Starting phenix.real_space_refine on Thu Sep 18 19:52:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d7p_46614/09_2025/9d7p_46614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d7p_46614/09_2025/9d7p_46614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d7p_46614/09_2025/9d7p_46614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d7p_46614/09_2025/9d7p_46614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d7p_46614/09_2025/9d7p_46614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d7p_46614/09_2025/9d7p_46614.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 127 5.16 5 C 12335 2.51 5 N 3257 2.21 5 O 3971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19690 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 Chain: "B" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3396 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 976 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 2 Chain: "E" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3461 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1003 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1254 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 13, 'TRANS': 153} Chain breaks: 3 Chain: "H" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1320 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1268 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 13, 'TRANS': 154} Chain breaks: 3 Chain: "J" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1245 Classifications: {'peptide': 165} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 155} Chain breaks: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" 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: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.69, per 1000 atoms: 0.24 Number of scatterers: 19690 At special positions: 0 Unit cell: (160.92, 124.2, 141.48, 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 127 16.00 O 3971 8.00 N 3257 7.00 C 12335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " 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 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 385 " distance=2.06 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " 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=2.09 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 445 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 355 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 355 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 197 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 137 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 448 " " NAG F 701 " - " ASN F 611 " " NAG K 1 " - " ASN A 386 " " NAG L 1 " - " ASN A 448 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 148 " " NAG O 1 " - " ASN A 152 " " NAG P 1 " - " ASN A 197 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 448 " " NAG Y 1 " - " ASN C 88 " " NAG Z 1 " - " ASN C 148 " " NAG a 1 " - " ASN C 152 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 262 " " NAG d 1 " - " ASN C 276 " " NAG e 1 " - " ASN C 295 " " NAG f 1 " - " ASN C 301 " " NAG g 1 " - " ASN C 332 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 148 " " NAG j 1 " - " ASN E 152 " " NAG k 1 " - " ASN E 262 " " NAG l 1 " - " ASN E 276 " " NAG m 1 " - " ASN E 295 " " NAG n 1 " - " ASN E 301 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 363 " " NAG q 1 " - " ASN E 386 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 815.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4386 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 47 sheets defined 17.6% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 123 through 126 removed outlier: 3.663A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.773A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.775A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 570 through 597 removed outlier: 4.298A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.504A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 641 through 661 removed outlier: 4.098A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.556A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN C 98 " --> pdb=" O MET C 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 98' Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.823A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.762A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 335 through 354 removed outlier: 5.112A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.909A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.701A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.994A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 113 removed outlier: 4.172A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.224A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.985A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.944A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 4.378A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.746A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 633 Processing helix chain 'F' and resid 635 through 637 No H-bonds generated for 'chain 'F' and resid 635 through 637' Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.883A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.591A pdb=" N ASP G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 