96.5255 Evaluate side-chains 162 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain Z residue 539 VAL 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 K residue 189 HIS 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 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 371 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 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: 7.9990 chunk 97 optimal weight: 30.0000 chunk 265 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 117 optimal weight: 50.0000 chunk 230 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 HIS J 59 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.089673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.051847 restraints weight = 95351.980| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.89 r_work: 0.2759 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 25532 Z= 0.323 Angle : 0.720 11.726 34887 Z= 0.354 Chirality : 0.047 0.339 4207 Planarity : 0.004 0.053 4269 Dihedral : 7.197 58.684 5172 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 2.53 % Allowed : 10.99 % Favored : 86.48 % 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: -0.28 (0.16), residues: 2989 helix: 0.83 (0.25), residues: 479 sheet: -0.06 (0.16), residues: 1072 loop : -0.54 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 112 HIS 0.014 0.002 HIS K 189 PHE 0.021 0.002 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 0.00590 ( 59) link_NAG-ASN : angle 1.97727 ( 177) link_ALPHA1-6 : bond 0.00385 ( 2) link_ALPHA1-6 : angle 1.81014 ( 6) link_BETA1-4 : bond 0.00709 ( 29) link_BETA1-4 : angle 2.63401 ( 87) link_ALPHA1-3 : bond 0.00789 ( 2) link_ALPHA1-3 : angle 2.25123 ( 6) hydrogen bonds : bond 0.03565 ( 911) hydrogen bonds : angle 5.19478 ( 2571) SS BOND : bond 0.00484 ( 48) SS BOND : angle 1.06758 ( 96) covalent geometry : bond 0.00742 (25392) covalent geometry : angle 0.69450 (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 196 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 128 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 543 ASN cc_start: 0.8803 (m-40) cc_final: 0.8444 (m-40) REVERT: Z 633 LYS cc_start: 0.9385 (mmmt) cc_final: 0.9033 (mmmm) REVERT: H 75 ASP cc_start: 0.9286 (p0) cc_final: 0.8677 (p0) REVERT: H 78 LYS cc_start: 0.9433 (tptp) cc_final: 0.9110 (pttp) REVERT: G 107 ASP cc_start: 0.8960 (m-30) cc_final: 0.8713 (t0) REVERT: E 104 MET cc_start: 0.9277 (ttm) cc_final: 0.8718 (tpp) REVERT: E 217 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: E 288 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.7867 (p90) REVERT: F 426 MET cc_start: 0.7889 (ptt) cc_final: 0.7605 (ptt) REVERT: X 626 MET cc_start: 0.8726 (ttm) cc_final: 0.8501 (ttm) REVERT: Y 530 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8722 (mtp) REVERT: Y 616 ASN cc_start: 0.9255 (p0) cc_final: 0.9024 (p0) outliers start: 68 outliers final: 47 residues processed: 188 average time/residue: 0.3212 time to fit residues: 100.9359 Evaluate side-chains 175 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain Z residue 536 THR 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 202 THR Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 77 SER 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 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 286 VAL Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 323 ILE 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 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 Y residue 515 ILE Chi-restraints excluded: chain Y residue 520 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 20 optimal weight: 50.0000 chunk 213 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 282 optimal weight: 0.8980 chunk 109 optimal weight: 10.9990 chunk 58 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 294 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** K 189 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.091382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.053449 restraints weight = 93993.914| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.93 r_work: 0.2805 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25532 Z= 0.116 Angle : 0.584 12.099 34887 Z= 0.286 Chirality : 0.044 0.324 4207 Planarity : 0.004 0.052 4269 Dihedral : 6.592 57.953 5172 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 1.34 % Allowed : 12.85 % Favored : 85.80 % 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: 0.05 (0.16), residues: 2989 helix: 1.29 (0.25), residues: 471 sheet: 0.18 (0.17), residues: 1039 loop : -0.41 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 479 HIS 0.032 0.001 HIS J 27 PHE 0.023 0.001 PHE H 81 TYR 0.024 0.001 TYR L 49 ARG 0.006 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 59) link_NAG-ASN : angle 1.73055 ( 177) link_ALPHA1-6 : bond 0.00407 ( 2) link_ALPHA1-6 : angle 1.50562 ( 6) link_BETA1-4 : bond 0.00826 ( 29) link_BETA1-4 : angle 2.47306 ( 87) link_ALPHA1-3 : bond 0.01021 ( 2) link_ALPHA1-3 : angle 1.89997 ( 6) hydrogen bonds : bond 0.02980 ( 911) hydrogen bonds : angle 4.87314 ( 2571) SS BOND : bond 0.00296 ( 48) SS BOND : angle 0.89398 ( 96) covalent geometry : bond 0.00258 (25392) covalent geometry : angle 0.55715 (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 178 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 543 ASN cc_start: 0.8827 (m-40) cc_final: 0.8083 (t0) REVERT: Z 626 MET cc_start: 0.7898 (ttt) cc_final: 0.7648 (ttt) REVERT: J 59 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8269 (p0) REVERT: H 78 LYS cc_start: 0.9412 (tptp) cc_final: 0.9159 (tptp) REVERT: E 104 MET cc_start: 0.9182 (ttm) cc_final: 0.8724 (tpp) REVERT: E 161 MET cc_start: 0.9367 (tpt) cc_final: 0.9166 (tpt) REVERT: E 217 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: F 426 MET cc_start: 0.7501 (ptt) cc_final: 0.7251 (ptt) REVERT: X 626 MET cc_start: 0.8627 (ttm) cc_final: 0.8082 (ttm) REVERT: Y 616 ASN cc_start: 0.9188 (p0) cc_final: 0.8984 (p0) REVERT: Y 625 ASN cc_start: 0.9143 (t0) cc_final: 0.8645 (t0) REVERT: Y 638 TYR cc_start: 0.9122 (m-10) cc_final: 0.8872 (m-10) outliers start: 36 outliers final: 22 residues processed: 170 average time/residue: 0.3356 time to fit residues: 93.5241 Evaluate side-chains 155 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain J residue 59 ASN 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 196 CYS Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 ASN 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 286 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 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 446 VAL Chi-restraints excluded: chain Y residue 515 ILE 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: 5.9990 chunk 159 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** F 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.090262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.052307 restraints weight = 94837.300| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 4.89 r_work: 0.2780 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 25532 Z= 0.243 Angle : 0.656 11.736 34887 Z= 0.321 Chirality : 0.045 0.325 4207 Planarity : 0.004 0.054 4269 Dihedral : 6.659 57.854 5172 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.88 % Rotamer: Outliers : 2.31 % Allowed : 12.78 % 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: 1.07 (0.25), residues: 479 sheet: 0.08 (0.16), residues: 1066 loop : -0.49 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 112 HIS 0.006 0.001 HIS E 330 PHE 0.019 0.002 PHE H 81 TYR 0.019 0.001 TYR L 49 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 59) link_NAG-ASN : angle 1.83941 ( 177) link_ALPHA1-6 : bond 0.00117 ( 2) link_ALPHA1-6 : angle 1.64686 ( 6) link_BETA1-4 : bond 0.00747 ( 29) link_BETA1-4 : angle 2.51333 ( 87) link_ALPHA1-3 : bond 0.00869 ( 2) link_ALPHA1-3 : angle 1.94546 ( 6) hydrogen bonds : bond 0.03227 ( 911) hydrogen bonds : angle 4.92923 ( 2571) SS BOND : bond 0.00375 ( 48) SS BOND : angle 1.02859 ( 96) covalent geometry : bond 0.00562 (25392) covalent geometry : angle 0.63041 (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 192 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 130 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 530 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5236 (mmt) REVERT: H 78 LYS cc_start: 0.9450 (tptp) cc_final: 0.9169 (tptp) REVERT: E 104 MET cc_start: 0.9263 (ttm) cc_final: 0.8710 (tpp) REVERT: E 217 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: F 426 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7529 (ptt) REVERT: X 626 MET cc_start: 0.8664 (ttm) cc_final: 0.8184 (ttm) REVERT: Y 616 ASN cc_start: 0.9256 (p0) cc_final: 0.9053 (p0) outliers start: 62 outliers final: 47 residues processed: 182 average time/residue: 0.3189 time to fit residues: 96.3612 Evaluate side-chains 178 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 208 ASN 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 208 ASN Chi-restraints excluded: chain H residue 77 SER 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 181 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 424 ILE Chi-restraints excluded: chain G residue 425 ASN Chi-restraints excluded: chain G residue 465 THR 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 426 MET Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain X residue 535 MET Chi-restraints excluded: chain Y residue 515 ILE 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: 0.2980 chunk 258 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 117 optimal weight: 50.0000 chunk 224 optimal weight: 6.9990 chunk 1 optimal weight: 40.0000 chunk 127 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.091504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.053744 restraints weight = 94837.120| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.81 r_work: 0.2829 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3428 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 : 0.594 12.039 34887 Z= 0.291 Chirality : 0.044 0.316 4207 Planarity : 0.003 0.050 4269 Dihedral : 6.328 59.372 5172 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 