Starting phenix.real_space_refine on Mon Aug 25 03:32:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnu_41426/08_2025/8tnu_41426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnu_41426/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tnu_41426/08_2025/8tnu_41426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnu_41426/08_2025/8tnu_41426.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tnu_41426/08_2025/8tnu_41426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnu_41426/08_2025/8tnu_41426.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.60, per 1000 atoms: 0.22 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: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.9 microseconds 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: 0.94 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: 4.04 Time building geometry restraints manager: 3.36 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 609)) selection = (chain 'F' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 609)) selection = (chain 'G' and (resid 32 through 58 or resid 66 through 398 or resid 412 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 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.670 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- 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 : 4.46 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.017 0.001 ARG X 542 TYR 0.041 0.002 TYR E 486 PHE 0.041 0.002 PHE H 81 TRP 0.018 0.002 TRP F 45 HIS 0.005 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00520 (25392) covalent geometry : angle 0.97132 (34515) SS BOND : bond 0.03816 ( 48) SS BOND : angle 5.55191 ( 96) hydrogen bonds : bond 0.13635 ( 911) hydrogen bonds : angle 6.77047 ( 2571) link_ALPHA1-3 : bond 0.00513 ( 2) link_ALPHA1-3 : angle 1.67368 ( 6) 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_NAG-ASN : bond 0.00301 ( 59) link_NAG-ASN : angle 2.24856 ( 177) *********************** 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 : 0.913 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: 0.1463 time to fit residues: 54.3587 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 : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0020 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 H 5 GLN H 80 GLN G 105 HIS E 246 GLN X 658 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.096809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.060715 restraints weight = 95874.870| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 5.08 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25532 Z= 0.114 Angle : 0.602 9.522 34887 Z= 0.295 Chirality : 0.044 0.302 4207 Planarity : 0.004 0.073 4269 Dihedral : 9.098 80.603 5172 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.67 % Allowed : 5.74 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 2989 helix: 0.35 (0.23), residues: 469 sheet: -0.00 (0.17), residues: 968 loop : -0.63 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 61 TYR 0.017 0.001 TYR H 187 PHE 0.028 0.001 PHE H 81 TRP 0.011 0.001 TRP G 96 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00250 (25392) covalent geometry : angle 0.57082 (34515) SS BOND : bond 0.00332 ( 48) SS BOND : angle 1.20437 ( 96) hydrogen bonds : bond 0.03546 ( 911) hydrogen bonds : angle 5.41240 ( 2571) link_ALPHA1-3 : bond 0.00953 ( 2) link_ALPHA1-3 : angle 2.19728 ( 6) link_ALPHA1-6 : bond 0.00269 ( 2) link_ALPHA1-6 : angle 1.76308 ( 6) link_BETA1-4 : bond 0.00880 ( 29) link_BETA1-4 : angle 2.72913 ( 87) link_NAG-ASN : bond 0.00190 ( 59) link_NAG-ASN : angle 1.76794 ( 177) *********************** 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 198 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.675 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: 0.5424 (mtp) cc_final: 0.4952 (ptp) REVERT: C 140 TYR cc_start: 0.4573 (t80) cc_final: 0.4180 (t80) REVERT: Z 603 ILE cc_start: 0.7536 (mm) cc_final: 0.6952 (tp) REVERT: H 75 ASP cc_start: 0.9147 (p0) cc_final: 0.8828 (p0) REVERT: H 78 LYS cc_start: 0.9169 (tptp) cc_final: 0.8791 (pttm) REVERT: L 49 TYR cc_start: 0.8905 (p90) cc_final: 0.8570 (p90) REVERT: L 62 PHE cc_start: 0.8679 (m-80) cc_final: 0.8409 (m-80) REVERT: L 189 HIS cc_start: 0.7549 (m-70) cc_final: 0.7345 (m-70) REVERT: X 584 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: Y 543 ASN cc_start: 0.7709 (m-40) cc_final: 0.7448 (m110) REVERT: Y 634 GLU cc_start: 0.8910 (tt0) cc_final: 0.8674 (tt0) outliers start: 18 outliers final: 12 residues processed: 191 average time/residue: 0.1342 time to fit residues: 41.6540 Evaluate side-chains 173 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 465 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 X residue 584 GLU 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 233 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 97 optimal weight: 0.0370 chunk 3 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 50.0000 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 overall best weight: 3.7664 ------------------------------------------------------------------------------- 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** H 105 HIS ** F 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.091554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.053492 restraints weight = 94802.429| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.89 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: 0.8445 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 25532 Z= 0.283 Angle : 0.715 9.596 34887 Z= 0.355 Chirality : 0.047 0.303 4207 Planarity : 0.004 0.059 4269 Dihedral : 7.667 68.454 5172 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.45 % Allowed : 8.53 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.16), residues: 2989 helix: 0.75 (0.25), residues: 479 sheet: -0.03 (0.16), residues: 1037 loop : -0.46 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG Z 542 TYR 0.012 0.002 TYR Z 638 PHE 0.023 0.002 PHE H 81 TRP 0.016 0.002 TRP X 628 HIS 0.007 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00645 (25392) covalent geometry : angle 0.68968 (34515) SS BOND : bond 0.00929 ( 48) SS BOND : angle 1.15694 ( 96) hydrogen bonds : bond 0.03703 ( 911) hydrogen bonds : angle 5.25489 ( 2571) link_ALPHA1-3 : bond 0.00900 ( 2) link_ALPHA1-3 : angle 2.21205 ( 6) link_ALPHA1-6 : bond 0.00487 ( 2) link_ALPHA1-6 : angle 1.82254 ( 6) link_BETA1-4 : bond 0.00737 ( 29) link_BETA1-4 : angle 2.73071 ( 87) link_NAG-ASN : bond 0.00449 ( 59) link_NAG-ASN : angle 1.81874 ( 177) *********************** 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 184 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 657 GLU cc_start: 0.9231 (tp30) cc_final: 0.8873 (tp30) REVERT: H 75 ASP cc_start: 0.9254 (p0) cc_final: 0.8790 (p0) REVERT: H 78 LYS cc_start: 0.9280 (tptp) cc_final: 0.8896 (pttm) REVERT: L 62 PHE cc_start: 0.8934 (m-80) cc_final: 0.8701 (m-80) REVERT: E 482 GLU cc_start: 0.9002 (tt0) cc_final: 0.8801 (tt0) REVERT: F 426 MET cc_start: 0.7585 (ptt) cc_final: 0.7266 (ptt) REVERT: Y 634 GLU cc_start: 0.9110 (tt0) cc_final: 0.8821 (tt0) outliers start: 39 outliers final: 27 residues processed: 173 average time/residue: 0.1411 time to fit residues: 39.8472 Evaluate side-chains 157 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 ILE 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 155 ASP Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL 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 38 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain Y residue 515 ILE Chi-restraints excluded: chain Y residue 608 VAL Chi-restraints excluded: chain Y residue 615 SER Chi-restraints excluded: chain Y residue 659 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 13 optimal weight: 6.9990 chunk 296 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 288 optimal weight: 0.8980 chunk 71 optimal weight: 30.0000 chunk 137 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS L 166 GLN F 478 ASN Y 543 ASN Y 616 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.091345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.053517 restraints weight = 94238.648| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.92 r_work: 0.2807 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25532 Z= 0.212 Angle : 0.620 10.298 34887 Z= 0.305 