495 Processing sheet with id=AA2, first strand: chain 'A' and resid 494 through 495 removed outlier: 4.229A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.572A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 121 removed outlier: 4.065A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 161 through 168 removed outlier: 3.577A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 260 removed outlier: 4.053A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.820A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.393A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.560A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.560A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 11.393A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.820A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.474A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.352A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.106A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.743A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB6, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AB7, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB8, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.376A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 274 removed outlier: 7.266A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.583A pdb=" N PHE C 288 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 304 through 312 removed outlier: 3.536A pdb=" N LYS C 305 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.414A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.899A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.594A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AC8, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.379A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.281A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS E 445 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.168A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.048A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.369A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.503A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 274 removed outlier: 12.503A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.369A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.048A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.168A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS E 445 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE E 359 " --> pdb=" O TRP E 395 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.464A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 9 through 13 removed outlier: 7.014A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AD5, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AD6, first strand: chain 'G' and resid 114 through 118 removed outlier: 3.639A pdb=" N VAL G 133 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR G 172 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 114 through 118 removed outlier: 3.639A pdb=" N VAL G 133 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR G 172 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.576A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 121 through 122 Processing sheet with id=AE2, first strand: chain 'I' and resid 9 through 13 removed outlier: 7.019A pdb=" N TRP I 35 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS I 39 " --> pdb=" O SER I 43 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SER I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 9 through 13 Processing sheet with id=AE4, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AE5, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.683A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU I 160 " --> pdb=" O TYR I 177 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.683A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER I 165 " --> pdb=" O ALA I 173 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 145 through 147 removed outlier: 3.533A pdb=" N THR I 145 " --> pdb=" O THR I 196 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AF1, first strand: chain 'J' and resid 57 through 59 removed outlier: 4.796A pdb=" N LEU J 45 " --> pdb=" O SER J 40 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER J 40 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 121 through 123 removed outlier: 3.502A pdb=" N LEU J 178 " --> pdb=" O VAL J 142 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP J 144 " --> pdb=" O TYR J 176 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1875 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: 4.03 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6169 1.36 - 1.49: 5495 1.49 - 1.63: 8246 1.63 - 1.77: 1 1.77 - 1.91: 164 Bond restraints: 20075 Sorted by residual: bond pdb=" C LYS C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.334 1.381 -0.047 8.40e-03 1.42e+04 3.18e+01 bond pdb=" C LYS H 201 " pdb=" N PRO H 202 " ideal model delta sigma weight residual 1.336 1.379 -0.044 1.23e-02 6.61e+03 1.26e+01 bond pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 1.808 1.905 -0.097 3.30e-02 9.18e+02 8.70e+00 bond pdb=" C LYS E 117 " pdb=" N PRO E 118 " ideal model delta sigma weight residual 1.340 1.400 -0.059 2.76e-02 1.31e+03 