1.64 % Allowed : 13.45 % 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: 0.04 (0.16), residues: 2989 helix: 1.24 (0.25), residues: 479 sheet: 0.21 (0.17), residues: 1043 loop : -0.44 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.003 0.001 HIS E 374 PHE 0.020 0.001 PHE H 81 TYR 0.021 0.001 TYR L 49 ARG 0.006 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 59) link_NAG-ASN : angle 1.71505 ( 177) link_ALPHA1-6 : bond 0.00173 ( 2) link_ALPHA1-6 : angle 1.65072 ( 6) link_BETA1-4 : bond 0.00796 ( 29) link_BETA1-4 : angle 2.42231 ( 87) link_ALPHA1-3 : bond 0.00942 ( 2) link_ALPHA1-3 : angle 1.67536 ( 6) hydrogen bonds : bond 0.02962 ( 911) hydrogen bonds : angle 4.78213 ( 2571) SS BOND : bond 0.00270 ( 48) SS BOND : angle 0.87509 ( 96) covalent geometry : bond 0.00302 (25392) covalent geometry : angle 0.56922 (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 182 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 543 ASN cc_start: 0.8817 (m-40) cc_final: 0.8089 (t0) REVERT: H 78 LYS cc_start: 0.9440 (tptp) cc_final: 0.9162 (tptp) REVERT: H 212 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8642 (mmtm) REVERT: G 271 MET cc_start: 0.8117 (mmm) cc_final: 0.7801 (mpp) REVERT: E 104 MET cc_start: 0.9206 (ttm) cc_final: 0.8728 (tpp) REVERT: E 217 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: F 426 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7359 (ptt) REVERT: X 626 MET cc_start: 0.8655 (ttm) cc_final: 0.7972 (ttm) REVERT: Y 616 ASN cc_start: 0.9222 (p0) cc_final: 0.9010 (p0) REVERT: Y 625 ASN cc_start: 0.9174 (t0) cc_final: 0.8713 (t0) REVERT: Y 638 TYR cc_start: 0.9119 (m-10) cc_final: 0.8912 (m-10) outliers start: 44 outliers final: 36 residues processed: 176 average time/residue: 0.3466 time to fit residues: 99.9449 Evaluate side-chains 173 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 605 CYS 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 181 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 424 ILE Chi-restraints excluded: chain G residue 465 THR 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 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 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 Y residue 515 ILE 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: 1.9990 chunk 263 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 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: 2.0586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.090973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053109 restraints weight = 94762.279| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.81 r_work: 0.2813 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25532 Z= 0.165 Angle : 0.607 12.170 34887 Z= 0.296 Chirality : 0.044 0.313 4207 Planarity : 0.004 0.050 4269 Dihedral : 6.277 57.563 5172 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 1.83 % Allowed : 13.30 % Favored : 84.87 % 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: 0.05 (0.16), residues: 2989 helix: 1.25 (0.25), residues: 478 sheet: 0.18 (0.16), residues: 1053 loop : -0.41 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 479 HIS 0.004 0.001 HIS J 27 PHE 0.019 0.001 PHE H 81 TYR 0.019 0.001 TYR L 49 ARG 0.007 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 59) link_NAG-ASN : angle 1.71942 ( 177) link_ALPHA1-6 : bond 0.00099 ( 2) link_ALPHA1-6 : angle 1.67343 ( 6) link_BETA1-4 : bond 0.00782 ( 29) link_BETA1-4 : angle 2.42529 ( 87) link_ALPHA1-3 : bond 0.00831 ( 2) link_ALPHA1-3 : angle 1.64297 ( 6) hydrogen bonds : bond 0.03015 ( 911) hydrogen bonds : angle 4.77727 ( 2571) SS BOND : bond 0.00295 ( 48) SS BOND : angle 0.85921 ( 96) covalent geometry : bond 0.00379 (25392) covalent geometry : angle 0.58237 (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: 49 poor density : 137 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 530 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.4947 (mmt) REVERT: Z 543 ASN cc_start: 0.8808 (m-40) cc_final: 0.8124 (t0) REVERT: H 78 LYS cc_start: 0.9451 (tptp) cc_final: 0.9178 (tptp) REVERT: H 212 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8674 (mmtm) REVERT: G 271 MET cc_start: 0.8148 (mmm) cc_final: 0.7840 (mpp) REVERT: E 104 MET cc_start: 0.9228 (ttm) cc_final: 0.8707 (tpp) REVERT: E 217 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: F 426 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7465 (ptt) REVERT: X 626 MET cc_start: 0.8683 (ttm) cc_final: 0.7879 (ttm) REVERT: Y 616 ASN cc_start: 0.9238 (p0) cc_final: 0.9026 (p0) REVERT: Y 638 TYR cc_start: 0.9128 (m-10) cc_final: 0.8873 (m-10) outliers start: 49 outliers final: 41 residues processed: 177 average time/residue: 0.3327 time to fit residues: 97.0796 Evaluate side-chains 178 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 208 ASN 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 89 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 181 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 424 ILE Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 120 