Starting phenix.real_space_refine on Fri Mar 6 20:07:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ll1_23411/03_2026/7ll1_23411.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ll1_23411/03_2026/7ll1_23411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ll1_23411/03_2026/7ll1_23411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ll1_23411/03_2026/7ll1_23411.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ll1_23411/03_2026/7ll1_23411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ll1_23411/03_2026/7ll1_23411.map" } resolution = 3.73 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= 0.004 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10164 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 16131 2.51 5 N 4329 2.21 5 O 5166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25773 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3533 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1205 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain: "C" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3533 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "D" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1205 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain: "G" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3533 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "I" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1205 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain: "H" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1729 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 213} Chain: "L" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1729 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 213} Chain: "F" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 203} Chain: "J" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1729 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 213} Chain: "K" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 203} Chain: "M" 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: "N" 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: "O" 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: 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: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "b" 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: "c" 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: "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: 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: "f" 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: "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: 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: "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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "l" 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: "m" 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: "n" 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: "o" 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: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 5.46, per 1000 atoms: 0.21 Number of scatterers: 25773 At special positions: 0 Unit cell: (176.04, 169.56, 133.92, 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 147 16.00 O 5166 8.00 N 4329 7.00 C 16131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 141 " - pdb=" SG CYS H 197 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 141 " - pdb=" SG CYS E 197 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 141 " - pdb=" SG CYS J 197 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN a 4 " - " MAN a 5 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " " BMA k 3 " - " MAN k 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA a 3 " - " MAN a 6 " " BMA k 3 " - " MAN k 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 355 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 355 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 363 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 88 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 363 " " NAG d 1 " - " ASN C 386 " " NAG e 1 " - " ASN C 392 " " NAG f 1 " - " ASN C 88 " " NAG g 1 " - " ASN G 156 " " NAG h 1 " - " ASN G 160 " " NAG i 1 " - " ASN G 234 " " NAG j 1 " - " ASN G 262 " " NAG k 1 " - " ASN G 276 " " NAG l 1 " - " ASN G 332 " " NAG m 1 " - " ASN G 363 " " NAG n 1 " - " ASN G 386 " " NAG o 1 " - " ASN G 392 " " NAG p 1 " - " ASN G 88 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5826 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 58 sheets defined 21.0% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.031A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 483 removed outlier: 4.072A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 removed outlier: 4.268A pdb=" N LEU B 520 " --> pdb=" O ALA B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.137A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 547 removed outlier: 5.850A pdb=" N GLY B 547 " --> pdb=" O LEU B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 544 through 547' Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 566 through 571 Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.558A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.721A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.668A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.684A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.509A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.224A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.737A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.243A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 521 removed outlier: 4.539A pdb=" N LEU D 520 " --> pdb=" O ALA D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 547 removed outlier: 3.985A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 553 Processing helix chain 'D' and resid 566 through 571 Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.556A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.653A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.971A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.577A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS D 655 " --> pdb=" O ASN D 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 Processing helix chain 'G' and resid 99 through 117 Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.605A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.827A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 483 removed outlier: 4.057A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 through 521 removed outlier: 4.426A pdb=" N LEU I 520 " --> pdb=" O ALA I 517 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.695A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 547 removed outlier: 3.969A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY I 547 " --> pdb=" O ASN I 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 553 Processing helix chain 'I' and resid 566 through 571 Processing helix chain 'I' and resid 572 through 596 removed outlier: 3.590A pdb=" N ASP I 589 " --> pdb=" O ARG I 585 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP I 596 " --> pdb=" O LEU I 592 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 625 removed outlier: 3.698A pdb=" N TRP I 623 " --> pdb=" O LEU I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 636 removed outlier: 4.038A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU I 634 " --> pdb=" O GLN I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 664 removed outlier: 3.671A pdb=" N GLY I 644 " --> pdb=" O GLN I 640 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS I 655 " --> pdb=" O ASN I 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.876A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'H' and resid 157 through 159 No H-bonds generated for 'chain 'H' and resid 157 through 159' Processing helix chain 'H' and resid 188 through 190 No H-bonds generated for 'chain 'H' and resid 188 through 190' Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.935A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 183 through 189 removed outlier: 3.632A pdb=" N HIS F 189 " --> pdb=" O ASP F 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.953A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 129 through 134 removed outlier: 3.881A pdb=" N GLY J 134 " --> pdb=" O LYS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'J' and resid 188 through 192 removed outlier: 4.181A pdb=" N GLY J 191 " --> pdb=" O SER J 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.455A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.923A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.445A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 361 removed outlier: 6.619A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.777A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.315A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.744A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.777A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.315A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.547A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.494A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.844A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.341A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.612A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 259 through 261 removed outlier: 10.546A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 315 through 323 removed outlier: 6.702A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.553A pdb=" N VAL I 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL G 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR I 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N TYR G 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N CYS I 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.732A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.351A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.667A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.164A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.801A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 271 through 273 removed outlier: 10.912A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.801A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 12.164A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 301 through 312 removed outlier: 6.713A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.790A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.624A pdb=" N PHE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 121 through 125 removed outlier: 4.621A pdb=" N ALA H 138 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL H 185 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY H 140 " --> pdb=" O VAL H 183 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL H 183 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU H 142 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER H 181 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS H 144 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU H 179 " --> pdb=" O LYS H 144 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 151 through 155 Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.408A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.408A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.402A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AE2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.505A pdb=" N GLN E 10 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.505A pdb=" N GLN E 10 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 121 through 125 removed outlier: 4.974A pdb=" N ALA E 138 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL E 185 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY E 140 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL E 183 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU E 142 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER E 181 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS E 144 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU E 179 " --> pdb=" O LYS E 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 121 through 125 removed outlier: 4.974A pdb=" N ALA E 138 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL E 185 