4.64e+00 bond pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.86e+00 ... (remaining 20070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.14: 27227 6.14 - 12.28: 41 12.28 - 18.42: 5 18.42 - 24.56: 0 24.56 - 30.70: 1 Bond angle restraints: 27274 Sorted by residual: angle pdb=" CA CYS C 331 " pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " ideal model delta sigma weight residual 114.40 145.10 -30.70 2.30e+00 1.89e-01 1.78e+02 angle pdb=" C ASN C 339 " pdb=" N GLU C 340 " pdb=" CA GLU C 340 " ideal model delta sigma weight residual 121.54 131.58 -10.04 1.91e+00 2.74e-01 2.76e+01 angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 125.74 -11.34 2.30e+00 1.89e-01 2.43e+01 angle pdb=" N ASN C 99 " pdb=" CA ASN C 99 " pdb=" C ASN C 99 " ideal model delta sigma weight residual 112.57 107.28 5.29 1.13e+00 7.83e-01 2.19e+01 angle pdb=" C2 NAG Y 1 " pdb=" N2 NAG Y 1 " pdb=" C7 NAG Y 1 " ideal model delta sigma weight residual 124.56 138.07 -13.51 3.00e+00 1.11e-01 2.03e+01 ... (remaining 27269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12005 17.96 - 35.92: 950 35.92 - 53.88: 198 53.88 - 71.84: 67 71.84 - 89.80: 14 Dihedral angle restraints: 13234 sinusoidal: 6450 harmonic: 6784 Sorted by residual: dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 385 " pdb=" CB CYS A 385 " ideal model delta sinusoidal sigma weight residual -86.00 -3.65 -82.35 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -8.87 -77.13 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 418 " pdb=" CB CYS A 418 " ideal model delta sinusoidal sigma weight residual -86.00 -155.66 69.66 1 1.00e+01 1.00e-02 6.26e+01 ... (remaining 13231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3024 0.089 - 0.177: 325 0.177 - 0.266: 17 0.266 - 0.354: 7 0.354 - 0.443: 2 Chirality restraints: 3375 Sorted by residual: chirality pdb=" C1 NAG C 603 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG C 603 " pdb=" O5 NAG C 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA CYS C 331 " pdb=" N CYS C 331 " pdb=" C CYS C 331 " pdb=" CB CYS C 331 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C2 NAG Y 1 " pdb=" C1 NAG Y 1 " pdb=" C3 NAG Y 1 " pdb=" N2 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.14 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 3372 not shown) Planarity restraints: 3394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 69 " -0.023 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP C 69 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 69 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 69 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 69 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 69 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 69 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 69 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 340 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C GLU C 340 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU C 340 " -0.019 2.00e-02 2.50e+03 pdb=" N THR C 341 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR G 140 " 0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO G 141 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 141 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 141 " 0.037 5.00e-02 4.00e+02 ... (remaining 3391 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 5814 2.83 - 3.35: 15304 3.35 - 3.87: 30840 3.87 - 4.38: 33666 4.38 - 4.90: 61729 Nonbonded interactions: 147353 Sorted by model distance: nonbonded pdb=" OG SER G 63 " pdb=" OG1 THR G 74 " model vdw 2.317 3.040 nonbonded pdb=" O VAL C 36 " pdb=" OG1 THR D 606 " model vdw 2.324 3.040 nonbonded pdb=" NH1 ARG C 192 " pdb=" O LEU C 193 " model vdw 2.324 3.120 nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.325 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.328 3.040 ... (remaining 147348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 133 or resid 142 through 177 or re \ sid 188 through 398 or resid 412 through 604)) selection = (chain 'C' and (resid 34 through 398 or resid 412 through 458 or resid 463 throu \ gh 604)) selection = (chain 'E' and (resid 34 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 133 or resid 142 through 177 or re \ sid 188 through 458 or resid 463 through 604)) } ncs_group { reference = (chain 'B' and (resid 519 through 547 or resid 572 through 701)) selection = (chain 'D' and (resid 519 through 547 or resid 572 through 701)) selection = (chain 'F' and (resid 519 through 547 or resid 572 through 701)) } ncs_group { reference = (chain 'G' and (resid 2 through 120 or resid 132 through 148 or resid 159 throug \ h 178 or resid 193 through 202)) selection = (chain 'I' and (resid 2 through 120 or resid 132 through 202)) } ncs_group { reference = (chain 'H' and (resid 1 through 152 or resid 165 through 182)) selection = (chain 'J' and (resid 1 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 124 or resid 139 through 182)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = 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 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' 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' } ncs_group { reference = chain 'Q' selection = chain 'V' selection = chain 'c' selection = chain 'k' selection = chain 'p' selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 