Chirality : 0.045 0.333 4207 Planarity : 0.004 0.060 4269 Dihedral : 6.985 57.268 5172 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.16 % Allowed : 9.61 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.16), residues: 2989 helix: 1.04 (0.25), residues: 473 sheet: 0.11 (0.16), residues: 1058 loop : -0.38 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 617 TYR 0.015 0.001 TYR K 49 PHE 0.023 0.002 PHE H 81 TRP 0.013 0.001 TRP E 96 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00485 (25392) covalent geometry : angle 0.59313 (34515) SS BOND : bond 0.00345 ( 48) SS BOND : angle 0.94143 ( 96) hydrogen bonds : bond 0.03243 ( 911) hydrogen bonds : angle 5.01996 ( 2571) link_ALPHA1-3 : bond 0.00912 ( 2) link_ALPHA1-3 : angle 2.27356 ( 6) link_ALPHA1-6 : bond 0.00552 ( 2) link_ALPHA1-6 : angle 1.79242 ( 6) link_BETA1-4 : bond 0.00829 ( 29) link_BETA1-4 : angle 2.58212 ( 87) link_NAG-ASN : bond 0.00318 ( 59) link_NAG-ASN : angle 1.74304 ( 177) *********************** 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 201 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 626 MET cc_start: 0.7671 (ttt) cc_final: 0.7362 (ttt) REVERT: Z 633 LYS cc_start: 0.9301 (mmmt) cc_final: 0.8977 (mmmt) REVERT: J 27 HIS cc_start: 0.8544 (OUTLIER) cc_final: 0.7810 (m-70) REVERT: H 75 ASP cc_start: 0.9292 (p0) cc_final: 0.8697 (p0) REVERT: H 78 LYS cc_start: 0.9321 (tptp) cc_final: 0.8982 (pttm) REVERT: H 82 PHE cc_start: 0.9544 (m-10) cc_final: 0.9303 (m-80) REVERT: L 62 PHE cc_start: 0.8947 (m-80) cc_final: 0.8735 (m-80) REVERT: G 475 MET cc_start: 0.9028 (tpp) cc_final: 0.8797 (tpp) REVERT: E 104 MET cc_start: 0.9238 (ttm) cc_final: 0.8845 (tpp) REVERT: F 426 MET cc_start: 0.7428 (ptt) cc_final: 0.7202 (ptt) REVERT: Y 634 GLU cc_start: 0.9112 (tt0) cc_final: 0.8837 (tt0) REVERT: Y 638 TYR cc_start: 0.9151 (m-10) cc_final: 0.8911 (m-10) outliers start: 58 outliers final: 34 residues processed: 185 average time/residue: 0.1435 time to fit residues: 43.6973 Evaluate side-chains 170 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 Z residue 606 THR Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 636 SER Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain 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 89 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 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 374 HIS 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 616 ASN 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 41 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 243 optimal weight: 0.9980 chunk 251 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 30.0000 chunk 253 optimal weight: 2.9990 chunk 212 optimal weight: 0.0060 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN K 90 GLN H 27 HIS E 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.092529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.054763 restraints weight = 94122.331| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 4.94 r_work: 0.2847 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25532 Z= 0.107 Angle : 0.573 10.884 34887 Z= 0.280 Chirality : 0.044 0.314 4207 Planarity : 0.003 0.052 4269 Dihedral : 6.588 56.953 5172 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.42 % Allowed : 11.03 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.16), residues: 2989 helix: 1.26 (0.25), residues: 472 sheet: 0.28 (0.16), residues: 1041 loop : -0.35 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Z 542 TYR 0.027 0.001 TYR L 49 PHE 0.022 0.001 PHE H 81 TRP 0.012 0.001 TRP F 479 HIS 0.003 0.001 HIS J 27 Details of bonding type rmsd covalent geometry : bond 0.00238 (25392) covalent geometry : angle 0.54738 (34515) SS BOND : bond 0.00256 ( 48) SS BOND : angle 0.84434 ( 96) hydrogen bonds : bond 0.02972 ( 911) hydrogen bonds : angle 4.83699 ( 2571) link_ALPHA1-3 : bond 0.01033 ( 2) link_ALPHA1-3 : angle 2.02716 ( 6) link_ALPHA1-6 : bond 0.00506 ( 2) link_ALPHA1-6 : angle 1.65746 ( 6) link_BETA1-4 : bond 0.00834 ( 29) link_BETA1-4 : angle 2.47721 ( 87) link_NAG-ASN : bond 0.00177 ( 59) link_NAG-ASN : angle 1.63565 ( 177) *********************** 