VAL 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 426 MET 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 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: 0.8980 chunk 129 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 253 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 17 optimal weight: 30.0000 chunk 184 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 209 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.091621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053886 restraints weight = 94714.439| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.84 r_work: 0.2840 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3500 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= 0.127 Angle : 0.587 11.999 34887 Z= 0.287 Chirality : 0.044 0.308 4207 Planarity : 0.003 0.050 4269 Dihedral : 6.108 57.178 5172 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 1.68 % Allowed : 13.49 % 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: 0.15 (0.16), residues: 2989 helix: 1.35 (0.25), residues: 476 sheet: 0.29 (0.17), residues: 1043 loop : -0.38 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 479 HIS 0.004 0.001 HIS J 27 PHE 0.020 0.001 PHE H 81 TYR 0.018 0.001 TYR L 49 ARG 0.008 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 59) link_NAG-ASN : angle 1.66002 ( 177) link_ALPHA1-6 : bond 0.00161 ( 2) link_ALPHA1-6 : angle 1.64985 ( 6) link_BETA1-4 : bond 0.00811 ( 29) link_BETA1-4 : angle 2.38086 ( 87) link_ALPHA1-3 : bond 0.00830 ( 2) link_ALPHA1-3 : angle 1.50646 ( 6) hydrogen bonds : bond 0.02877 ( 911) hydrogen bonds : angle 4.68747 ( 2571) SS BOND : bond 0.00257 ( 48) SS BOND : angle 0.81504 ( 96) covalent geometry : bond 0.00290 (25392) covalent geometry : angle 0.56289 (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 188 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.8564 (mpp) cc_final: 0.8262 (mpp) REVERT: Z 530 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.5050 (mmt) REVERT: Z 543 ASN cc_start: 0.8816 (m-40) cc_final: 0.8154 (t0) REVERT: J 155 ASP cc_start: 0.9384 (m-30) cc_final: 0.8950 (p0) REVERT: H 78 LYS cc_start: 0.9445 (tptp) cc_final: 0.9178 (tptp) REVERT: H 212 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8669 (mmtm) REVERT: G 271 MET cc_start: 0.8130 (mmm) cc_final: 0.7817 (mpp) REVERT: E 104 MET cc_start: 0.9210 (ttm) cc_final: 0.8725 (tpp) REVERT: E 217 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: X 616 ASN cc_start: 0.9204 (m-40) cc_final: 0.8580 (p0) REVERT: X 626 MET cc_start: 0.8655 (ttm) cc_final: 0.8049 (ttm) REVERT: Y 616 ASN cc_start: 0.9244 (p0) cc_final: 0.9031 (p0) REVERT: Y 625 ASN cc_start: 0.9165 (t0) cc_final: 0.8689 (t0) REVERT: Y 638 TYR cc_start: 0.9139 (m-10) cc_final: 0.8889 (m-10) outliers start: 45 outliers final: 37 residues processed: 180 average time/residue: 0.3456 time to fit residues: 101.7164 Evaluate side-chains 176 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 208 ASN 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 89 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 181 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 465 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 120 VAL 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 126 CYS Chi-restraints excluded: chain F residue 202 THR 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 543 ASN Chi-restraints excluded: chain Y residue 515 ILE 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: 4.9990 chunk 192 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 72 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 231 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.088972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050266 restraints weight = 93096.812| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.70 r_work: 0.2748 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 25532 Z= 0.301 Angle : 0.719 12.393 34887 Z= 0.352 Chirality : 0.046 0.316 4207 Planarity : 0.004 0.048 4269 Dihedral : 6.456 58.331 5172 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 1.75 % Allowed : 13.41 % 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: -0.07 (0.16), residues: 2989 helix: 1.06 (0.25), residues: 479 sheet: 0.13 (0.16), residues: 1075 loop : -0.48 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 35 HIS 0.007 0.001 HIS E 330 PHE 0.021 0.002 PHE G 382 TYR 0.017 0.001 TYR L 49 ARG 0.008 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 59) link_NAG-ASN : angle 1.88955 ( 177) link_ALPHA1-6 : bond 0.00048 ( 2) link_ALPHA1-6 : angle 1.76034 ( 6) link_BETA1-4 : bond 0.00720 ( 29) link_BETA1-4 : angle 2.48033 ( 87) link_ALPHA1-3 : bond 0.00661 ( 2) link_ALPHA1-3 : angle 1.65637 ( 6) hydrogen bonds : bond 0.03327 ( 911) hydrogen bonds : angle 4.92490 ( 2571) SS BOND : bond 0.00433 ( 48) SS BOND : angle 1.00524 ( 96) covalent geometry : bond 0.00695 (25392) covalent geometry : angle 0.69642 (34515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16123.00 seconds wall clock time: 278 minutes 52.88 seconds (16732.88 seconds total)