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY E 140 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL E 183 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU E 142 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER E 181 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS E 144 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU E 179 " --> pdb=" O LYS E 144 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 151 through 155 Processing sheet with id=AE8, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.398A pdb=" N LEU F 11 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.398A pdb=" N LEU F 11 " --> pdb=" O ASP F 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.331A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 153 through 155 removed outlier: 4.579A pdb=" N TRP F 148 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.848A pdb=" N ILE J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.671A pdb=" N PHE J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 121 through 125 removed outlier: 3.645A pdb=" N PHE J 123 " --> pdb=" O LEU J 142 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA J 138 " --> pdb=" O VAL J 185 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL J 185 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY J 140 " --> pdb=" O VAL J 183 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL J 183 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU J 142 " --> pdb=" O SER J 181 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER J 181 " --> pdb=" O LEU J 142 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS J 144 " --> pdb=" O LEU J 179 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU J 179 " --> pdb=" O LYS J 144 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 151 through 155 Processing sheet with id=AF9, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.236A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR K 49 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.236A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 114 through 118 removed outlier: 5.455A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.468A pdb=" N TRP K 148 " --> pdb=" O GLN K 155 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2565 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: 4.66 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4735 1.32 - 1.44: 6171 1.44 - 1.57: 15189 1.57 - 1.69: 2 1.69 - 1.82: 195 Bond restraints: 26292 Sorted by residual: bond pdb=" CA PRO C 437 " pdb=" C PRO C 437 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.83e+01 bond pdb=" C2 MAN a 4 " pdb=" O2 MAN a 4 " ideal model delta sigma weight residual 1.407 1.490 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C4 NAG e 1 " pdb=" O4 NAG e 1 " ideal model delta sigma weight residual 1.409 1.492 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C4 NAG U 1 " pdb=" O4 NAG U 1 " ideal model delta sigma weight residual 1.409 1.492 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C2 MAN k 4 " pdb=" O2 MAN k 4 " ideal model delta sigma weight residual 1.407 1.489 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 26287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 34372 4.03 - 8.06: 1318 8.06 - 12.10: 13 12.10 - 16.13: 5 16.13 - 20.16: 4 Bond angle restraints: 35712 Sorted by residual: angle pdb=" CA VAL C 89 " pdb=" CB VAL C 89 " pdb=" CG1 VAL C 89 " ideal model delta sigma weight residual 110.40 130.56 -20.16 1.70e+00 3.46e-01 1.41e+02 angle pdb=" CA VAL A 89 " pdb=" CB VAL A 89 " pdb=" CG1 VAL A 89 " ideal model delta sigma weight residual 110.40 129.91 -19.51 1.70e+00 3.46e-01 1.32e+02 angle pdb=" CA VAL G 89 " pdb=" CB VAL G 89 " pdb=" CG1 VAL G 89 " ideal model delta sigma weight residual 110.40 129.03 -18.63 1.70e+00 3.46e-01 1.20e+02 angle pdb=" CA ILE G 84 " pdb=" CB ILE G 84 " pdb=" CG1 ILE G 84 " ideal model delta sigma weight residual 110.40 127.61 -17.21 1.70e+00 3.46e-01 1.02e+02 angle pdb=" N VAL C 89 " pdb=" CA VAL C 89 " pdb=" C VAL C 89 " ideal model delta sigma weight residual 109.55 122.23 -12.68 1.38e+00 5.25e-01 8.45e+01 ... (remaining 35707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 15706 21.67 - 43.34: 946 43.34 - 65.01: 227 65.01 - 86.68: 206 86.68 - 108.35: 123 Dihedral angle restraints: 17208 sinusoidal: 8169 harmonic: 9039 Sorted by residual: dihedral pdb=" C VAL C 89 " pdb=" N VAL C 89 " pdb=" CA VAL C 89 " pdb=" CB VAL C 89 " ideal model delta harmonic sigma weight residual -122.00 -149.50 27.50 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C VAL G 89 " pdb=" N VAL G 89 " pdb=" CA VAL G 89 " pdb=" CB VAL G 89 " ideal model delta harmonic sigma weight residual -122.00 -149.26 27.26 0 2.50e+00 1.60e-01 1.19e+02 dihedral pdb=" C VAL A 89 " pdb=" N VAL A 89 " pdb=" CA VAL A 89 " pdb=" CB VAL A 89 " ideal model delta harmonic sigma weight residual -122.00 -148.97 26.97 0 2.50e+00 1.60e-01 1.16e+02 ... (remaining 17205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.300: 4289 0.300 - 0.600: 56 0.600 - 0.900: 0 0.900 - 1.200: 3 1.200 - 1.500: 11 Chirality restraints: 4359 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.79e+03 chirality pdb=" C1 BMA c 3 " pdb=" O4 NAG c 2 " pdb=" C2 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.77e+03 chirality pdb=" C1 BMA m 3 " pdb=" O4 NAG m 2 " pdb=" C2 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.76e+03 ... (remaining 4356 not shown) Planarity restraints: 4446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 88 " -0.139 2.00e-02 2.50e+03 1.48e-01 2.73e+02 pdb=" CG ASN C 88 " 0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C 88 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 88 " 0.229 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " -0.179 2.00e-02 2.50e+03 1.48e-01 2.73e+02 pdb=" C7 NAG Z 2 " 0.058 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " -0.133 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " 0.236 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 88 " -0.141 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN G 88 " 0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN G 88 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN G 88 " 0.217 2.00e-02 2.50e+03 pdb=" C1 NAG p 1 " -0.175 2.00e-02 2.50e+03 ... (remaining 4443 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 5 2.53 - 3.12: 19183 3.12 - 3.72: 38004 3.72 - 4.31: 55985 4.31 - 4.90: 90917 Nonbonded interactions: 204094 Sorted by model distance: nonbonded pdb=" OE2 GLU A 102 " pdb=" CD1 ILE D 559 " model vdw 1.939 3.460 nonbonded pdb=" CD1 ILE B 559 " pdb=" CG2 THR G 106 " model vdw 2.457 3.880 nonbonded pdb=" N ALA K 50 " pdb=" O ALA K 50 " model vdw 2.521 2.496 nonbonded pdb=" N ALA F 50 " pdb=" O ALA F 50 " model vdw 2.523 2.496 nonbonded pdb=" N ALA L 50 " pdb=" O ALA L 50 " model vdw 2.523 2.496 ... (remaining 204089 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'a' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.880 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.100 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 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 : 0.014 0.083 26445 Z= 0.821 Angle : 1.978 20.162 36126 Z= 1.230 Chirality : 0.133 1.500 4359 Planarity : 0.017 0.203 4407 Dihedral : 19.959 108.354 11247 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.79 % Favored : 92.82 % Rotamer: Outliers : 1.46 % Allowed : 7.61 % Favored : 90.93 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.71 (0.14), residues: 3093 helix: -2.09 (0.18), residues: 525 sheet: -0.24 (0.18), residues: 813 loop : -1.24 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 298 TYR 0.183 0.028 TYR A 217 PHE 0.065 0.013 PHE K 71 TRP 0.153 0.024 TRP A 96 HIS 0.018 0.005 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.01426 (26292) covalent geometry : angle 1.90890 (35712) SS BOND : bond 0.00644 ( 45) SS BOND : angle 2.03695 ( 90) hydrogen bonds : bond 0.16462 ( 919) hydrogen bonds : angle 8.50993 ( 2565) link_ALPHA1-2 : bond 0.01998 ( 3) link_ALPHA1-2 : angle 6.06440 ( 9) link_ALPHA1-3 : bond 0.02232 ( 3) link_ALPHA1-3 : angle 3.73428 ( 9) link_ALPHA1-6 : bond 0.01531 ( 3) link_ALPHA1-6 : angle 3.39253 ( 9) link_BETA1-4 : bond 0.03015 ( 60) link_BETA1-4 : angle 6.34289 ( 180) link_NAG-ASN : bond 0.01090 ( 39) link_NAG-ASN : angle 5.03924 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9347 (ttm) cc_final: 0.9085 (tpp) REVERT: A 150 MET cc_start: 0.8722 (mmm) cc_final: 0.8001 (tpt) REVERT: G 150 MET cc_start: 0.8826 (mmm) cc_final: 0.8596 (mmp) REVERT: I 574 LYS cc_start: 0.9176 (mttt) cc_final: 0.8947 (ptmt) outliers start: 40 outliers final: 11 residues processed: 146 average time/residue: 0.1923 time to fit residues: 43.4033 Evaluate side-chains 82 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain H residue 99 PHE Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 650 GLN D 650 GLN G 82 GLN G 478 ASN I 554 ASN I 616 ASN I 650 GLN L 89 GLN L 137 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 ASN ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.044900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.033637 restraints weight = 196403.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.034631 restraints weight = 115294.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.035258 restraints weight = 84242.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.035644 restraints weight = 69606.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.035880 restraints weight = 61899.001| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26445 Z= 0.189 Angle : 0.946 14.325 36126 Z= 0.441 Chirality : 0.053 0.330 4359 Planarity : 0.005 0.045 4407 Dihedral : 16.573 80.794 5567 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 1.83 % Allowed : 9.22 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 are not related in a simple way. whole: -0.86 (0.15), residues: 3093 helix: -0.49 (0.22), residues: 504 sheet: -0.01 (0.16), residues: 957 loop : -0.89 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 617 TYR 0.019 0.002 TYR H 177 PHE 0.018 0.002 PHE L 71 TRP 0.028 0.002 TRP D 571 HIS 0.007 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00411 (26292) covalent geometry : angle 0.84311 (35712) SS BOND : bond 0.00280 ( 45) SS BOND : angle 1.24956 ( 90) hydrogen bonds : bond 0.05305 ( 919) hydrogen bonds : angle 6.39604 ( 2565) link_ALPHA1-2 : bond 0.01824 ( 3) link_ALPHA1-2 : angle 4.21570 ( 9) link_ALPHA1-3 : bond 0.01102 ( 3) link_ALPHA1-3 : angle 2.24467 ( 9) link_ALPHA1-6 : bond 0.00090 ( 3) link_ALPHA1-6 : angle 1.86061 ( 9) link_BETA1-4 : bond 0.01382 ( 60) link_BETA1-4 : angle 4.42688 ( 180) link_NAG-ASN : bond 0.00855 ( 39) link_NAG-ASN : angle 5.09460 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 71 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.7055 (p-80) REVERT: A 104 MET cc_start: 0.9285 (ttm) cc_final: 0.8962 (tpp) REVERT: A 150 MET cc_start: 0.8703 (mmm) cc_final: 0.8079 (tpt) REVERT: G 72 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7911 (p90) REVERT: G 104 MET cc_start: 0.9347 (tpp) cc_final: 0.9030 (tpp) REVERT: G 467 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8490 (p) outliers start: 50 outliers final: 15 residues processed: 116 average time/residue: 0.1616 time to fit residues: 30.9169 Evaluate side-chains 79 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain L residue 108 ARG Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 210 optimal weight: 9.9990 chunk 265 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 297 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 170 GLN G 82 GLN G 99 ASN I 540 GLN H 156 ASN H 193 GLN L 138 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.044670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.033602 restraints weight = 192363.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.034598 restraints weight = 112832.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.035220 restraints weight = 82351.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.035597 restraints weight = 68090.