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 185 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 626 MET cc_start: 0.7605 (ttt) cc_final: 0.7236 (ttt) REVERT: Z 632 ASP cc_start: 0.8829 (t70) cc_final: 0.8585 (t0) REVERT: Z 633 LYS cc_start: 0.9302 (mmmt) cc_final: 0.8935 (mmmt) REVERT: J 27 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7703 (m-70) REVERT: K 90 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8152 (pp30) REVERT: H 75 ASP cc_start: 0.9288 (p0) cc_final: 0.8841 (p0) REVERT: H 78 LYS cc_start: 0.9300 (tptp) cc_final: 0.8937 (pttm) REVERT: L 62 PHE cc_start: 0.8926 (m-80) cc_final: 0.8686 (m-80) REVERT: E 104 MET cc_start: 0.9212 (ttm) cc_final: 0.8881 (tpp) REVERT: F 426 MET cc_start: 0.7272 (ptt) cc_final: 0.7038 (ptt) REVERT: X 654 GLU cc_start: 0.9046 (tp30) cc_final: 0.8695 (tp30) REVERT: Y 634 GLU cc_start: 0.9085 (tt0) cc_final: 0.8844 (tt0) REVERT: Y 638 TYR cc_start: 0.9117 (m-10) cc_final: 0.8883 (m-10) outliers start: 38 outliers final: 24 residues processed: 179 average time/residue: 0.1469 time to fit residues: 43.3585 Evaluate side-chains 165 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU 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 465 THR 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 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 202 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain X residue 587 LEU Chi-restraints excluded: chain Y residue 608 VAL Chi-restraints excluded: chain Y residue 654 GLU 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 50 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 32 optimal weight: 40.0000 chunk 131 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 265 optimal weight: 0.2980 chunk 190 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN E 80 ASN F 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.090629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.052472 restraints weight = 94540.971| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.94 r_work: 0.2804 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 25532 Z= 0.249 Angle : 0.655 10.743 34887 Z= 0.323 Chirality : 0.045 0.319 4207 Planarity : 0.004 0.049 4269 Dihedral : 6.670 58.115 5172 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 2.01 % Allowed : 11.44 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.16), residues: 2989 helix: 1.13 (0.25), residues: 473 sheet: 0.17 (0.16), residues: 1048 loop : -0.36 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG Z 542 TYR 0.023 0.001 TYR L 49 PHE 0.021 0.002 PHE H 81 TRP 0.012 0.001 TRP X 623 HIS 0.006 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00573 (25392) covalent geometry : angle 0.63030 (34515) SS BOND : bond 0.00370 ( 48) SS BOND : angle 0.98101 ( 96) hydrogen bonds : bond 0.03306 ( 911) hydrogen bonds : angle 4.93711 ( 2571) link_ALPHA1-3 : bond 0.00874 ( 2) link_ALPHA1-3 : angle 2.09090 ( 6) link_ALPHA1-6 : bond 0.00298 ( 2) link_ALPHA1-6 : angle 1.65904 ( 6) link_BETA1-4 : bond 0.00750 ( 29) link_BETA1-4 : angle 2.52847 ( 87) link_NAG-ASN : bond 0.00415 ( 59) link_NAG-ASN : angle 1.77361 ( 177) *********************** 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 185 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.4137 (ptp) cc_final: 0.3758 (ptt) REVERT: Z 626 MET cc_start: 0.7785 (ttt) cc_final: 0.7387 (ttt) REVERT: Z 633 LYS cc_start: 0.9350 (mmmt) cc_final: 0.8949 (mmmt) REVERT: J 27 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8101 (m-70) REVERT: H 75 ASP cc_start: 0.9326 (p0) cc_final: 0.8811 (p0) REVERT: H 78 LYS cc_start: 0.9322 (tptp) cc_final: 0.8998 (pttm) REVERT: L 62 PHE cc_start: 0.8988 (m-80) cc_final: 0.8779 (m-80) REVERT: E 104 MET cc_start: 0.9287 (ttm) cc_final: 0.8619 (tpp) REVERT: E 217 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: Y 634 GLU cc_start: 0.9091 (tt0) cc_final: 0.8795 (tt0) outliers start: 54 outliers final: 39 residues processed: 176 average time/residue: 0.1485 time to fit residues: 43.3742 Evaluate side-chains 170 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 LYS 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 Z residue 606 THR Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 17 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 139 optimal weight: 50.0000 chunk 5 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 278 optimal weight: 2.9990 chunk 279 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 72 optimal weight: 40.