18.970 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.004 0.097 20202 Z= 0.185 Angle : 0.915 30.704 27623 Z= 0.440 Chirality : 0.054 0.443 3375 Planarity : 0.006 0.066 3338 Dihedral : 13.323 89.799 8752 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.16), residues: 2290 helix: -1.73 (0.22), residues: 393 sheet: 0.01 (0.20), residues: 721 loop : -1.56 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 542 TYR 0.020 0.001 TYR A 191 PHE 0.030 0.002 PHE C 53 TRP 0.055 0.001 TRP C 69 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00371 (20075) covalent geometry : angle 0.85112 (27274) SS BOND : bond 0.01367 ( 32) SS BOND : angle 3.74511 ( 64) hydrogen bonds : bond 0.13807 ( 640) hydrogen bonds : angle 6.51624 ( 1875) link_BETA1-4 : bond 0.00698 ( 39) link_BETA1-4 : angle 2.34751 ( 117) link_NAG-ASN : bond 0.00664 ( 56) link_NAG-ASN : angle 3.28879 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.6417 (p0) cc_final: 0.6201 (p0) REVERT: B 544 LEU cc_start: 0.8865 (mm) cc_final: 0.8613 (mm) REVERT: B 588 ARG cc_start: 0.8476 (ttm110) cc_final: 0.8273 (ttm170) REVERT: D 634 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8203 (mt-10) REVERT: E 500 ARG cc_start: 0.7439 (tpt170) cc_final: 0.7189 (ttt180) REVERT: I 165 SER cc_start: 0.8787 (p) cc_final: 0.8586 (p) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1475 time to fit residues: 59.5819 Evaluate side-chains 209 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.0770 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 chunk 227 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.0970 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 428 GLN E 99 ASN E 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.136934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106796 restraints weight = 24865.928| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.48 r_work: 0.2894 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20202 Z= 0.100 Angle : 0.636 15.770 27623 Z= 0.298 Chirality : 0.045 0.357 3375 Planarity : 0.004 0.055 3338 Dihedral : 7.344 58.318 4478 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.53 % Allowed : 4.63 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.17), residues: 2290 helix: -0.36 (0.27), residues: 384 sheet: 0.07 (0.19), residues: 734 loop : -1.41 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.015 0.001 TYR A 484 PHE 0.028 0.001 PHE E 53 TRP 0.014 0.001 TRP C 69 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00212 (20075) covalent geometry : angle 0.56311 (27274) SS BOND : bond 0.00852 ( 32) SS BOND : angle 3.56218 ( 64) hydrogen bonds : bond 0.03779 ( 640) hydrogen bonds : angle 5.22243 ( 1875) link_BETA1-4 : bond 0.00540 ( 39) link_BETA1-4 : angle 2.03445 ( 117) link_NAG-ASN : bond 0.00486 ( 56) link_NAG-ASN : angle 2.71361 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7752 (mttt) cc_final: 0.7385 (mtpt) REVERT: B 588 ARG cc_start: 0.8378 (ttm110) cc_final: 0.7531 (mtt180) REVERT: C 160 LYS cc_start: 0.8320 (mttm) cc_final: 0.8086 (mttm) REVERT: C 484 TYR cc_start: 0.9147 (p90) cc_final: 0.8824 (p90) REVERT: D 542 ARG cc_start: 0.8311 (ptp-110) cc_final: 0.7996 (ptp-110) REVERT: E 46 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8623 (mmtt) REVERT: E 500 ARG cc_start: 0.7318 (tpt170) cc_final: 0.7015 (ttt180) REVERT: H 75 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7798 (tp30) REVERT: J 64 LYS cc_start: 0.7730 (tptp) cc_final: 0.7145 (tttm) outliers start: 11 outliers final: 6 residues processed: 235 average time/residue: 0.1478 time to fit residues: 52.3536 Evaluate side-chains 212 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain J residue 107 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101393 restraints weight = 25266.678| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.66 r_work: 0.2805 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20202 Z= 0.156 Angle : 0.673 16.154 27623 Z= 0.316 Chirality : 0.047 0.375 3375 Planarity : 0.004 0.049 3338 Dihedral : 7.311 58.875 4478 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.25 % Allowed : 6.75 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.17), residues: 2290 helix: 0.07 (0.28), residues: 400 sheet: 0.24 (0.20), residues: 721 loop : -1.36 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.019 0.001 TYR H 50 PHE 0.024 0.002 PHE E 53 TRP 0.010 0.001 TRP C 69 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00369 (20075) covalent geometry : angle 0.59809 (27274) SS BOND : bond 0.00989 ( 32) SS BOND : angle 3.98784 ( 64) hydrogen bonds : bond 0.03822 ( 640) hydrogen bonds : angle 4.97211 ( 1875) link_BETA1-4 : bond 0.00497 ( 39) link_BETA1-4 : angle 1.98049 ( 117) link_NAG-ASN : bond 0.00576 ( 56) link_NAG-ASN : angle 2.74051 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7787 (mttt) cc_final: 0.7550 (mtpt) REVERT: A 195 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7961 (p0) REVERT: B 588 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7591 (mtt180) REVERT: B 633 LYS cc_start: 0.8692 (mptt) cc_final: 0.8438 (mmtm) REVERT: C 484 TYR cc_start: 0.9235 (p90) cc_final: 0.8980 (p90) outliers start: 26 outliers final: 15 residues processed: 217 average time/residue: 0.1477 time to fit residues: 48.3310 Evaluate side-chains 214 