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.035815 restraints weight = 60652.807| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26445 Z= 0.152 Angle : 0.817 11.683 36126 Z= 0.372 Chirality : 0.051 0.335 4359 Planarity : 0.004 0.063 4407 Dihedral : 12.287 66.087 5554 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.30 % Favored : 95.64 % Rotamer: Outliers : 1.61 % Allowed : 10.65 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 are not related in a simple way. whole: -0.65 (0.15), residues: 3093 helix: -0.15 (0.23), residues: 522 sheet: -0.02 (0.16), residues: 990 loop : -0.73 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 585 TYR 0.017 0.002 TYR K 93 PHE 0.014 0.002 PHE G 93 TRP 0.020 0.001 TRP D 571 HIS 0.006 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00327 (26292) covalent geometry : angle 0.73209 (35712) SS BOND : bond 0.00178 ( 45) SS BOND : angle 0.96572 ( 90) hydrogen bonds : bond 0.04165 ( 919) hydrogen bonds : angle 5.71899 ( 2565) link_ALPHA1-2 : bond 0.01715 ( 3) link_ALPHA1-2 : angle 4.32285 ( 9) link_ALPHA1-3 : bond 0.01339 ( 3) link_ALPHA1-3 : angle 2.08017 ( 9) link_ALPHA1-6 : bond 0.00193 ( 3) link_ALPHA1-6 : angle 2.54989 ( 9) link_BETA1-4 : bond 0.01180 ( 60) link_BETA1-4 : angle 3.84199 ( 180) link_NAG-ASN : bond 0.00687 ( 39) link_NAG-ASN : angle 4.09387 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 66 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.7290 (p-80) REVERT: A 104 MET cc_start: 0.9297 (ttm) cc_final: 0.9027 (tpp) REVERT: A 150 MET cc_start: 0.8725 (mmm) cc_final: 0.8071 (tpt) REVERT: A 259 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8481 (pp) REVERT: C 259 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8794 (pt) REVERT: D 520 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6428 (mt) REVERT: G 104 MET cc_start: 0.9284 (tpp) cc_final: 0.8902 (tpp) REVERT: G 259 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8739 (pt) REVERT: G 293 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: I 554 ASN cc_start: 0.2665 (OUTLIER) cc_final: 0.2192 (p0) outliers start: 44 outliers final: 13 residues processed: 105 average time/residue: 0.1517 time to fit residues: 26.8961 Evaluate side-chains 81 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain I residue 554 ASN Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 239 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 259 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** I 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 ASN F 89 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN K 89 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.043579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.032295 restraints weight = 196643.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.033239 restraints weight = 117392.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.033828 restraints weight = 86976.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.034199 restraints weight = 72460.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.034427 restraints weight = 64792.271| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 26445 Z= 0.252 Angle : 0.849 12.311 36126 Z= 0.391 Chirality : 0.051 0.348 4359 Planarity : 0.005 0.048 4407 Dihedral : 10.862 65.019 5554 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 1.90 % Allowed : 12.04 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 are not related in a simple way. whole: -0.79 (0.15), residues: 3093 helix: -0.22 (0.23), residues: 510 sheet: -0.01 (0.16), residues: 996 loop : -0.90 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 71 TYR 0.024 0.002 TYR K 49 PHE 0.018 0.002 PHE K 98 TRP 0.017 0.002 TRP G 96 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00582 (26292) covalent geometry : angle 0.76498 (35712) SS BOND : bond 0.00262 ( 45) SS BOND : angle 1.15290 ( 90) hydrogen bonds : bond 0.04373 ( 919) hydrogen bonds : angle 5.71617 ( 2565) link_ALPHA1-2 : bond 0.01394 ( 3) link_ALPHA1-2 : angle 4.31342 ( 9) link_ALPHA1-3 : bond 0.00736 ( 3) link_ALPHA1-3 : angle 2.49365 ( 9) link_ALPHA1-6 : bond 0.00356 ( 3) link_ALPHA1-6 : angle 1.83745 ( 9) link_BETA1-4 : bond 0.01066 ( 60) link_BETA1-4 : angle 3.73073 ( 180) link_NAG-ASN : bond 0.00636 ( 39) link_NAG-ASN : angle 4.39267 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 66 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7386 (p-80) REVERT: A 74 CYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7288 (t) REVERT: A 104 MET cc_start: 0.9382 (ttm) cc_final: 0.9026 (tpp) REVERT: A 259 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8581 (pp) REVERT: C 259 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8884 (pt) REVERT: D 518 VAL cc_start: 0.5434 (OUTLIER) cc_final: 0.5191 (m) REVERT: G 104 MET cc_start: 0.9299 (tpp) cc_final: 0.8892 (tpp) REVERT: G 259 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8765 (pp) REVERT: I 554 ASN cc_start: 0.3084 (OUTLIER) cc_final: 0.2222 (p0) REVERT: H 57 MET cc_start: 0.8962 (ptt) cc_final: 0.8758 (ptt) outliers start: 52 outliers final: 20 residues processed: 116 average time/residue: 0.1537 time to fit residues: 30.3398 Evaluate side-chains 90 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain I residue 554 ASN Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 255 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 303 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 551 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 GLN L 147 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.043786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.032507 restraints weight = 195838.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.033453 restraints weight = 116904.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.034052 restraints weight = 86495.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.034421 restraints weight = 72096.