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 HIS K 90 GLN L 124 GLN E 80 ASN E 428 GLN F 352 HIS F 432 GLN Y 616 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.090134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052187 restraints weight = 94661.114| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.90 r_work: 0.2775 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25532 Z= 0.267 Angle : 0.682 11.582 34887 Z= 0.336 Chirality : 0.046 0.336 4207 Planarity : 0.004 0.050 4269 Dihedral : 6.781 57.550 5172 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.58 % Rotamer: Outliers : 2.09 % Allowed : 12.00 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.16), residues: 2989 helix: 0.92 (0.25), residues: 478 sheet: 0.06 (0.16), residues: 1090 loop : -0.43 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Z 542 TYR 0.025 0.001 TYR L 49 PHE 0.021 0.002 PHE H 81 TRP 0.014 0.002 TRP G 112 HIS 0.007 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00615 (25392) covalent geometry : angle 0.65631 (34515) SS BOND : bond 0.00411 ( 48) SS BOND : angle 1.07342 ( 96) hydrogen bonds : bond 0.03382 ( 911) hydrogen bonds : angle 5.00705 ( 2571) link_ALPHA1-3 : bond 0.00835 ( 2) link_ALPHA1-3 : angle 1.92862 ( 6) link_ALPHA1-6 : bond 0.00164 ( 2) link_ALPHA1-6 : angle 1.62462 ( 6) link_BETA1-4 : bond 0.00740 ( 29) link_BETA1-4 : angle 2.54712 ( 87) link_NAG-ASN : bond 0.00480 ( 59) link_NAG-ASN : angle 1.91721 ( 177) *********************** 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 187 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 131 time to evaluate : 0.932 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: 0.4223 (ptp) cc_final: 0.3849 (ptt) REVERT: K 90 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8476 (pp30) REVERT: G 107 ASP cc_start: 0.8855 (m-30) cc_final: 0.8647 (t0) REVERT: E 104 MET cc_start: 0.9266 (ttm) cc_final: 0.8726 (tpp) REVERT: E 217 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: E 288 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8311 (p90) outliers start: 56 outliers final: 43 residues processed: 177 average time/residue: 0.1372 time to fit residues: 40.1745 Evaluate side-chains 172 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 636 SER Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain G residue 89 VAL 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 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 14 optimal weight: 50.0000 chunk 125 optimal weight: 20.0000 chunk 239 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 191 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 95 optimal weight: 30.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 90 GLN E 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.091578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.054133 restraints weight = 94491.454| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.85 r_work: 0.2830 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25532 Z= 0.123 Angle : 0.603 12.294 34887 Z= 0.294 Chirality : 0.044 0.321 4207 Planarity : 0.003 0.049 4269 Dihedral : 6.400 59.201 5172 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 1.68 % Allowed : 12.85 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.16), residues: 2989 helix: 1.20 (0.25), residues: 473 sheet: 0.22 (0.16), residues: 1054 loop : -0.38 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 542 TYR 0.023 0.001 TYR L 49 PHE 0.022 0.001 PHE H 81 TRP 0.014 0.001 TRP F 479 HIS 0.014 0.001 HIS J 27 Details of bonding type rmsd covalent geometry : bond 0.00278 (25392) covalent geometry : angle 0.57792 (34515) SS BOND : bond 0.00263 ( 48) SS BOND : angle 0.88417 ( 96) hydrogen bonds : bond 0.03020 ( 911) hydrogen bonds : angle 4.82079 ( 2571) link_ALPHA1-3 : bond 0.00924 ( 2) link_ALPHA1-3 : angle 1.69723 ( 6) link_ALPHA1-6 : bond 0.00178 ( 2) link_ALPHA1-6 : angle 1.63866 ( 6) link_BETA1-4 : bond 0.00793 ( 29) link_BETA1-4 : angle 2.43945 ( 87) link_NAG-ASN : bond 0.00211 ( 59) link_NAG-ASN : angle 1.74099 ( 177) *********************** 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 185 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.4136 (ptp) cc_final: 0.3814 (ptt) REVERT: H 75 ASP cc_start: 0.9361 (p0) cc_final: 0.8707 (p0) REVERT: H 78 LYS cc_start: 0.9334 (tptp) cc_final: 0.9034 (pttm) REVERT: G 107 ASP cc_start: 0.8831 (m-30) cc_final: 0.8597 (t0) REVERT: E 104 MET cc_start: 0.9230 (ttm) cc_final: 0.8746 (tpp) REVERT: E 161 MET cc_start: 0.9339 (tpt) cc_final: 0.9115 (tpt) REVERT: E 217 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.8121 (m-80) outliers start: 45 outliers final: 34 residues processed: 177 average time/residue: 0.1290 time to fit residues: 38.3833 Evaluate side-chains 168 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 636 SER Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 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 424 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 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 216 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 20 optimal weight: 50.0000 chunk 115 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 256 optimal weight: 0.3980 chunk 184 optimal weight: 0.4980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN E 80 ASN X 543 ASN Y 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.091215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053613 restraints weight = 94472.809| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 4.95 r_work: 0.2823 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25532 Z= 0.161 Angle : 0.616 12.696 34887 Z= 0.300 Chirality : 0.044 0.313 4207 Planarity : 0.003 0.049 4269 Dihedral : 6.311 58.416 5172 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 1.75 % Allowed : 12.85 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.16), residues: 2989 helix: 1.19 (0.25), residues: 477 sheet: 0.25 (0.16), residues: 1052 loop : -0.39 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 542 TYR 0.020 0.001 TYR L 49 PHE 0.021 0.001 PHE H 81 TRP 0.022 0.001 TRP F 479 HIS 0.004 0.001 HIS J 27 Details of bonding type rmsd covalent geometry : bond 0.00371 (25392) covalent geometry : angle 0.59206 (34515) SS BOND : bond 0.00322 ( 48) SS BOND : angle 0.95061 ( 96) hydrogen bonds : bond 0.03018 ( 911) hydrogen bonds : angle 4.77760 ( 2571) link_ALPHA1-3 : bond 0.00856 ( 2) link_ALPHA1-3 : angle 1.64694 ( 6) link_ALPHA1-6 : bond 0.00109 ( 2) link_ALPHA1-6 : angle 1.67051 ( 6) link_BETA1-4 : bond 0.00788 ( 29) link_BETA1-4 : angle 2.42666 ( 87) link_NAG-ASN : bond 0.00257 ( 59) link_NAG-ASN : angle 1.72526 ( 177) *********************** 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 181 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.4183 (ptp) cc_final: 0.3866 (ptt) REVERT: H 75 ASP cc_start: 0.9348 (p0) cc_final: 0.8662 (p0) REVERT: H 78 LYS cc_start: 0.9349 (tptp) cc_final: 0.9044 (pttm) REVERT: L 195 GLU cc_start: 0.8986 (pm20) cc_final: 0.8705 (tp30) REVERT: E 104 MET cc_start: 0.9238 (ttm) cc_final: 0.8705 (tpp) REVERT: E 217 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: E 288 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8075 (p90) outliers start: 47 outliers final: 40 residues processed: 172 average time/residue: 0.1351 time to fit residues: 38.7283 Evaluate side-chains 174 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 636 SER Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain G residue 89 VAL 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 465 THR Chi-restraints excluded: chain E residue 36 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 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 288 PHE 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 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 100 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 284 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 398 ASN E 80 ASN ** X 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.091332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.053658 