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain J residue 107 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 18 optimal weight: 0.0770 chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN F 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.101129 restraints weight = 25262.783| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.63 r_work: 0.2790 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20202 Z= 0.151 Angle : 0.649 16.270 27623 Z= 0.307 Chirality : 0.047 0.364 3375 Planarity : 0.004 0.050 3338 Dihedral : 7.325 58.472 4478 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.25 % Allowed : 8.87 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.17), residues: 2290 helix: 0.26 (0.28), residues: 400 sheet: 0.20 (0.20), residues: 721 loop : -1.32 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.015 0.001 TYR H 50 PHE 0.031 0.001 PHE E 53 TRP 0.008 0.001 TRP A 112 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00360 (20075) covalent geometry : angle 0.58182 (27274) SS BOND : bond 0.01115 ( 32) SS BOND : angle 3.76685 ( 64) hydrogen bonds : bond 0.03673 ( 640) hydrogen bonds : angle 4.88970 ( 1875) link_BETA1-4 : bond 0.00493 ( 39) link_BETA1-4 : angle 1.93145 ( 117) link_NAG-ASN : bond 0.00401 ( 56) link_NAG-ASN : angle 2.49765 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 588 ARG cc_start: 0.8436 (ttm110) cc_final: 0.7626 (mtt180) REVERT: B 633 LYS cc_start: 0.8674 (mptt) cc_final: 0.8367 (mmtm) REVERT: C 484 TYR cc_start: 0.9246 (p90) cc_final: 0.9004 (p90) REVERT: E 46 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8471 (mmtt) REVERT: E 195 ASN cc_start: 0.7874 (p0) cc_final: 0.6898 (p0) REVERT: E 271 MET cc_start: 0.9191 (mmm) cc_final: 0.8986 (mmp) outliers start: 26 outliers final: 18 residues processed: 215 average time/residue: 0.1704 time to fit residues: 54.6663 Evaluate side-chains 216 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 57 optimal weight: 0.2980 chunk 215 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 577 GLN E 99 ASN F 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.100509 restraints weight = 25313.416| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.49 r_work: 0.2761 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20202 Z= 0.197 Angle : 0.691 16.773 27623 Z= 0.328 Chirality : 0.048 0.365 3375 Planarity : 0.004 0.054 3338 Dihedral : 7.560 59.928 4478 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.88 % Allowed : 9.79 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.17), residues: 2290 helix: 0.40 (0.29), residues: 390 sheet: 0.17 (0.19), residues: 752 loop : -1.38 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.018 0.001 TYR J 50 PHE 0.028 0.002 PHE E 53 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00479 (20075) covalent geometry : angle 0.62139 (27274) SS BOND : bond 0.01238 ( 32) SS BOND : angle 3.95379 ( 64) hydrogen bonds : bond 0.04033 ( 640) hydrogen bonds : angle 4.98149 ( 1875) link_BETA1-4 : bond 0.00478 ( 39) link_BETA1-4 : angle 1.98714 ( 117) link_NAG-ASN : bond 0.00434 ( 56) link_NAG-ASN : angle 2.65752 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8116 (p0) REVERT: A 272 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8444 (mp) REVERT: B 588 ARG cc_start: 0.8457 (ttm110) cc_final: 0.7658 (mtt180) REVERT: C 484 TYR cc_start: 0.9299 (p90) cc_final: 0.9073 (p90) REVERT: D 542 ARG cc_start: 0.8406 (ptp-110) cc_final: 0.7952 (ptp-110) REVERT: E 46 LYS cc_start: 0.8780 (mmtm) cc_final: 0.8450 (mmtt) REVERT: E 195 ASN cc_start: 0.8294 (p0) cc_final: 0.7468 (p0) REVERT: E 271 MET cc_start: 0.9223 (mmm) cc_final: 0.8973 (mmp) REVERT: G 82 ASP cc_start: 0.8576 (m-30) cc_final: 0.8339 (m-30) REVERT: H 171 GLN cc_start: 0.7985 (mt0) cc_final: 0.7468 (mt0) outliers start: 39 outliers final: 21 residues processed: 226 average time/residue: 0.1683 time to fit residues: 57.0639 Evaluate side-chains 216 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 107 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 97 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 177 ASN F 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.129332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099912 restraints weight = 24965.073| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.63 r_work: 0.2770 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20202 Z= 0.142 Angle : 0.654 16.440 27623 Z= 0.307 Chirality : 0.046 0.354 3375 Planarity : 0.004 0.055 3338 Dihedral : 7.410 59.735 4478 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.03 % Allowed : 10.85 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.17), residues: 2290 helix: 0.51 (0.29), residues: 390 sheet: 0.16 (0.19), residues: 743 loop : -1.30 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 617 TYR 0.014 0.001 TYR J 50 PHE 0.023 0.001 PHE E 53 TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00337 (20075) covalent geometry : angle 0.58102 (27274) SS BOND : bond 0.01072 ( 32) SS BOND : angle 3.70456 ( 64) hydrogen bonds : bond 0.03657 ( 640) hydrogen bonds : angle 4.85650 ( 1875) link_BETA1-4 : bond 0.00476 ( 39) link_BETA1-4 : angle 1.92539 ( 117) link_NAG-ASN : bond 0.00444 ( 56) link_NAG-ASN : angle 2.75825 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7789 (mttt) cc_final: 0.7546 (mtpt) REVERT: A 195 ASN cc_start: 