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034605 restraints weight = 64568.316| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26445 Z= 0.197 Angle : 0.780 11.204 36126 Z= 0.358 Chirality : 0.049 0.344 4359 Planarity : 0.004 0.049 4407 Dihedral : 10.328 59.773 5554 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 2.31 % Allowed : 12.88 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 are not related in a simple way. whole: -0.70 (0.15), residues: 3093 helix: -0.12 (0.23), residues: 522 sheet: -0.01 (0.16), residues: 987 loop : -0.82 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.018 0.002 TYR K 49 PHE 0.014 0.002 PHE K 98 TRP 0.016 0.001 TRP A 112 HIS 0.018 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00447 (26292) covalent geometry : angle 0.70203 (35712) SS BOND : bond 0.00379 ( 45) SS BOND : angle 1.23626 ( 90) hydrogen bonds : bond 0.03933 ( 919) hydrogen bonds : angle 5.55913 ( 2565) link_ALPHA1-2 : bond 0.01553 ( 3) link_ALPHA1-2 : angle 4.32587 ( 9) link_ALPHA1-3 : bond 0.01037 ( 3) link_ALPHA1-3 : angle 2.30176 ( 9) link_ALPHA1-6 : bond 0.00130 ( 3) link_ALPHA1-6 : angle 2.12540 ( 9) link_BETA1-4 : bond 0.01014 ( 60) link_BETA1-4 : angle 3.40991 ( 180) link_NAG-ASN : bond 0.00526 ( 39) link_NAG-ASN : angle 4.04774 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 64 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7402 (p-80) REVERT: A 74 CYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7387 (t) REVERT: A 104 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9015 (tpp) REVERT: A 150 MET cc_start: 0.7412 (tpt) cc_final: 0.7103 (tpt) REVERT: A 259 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8726 (pp) REVERT: C 259 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8822 (pt) REVERT: G 104 MET cc_start: 0.9277 (tpp) cc_final: 0.8892 (tpp) REVERT: G 271 MET cc_start: 0.8341 (mmm) cc_final: 0.8123 (tpt) REVERT: G 467 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8350 (p) REVERT: I 554 ASN cc_start: 0.3269 (OUTLIER) cc_final: 0.2343 (p0) outliers start: 63 outliers final: 27 residues processed: 123 average time/residue: 0.1472 time to fit residues: 30.8055 Evaluate side-chains 97 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 554 ASN Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 133 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 551 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN C 374 HIS ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN ** I 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 ASN J 193 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.043057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.032039 restraints weight = 195162.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.032866 restraints weight = 123524.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.033392 restraints weight = 94217.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.033715 restraints weight = 80022.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.033923 restraints weight = 72322.048| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26445 Z= 0.142 Angle : 0.726 10.874 36126 Z= 0.331 Chirality : 0.047 0.341 4359 Planarity : 0.004 0.047 4407 Dihedral : 9.776 58.525 5551 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.25 % Rotamer: Outliers : 1.76 % Allowed : 13.54 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 are not related in a simple way. whole: -0.56 (0.15), residues: 3093 helix: 0.06 (0.23), residues: 522 sheet: 0.19 (0.16), residues: 975 loop : -0.83 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 24 TYR 0.016 0.001 TYR K 93 PHE 0.011 0.001 PHE C 53 TRP 0.013 0.001 TRP D 571 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00314 (26292) covalent geometry : angle 0.65231 (35712) SS BOND : bond 0.00349 ( 45) SS BOND : angle 1.08559 ( 90) hydrogen bonds : bond 0.03496 ( 919) hydrogen bonds : angle 5.34829 ( 2565) link_ALPHA1-2 : bond 0.01534 ( 3) link_ALPHA1-2 : angle 4.02563 ( 9) link_ALPHA1-3 : bond 0.01081 ( 3) link_ALPHA1-3 : angle 2.29740 ( 9) link_ALPHA1-6 : bond 0.00161 ( 3) link_ALPHA1-6 : angle 2.13551 ( 9) link_BETA1-4 : bond 0.00999 ( 60) link_BETA1-4 : angle 3.18268 ( 180) link_NAG-ASN : bond 0.00541 ( 39) link_NAG-ASN : angle 3.77966 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 63 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7408 (p-80) REVERT: A 74 CYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7419 (t) REVERT: A 104 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.9045 (tpp) REVERT: A 259 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8394 (pp) REVERT: C 259 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8785 (pt) REVERT: G 104 MET cc_start: 0.9242 (tpp) cc_final: 0.8817 (tpp) REVERT: G 161 MET cc_start: 0.8588 (mmm) cc_final: 0.7852 (mmm) REVERT: G 271 MET cc_start: 0.8298 (mmm) cc_final: 0.8097 (tpt) REVERT: G 467 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8305 (p) REVERT: I 554 ASN cc_start: 0.3229 (OUTLIER) cc_final: 0.2352 (p0) REVERT: H 57 MET cc_start: 0.8863 (ptt) cc_final: 0.8540 (ptt) REVERT: L 106 MET cc_start: 0.7805 (tmm) cc_final: 0.7213 (tmm) REVERT: F 4 MET cc_start: 0.7950 (mmm) cc_final: 0.7746 (mmm) outliers start: 48 outliers final: 26 residues processed: 108 average time/residue: 0.1481 time to fit residues: 27.5477 Evaluate side-chains 95 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 554 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 214 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 551 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.042749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.031722 restraints weight = 195170.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.032530 restraints weight = 124087.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.033023 restraints weight = 95236.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.033360 restraints weight = 81301.