restraints weight = 94987.130| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.97 r_work: 0.2818 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25532 Z= 0.158 Angle : 0.618 12.604 34887 Z= 0.302 Chirality : 0.044 0.311 4207 Planarity : 0.004 0.049 4269 Dihedral : 6.251 57.429 5172 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 1.64 % Allowed : 13.34 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 2989 helix: 1.23 (0.25), residues: 477 sheet: 0.28 (0.17), residues: 1050 loop : -0.39 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 542 TYR 0.020 0.001 TYR L 49 PHE 0.021 0.001 PHE H 81 TRP 0.020 0.001 TRP F 479 HIS 0.005 0.001 HIS J 27 Details of bonding type rmsd covalent geometry : bond 0.00365 (25392) covalent geometry : angle 0.59452 (34515) SS BOND : bond 0.00282 ( 48) SS BOND : angle 0.90728 ( 96) hydrogen bonds : bond 0.02989 ( 911) hydrogen bonds : angle 4.73666 ( 2571) link_ALPHA1-3 : bond 0.00816 ( 2) link_ALPHA1-3 : angle 1.59188 ( 6) link_ALPHA1-6 : bond 0.00116 ( 2) link_ALPHA1-6 : angle 1.67001 ( 6) link_BETA1-4 : bond 0.00781 ( 29) link_BETA1-4 : angle 2.41986 ( 87) link_NAG-ASN : bond 0.00254 ( 59) link_NAG-ASN : angle 1.71925 ( 177) ********************** 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 181 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.4137 (ptp) cc_final: 0.3833 (ptt) REVERT: H 75 ASP cc_start: 0.9342 (p0) cc_final: 0.8808 (p0) REVERT: H 78 LYS cc_start: 0.9354 (tptp) cc_final: 0.9016 (pttp) REVERT: H 212 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8649 (mmtm) REVERT: E 104 MET cc_start: 0.9238 (ttm) cc_final: 0.8699 (tpp) REVERT: E 161 MET cc_start: 0.9325 (tpt) cc_final: 0.9096 (tpt) REVERT: E 217 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: E 288 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8044 (p90) outliers start: 44 outliers final: 39 residues processed: 172 average time/residue: 0.1360 time to fit residues: 38.9122 Evaluate side-chains 175 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 605 CYS Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 636 SER Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain G residue 89 VAL 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 465 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 288 PHE 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 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 67 optimal weight: 20.0000 chunk 290 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 263 optimal weight: 7.9990 chunk 37 optimal weight: 50.0000 chunk 282 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 104 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 119 GLN F 432 GLN ** X 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.088397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.049235 restraints weight = 95452.132| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 4.77 r_work: 0.2720 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 25532 Z= 0.370 Angle : 0.786 13.033 34887 Z= 0.385 Chirality : 0.048 0.343 4207 Planarity : 0.004 0.047 4269 Dihedral : 6.949 58.970 5172 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 1.71 % Allowed : 13.30 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.16), residues: 2989 helix: 0.81 (0.25), residues: 478 sheet: 0.07 (0.16), residues: 1077 loop : -0.54 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.024 0.002 TYR L 49 PHE 0.024 0.002 PHE Z 522 TRP 0.021 0.002 TRP F 427 HIS 0.007 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00848 (25392) covalent geometry : angle 0.76053 (34515) SS BOND : bond 0.00509 ( 48) SS BOND : angle 1.18147 ( 96) hydrogen bonds : bond 0.03692 ( 911) hydrogen bonds : angle 5.16397 ( 2571) link_ALPHA1-3 : bond 0.00570 ( 2) link_ALPHA1-3 : angle 1.85443 ( 6) link_ALPHA1-6 : bond 0.00072 ( 2) link_ALPHA1-6 : angle 1.78743 ( 6) link_BETA1-4 : bond 0.00699 ( 29) link_BETA1-4 : angle 2.62047 ( 87) link_NAG-ASN : bond 0.00753 ( 59) link_NAG-ASN : angle 2.14394 ( 177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7213.31 seconds wall clock time: 124 minutes 5.42 seconds (7445.42 seconds total)