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.033552 restraints weight = 73566.917| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26445 Z= 0.183 Angle : 0.744 11.033 36126 Z= 0.340 Chirality : 0.047 0.343 4359 Planarity : 0.004 0.047 4407 Dihedral : 9.733 58.757 5551 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.99 % Rotamer: Outliers : 2.09 % Allowed : 13.83 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 are not related in a simple way. whole: -0.56 (0.15), residues: 3093 helix: 0.09 (0.24), residues: 522 sheet: 0.11 (0.16), residues: 990 loop : -0.78 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.022 0.001 TYR K 93 PHE 0.025 0.002 PHE G 382 TRP 0.015 0.001 TRP G 112 HIS 0.026 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00418 (26292) covalent geometry : angle 0.67198 (35712) SS BOND : bond 0.00323 ( 45) SS BOND : angle 0.97397 ( 90) hydrogen bonds : bond 0.03599 ( 919) hydrogen bonds : angle 5.33474 ( 2565) link_ALPHA1-2 : bond 0.01413 ( 3) link_ALPHA1-2 : angle 4.12366 ( 9) link_ALPHA1-3 : bond 0.00925 ( 3) link_ALPHA1-3 : angle 2.52614 ( 9) link_ALPHA1-6 : bond 0.00154 ( 3) link_ALPHA1-6 : angle 1.95727 ( 9) link_BETA1-4 : bond 0.00982 ( 60) link_BETA1-4 : angle 3.21891 ( 180) link_NAG-ASN : bond 0.00543 ( 39) link_NAG-ASN : angle 3.80375 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 63 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7404 (p-80) REVERT: A 74 CYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7305 (t) REVERT: A 104 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9037 (tpp) REVERT: A 259 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8605 (pp) REVERT: G 104 MET cc_start: 0.9260 (tpp) cc_final: 0.8831 (tpp) REVERT: G 467 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8457 (p) REVERT: I 554 ASN cc_start: 0.3322 (OUTLIER) cc_final: 0.2683 (p0) REVERT: L 106 MET cc_start: 0.7899 (tmm) cc_final: 0.7294 (tmm) outliers start: 57 outliers final: 42 residues processed: 117 average time/residue: 0.1392 time to fit residues: 28.4687 Evaluate side-chains 110 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 62 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 554 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 228 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 261 optimal weight: 30.0000 chunk 256 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.042998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.031986 restraints weight = 194846.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.032807 restraints weight = 123563.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.033306 restraints weight = 94510.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.033648 restraints weight = 80521.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.033828 restraints weight = 72719.756| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26445 Z= 0.144 Angle : 0.720 11.376 36126 Z= 0.326 Chirality : 0.047 0.342 4359 Planarity : 0.004 0.046 4407 Dihedral : 9.499 58.115 5551 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 1.83 % Allowed : 14.49 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 are not related in a simple way. whole: -0.45 (0.15), residues: 3093 helix: 0.21 (0.24), residues: 522 sheet: 0.22 (0.17), residues: 954 loop : -0.74 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 71 TYR 0.016 0.001 TYR K 93 PHE 0.019 0.001 PHE G 382 TRP 0.014 0.001 TRP G 112 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00320 (26292) covalent geometry : angle 0.64985 (35712) SS BOND : bond 0.00274 ( 45) SS BOND : angle 0.90597 ( 90) hydrogen bonds : bond 0.03390 ( 919) hydrogen bonds : angle 5.22854 ( 2565) link_ALPHA1-2 : bond 0.01504 ( 3) link_ALPHA1-2 : angle 3.99739 ( 9) link_ALPHA1-3 : bond 0.01051 ( 3) link_ALPHA1-3 : angle 2.42405 ( 9) link_ALPHA1-6 : bond 0.00187 ( 3) link_ALPHA1-6 : angle 2.05354 ( 9) link_BETA1-4 : bond 0.00963 ( 60) link_BETA1-4 : angle 3.07401 ( 180) link_NAG-ASN : bond 0.00565 ( 39) link_NAG-ASN : angle 3.71266 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 64 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7320 (p-80) REVERT: A 74 CYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7248 (t) REVERT: A 104 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.9015 (tpp) REVERT: A 259 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8398 (pp) REVERT: C 125 LEU cc_start: 0.9499 (tp) cc_final: 0.9120 (tp) REVERT: G 87 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6395 (pp20) REVERT: G 104 MET cc_start: 0.9233 (tpp) cc_final: 0.8804 (tpp) REVERT: G 467 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8359 (p) REVERT: I 554 ASN cc_start: 0.3203 (OUTLIER) cc_final: 0.2585 (p0) REVERT: L 106 MET cc_start: 0.7833 (tmm) cc_final: 0.7241 (tmm) REVERT: F 4 MET cc_start: 0.8072 (mmm) cc_final: 0.7825 (tpt) REVERT: K 4 MET cc_start: 0.8210 (mmm) cc_final: 0.7520 (tpt) outliers start: 50 outliers final: 36 residues processed: 110 average time/residue: 0.1453 time to fit residues: 27.8598 Evaluate side-chains 106 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 63 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 554 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 61 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 287 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 96 optimal weight: 0.2980 chunk 57 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 257 optimal weight: 20.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.042184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.031145 restraints weight = 197152.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.032308 restraints weight = 133761.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.032521 restraints weight = 90101.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.032583 restraints weight = 85859.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.032683 restraints weight = 79047.614| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 26445 Z= 0.256 Angle : 0.800 11.643 36126 Z= 0.368 Chirality : 0.049 0.349 4359 Planarity : 0.005 0.048 4407 Dihedral : 9.924 59.622 5551 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 2.20 % Allowed : 14.45 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.69 (0.15), residues: 3093 helix: 0.11 (0.24), residues: 522 sheet: -0.13 (0.16), residues: 1023 loop : -0.82 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 557 TYR 0.022 0.002 TYR K 49 PHE 0.021 0.002 PHE G 382 TRP 0.015 0.002 TRP G 112 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00587 (26292) covalent geometry : angle 0.72897 (35712) SS BOND : bond 0.00388 ( 45) SS BOND : angle 1.05841 ( 90) hydrogen bonds : bond 0.03939 ( 919) hydrogen bonds : angle 5.44445 ( 2565) link_ALPHA1-2 : bond 0.01328 ( 3) link_ALPHA1-2 : angle 4.17959 ( 9) link_ALPHA1-3 : bond 0.00601 ( 3) link_ALPHA1-3 : angle 2.92051 ( 9) link_ALPHA1-6 : bond 0.00538 ( 3) link_ALPHA1-6 : angle 1.86436 ( 9) link_BETA1-4 : bond 0.00958 ( 60) link_BETA1-4 : angle 3.25397 ( 180) link_NAG-ASN : bond 0.00585 ( 39) link_NAG-ASN : angle 3.98679 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 62 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7582 (p-80) REVERT: A 74 CYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7052 (t) REVERT: A 104 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.9063 (tpp) REVERT: A 259 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8790 (pp) REVERT: G 104 MET cc_start: 0.9268 (tpp) cc_final: 0.8870 (tpp) REVERT: I 554 ASN cc_start: 0.3439 (OUTLIER) cc_final: 0.2747 (p0) REVERT: L 106 MET cc_start: 0.7894 (tmm) cc_final: 0.7291 (tmm) REVERT: F 4 MET cc_start: 0.7929 (mmm) cc_final: 0.7705 (tpt) REVERT: K 4 MET cc_start: 0.8134 (mmm) cc_final: 0.7395 (tpt) outliers start: 60 outliers final: 45 residues processed: 118 average time/residue: 0.1375 time to fit residues: 28.3366 Evaluate side-chains 112 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 62 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 554 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 122 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 27 optimal weight: 9.9990 chunk 299 optimal weight: 2.9990 chunk 270 optimal weight: 0.0770 chunk 221 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 260 optimal weight: 0.9980 chunk 226 optimal weight: 0.5980 chunk 224 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.043142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.032101 restraints weight = 194386.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.032935 restraints weight = 123042.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.033462 restraints weight = 93866.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.033789 restraints weight = 79760.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.033994 restraints weight = 72067.321| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26445 Z= 0.126 Angle : 0.714 11.091 36126 Z= 0.324 Chirality : 0.047 0.344 4359 Planarity : 0.004 0.047 4407 Dihedral : 9.401 59.253 5551 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Rotamer: Outliers : 1.65 % Allowed : 15.08 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 are not related in a simple way. whole: -0.47 (0.15), residues: 3093 helix: 0.27 (0.24), residues: 522 sheet: 0.17 (0.17), residues: 957 loop : -0.76 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 273 TYR 0.013 0.001 TYR K 93 PHE 0.014 0.001 PHE G 382 TRP 0.024 0.001 TRP K 148 HIS 0.006 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00276 (26292) covalent geometry : angle 0.64720 (35712) SS BOND : bond 0.00265 ( 45) SS BOND : angle 1.08507 ( 90) hydrogen bonds : bond 0.03313 ( 919) hydrogen bonds : angle 5.18514 ( 2565) link_ALPHA1-2 : bond 0.01553 ( 3) link_ALPHA1-2 : angle 3.96043 ( 9) link_ALPHA1-3 : bond 0.01166 ( 3) link_ALPHA1-3 : angle 2.28320 ( 9) link_ALPHA1-6 : bond 0.00309 ( 3) link_ALPHA1-6 : angle 2.10847 ( 9) link_BETA1-4 : bond 0.00959 ( 60) link_BETA1-4 : angle 2.97713 ( 180) link_NAG-ASN : bond 0.00581 ( 39) link_NAG-ASN : angle 3.62174 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 64 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7354 (p-80) REVERT: A 74 CYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7217 (t) REVERT: A 104 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.9067 (tpp) REVERT: A 259 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8654 (pp) REVERT: C 125 LEU cc_start: 0.9498 (tp) cc_final: 0.8952 (tt) REVERT: G 104 MET cc_start: 0.9234 (tpp) cc_final: 0.8851 (tpp) REVERT: G 475 MET cc_start: 0.7481 (mmt) cc_final: 0.6999 (mmt) REVERT: I 554 ASN cc_start: 0.3033 (OUTLIER) cc_final: 0.2435 (p0) REVERT: L 106 MET cc_start: 0.7919 (tmm) cc_final: 0.7222 (tmm) REVERT: K 4 MET cc_start: 0.8142 (mmm) cc_final: 0.7371 (tpt) outliers start: 45 outliers final: 37 residues processed: 105 average time/residue: 0.1549 time to fit residues: 28.1147 Evaluate side-chains 105 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 63 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 554 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 222 optimal weight: 4.9990 chunk 134 optimal weight: 0.4980 chunk 16 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.042996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.031950 restraints weight = 194059.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.032766 restraints weight = 123278.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.033288 restraints weight = 94513.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.033614 restraints weight = 80366.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.033788 restraints weight = 72732.210| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26445 Z= 0.143 Angle : 0.709 11.128 36126 Z= 0.321 Chirality : 0.046 0.340 4359 Planarity : 0.004 0.046 4407 Dihedral : 9.218 58.842 5551 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 1.68 % Allowed : 15.15 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 are not related in a simple way. whole: -0.42 (0.15), residues: 3093 helix: 0.45 (0.24), residues: 504 sheet: 0.08 (0.17), residues: 987 loop : -0.69 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 50 TYR 0.013 0.001 TYR K 93 PHE 0.015 0.001 PHE G 382 TRP 0.017 0.001 TRP K 148 HIS 0.006 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00320 (26292) covalent geometry : angle 0.64102 (35712) SS BOND : bond 0.00256 ( 45) SS BOND : angle 1.00704 ( 90) hydrogen bonds : bond 0.03298 ( 919) hydrogen bonds : angle 5.12942 ( 2565) link_ALPHA1-2 : bond 0.01454 ( 3) link_ALPHA1-2 : angle 3.91285 ( 9) link_ALPHA1-3 : bond 0.00961 ( 3) link_ALPHA1-3 : angle 2.59620 ( 9) link_ALPHA1-6 : bond 0.00199 ( 3) link_ALPHA1-6 : angle 1.93199 ( 9) link_BETA1-4 : bond 0.00940 ( 60) link_BETA1-4 : angle 2.97004 ( 180) link_NAG-ASN : bond 0.00546 ( 39) link_NAG-ASN : angle 3.64754 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3686.59 seconds wall clock time: 65 minutes 13.10 seconds (3913.10 seconds total)