0.8530 (p0) cc_final: 0.8247 (p0) REVERT: A 272 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8424 (mp) REVERT: B 536 THR cc_start: 0.8912 (t) cc_final: 0.8661 (p) REVERT: B 588 ARG cc_start: 0.8451 (ttm110) cc_final: 0.7654 (mtt180) REVERT: C 484 TYR cc_start: 0.9267 (p90) cc_final: 0.9044 (p90) REVERT: D 542 ARG cc_start: 0.8375 (ptp-110) cc_final: 0.7915 (ptp-110) REVERT: E 46 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8440 (mmtt) REVERT: E 195 ASN cc_start: 0.8168 (p0) cc_final: 0.7353 (p0) REVERT: E 271 MET cc_start: 0.9212 (mmm) cc_final: 0.9011 (mmp) REVERT: H 171 GLN cc_start: 0.8003 (mt0) cc_final: 0.7495 (mt0) outliers start: 42 outliers final: 26 residues processed: 226 average time/residue: 0.1666 time to fit residues: 56.6766 Evaluate side-chains 220 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 64 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 218 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 196 optimal weight: 0.0370 chunk 144 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN F 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.100103 restraints weight = 25093.104| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.59 r_work: 0.2786 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20202 Z= 0.124 Angle : 0.632 16.791 27623 Z= 0.297 Chirality : 0.046 0.344 3375 Planarity : 0.004 0.057 3338 Dihedral : 7.217 59.370 4478 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.78 % Allowed : 11.43 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.18), residues: 2290 helix: 0.64 (0.29), residues: 389 sheet: 0.22 (0.20), residues: 741 loop : -1.23 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.012 0.001 TYR J 50 PHE 0.024 0.001 PHE E 53 TRP 0.008 0.001 TRP A 112 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00290 (20075) covalent geometry : angle 0.56225 (27274) SS BOND : bond 0.01176 ( 32) SS BOND : angle 3.70459 ( 64) hydrogen bonds : bond 0.03402 ( 640) hydrogen bonds : angle 4.71593 ( 1875) link_BETA1-4 : bond 0.00490 ( 39) link_BETA1-4 : angle 1.87018 ( 117) link_NAG-ASN : bond 0.00455 ( 56) link_NAG-ASN : angle 2.59444 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7728 (mttt) cc_final: 0.7479 (mtpt) REVERT: A 195 ASN cc_start: 0.8507 (p0) cc_final: 0.8266 (p0) REVERT: A 272 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 323 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8737 (mp) REVERT: B 536 THR cc_start: 0.8904 (t) cc_final: 0.8662 (p) REVERT: B 588 ARG cc_start: 0.8418 (ttm110) cc_final: 0.7667 (mtt180) REVERT: B 626 MET cc_start: 0.8728 (ttm) cc_final: 0.8239 (ttm) REVERT: C 484 TYR cc_start: 0.9237 (p90) cc_final: 0.9018 (p90) REVERT: E 46 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8402 (mmtt) REVERT: E 195 ASN cc_start: 0.8121 (p0) cc_final: 0.7297 (p0) REVERT: E 271 MET cc_start: 0.9203 (mmm) cc_final: 0.8992 (mmp) REVERT: H 171 GLN cc_start: 0.8010 (mt0) cc_final: 0.7521 (mt0) outliers start: 37 outliers final: 28 residues processed: 219 average time/residue: 0.1631 time to fit residues: 53.6102 Evaluate side-chains 224 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 178 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 151 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 229 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 0.0980 chunk 207 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.101006 restraints weight = 25123.720| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.59 r_work: 0.2801 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20202 Z= 0.110 Angle : 0.610 16.784 27623 Z= 0.286 Chirality : 0.045 0.336 3375 Planarity : 0.004 0.056 3338 Dihedral : 6.980 58.655 4478 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.49 % Allowed : 12.05 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.18), residues: 2290 helix: 0.79 (0.29), residues: 384 sheet: 0.33 (0.20), residues: 736 loop : -1.17 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.015 0.001 TYR A 191 PHE 0.016 0.001 PHE I 49 TRP 0.008 0.001 TRP A 112 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00253 (20075) covalent geometry : angle 0.54422 (27274) SS BOND : bond 0.01031 ( 32) SS BOND : angle 3.52632 ( 64) hydrogen bonds : bond 0.03198 ( 640) hydrogen bonds : angle 4.57356 ( 1875) link_BETA1-4 : bond 0.00488 ( 39) link_BETA1-4 : angle 1.79049 ( 117) link_NAG-ASN : bond 0.00431 ( 56) link_NAG-ASN : angle 2.46754 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7674 (mttt) cc_final: 0.7428 (mtpt) REVERT: A 195 ASN cc_start: 0.8485 (p0) cc_final: 0.8233 (p0) REVERT: A 272 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8431 (mp) REVERT: A 323 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8723 (mp) REVERT: B 536 THR cc_start: 0.8900 (t) cc_final: 0.8666 (p) REVERT: B 588 ARG cc_start: 0.8421 (ttm110) cc_final: 0.7654 (mtt180) REVERT: C 484 TYR cc_start: 0.9215 (p90) cc_final: 0.9002 (p90) REVERT: D 542 ARG cc_start: 0.8423 (ptp-110) cc_final: 0.7850 (ptp-110) REVERT: E 46 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8415 (mmtt) REVERT: E 271 MET cc_start: 0.9203 (mmm) cc_final: 0.8982 (mmp) REVERT: H 171 GLN cc_start: 0.8023 (mt0) cc_final: 0.7511 (mt0) REVERT: J 105 ARG cc_start: 0.8983 (mtm180) cc_final: 0.8739 (mtm180) outliers start: 31 outliers final: 23 residues processed: 221 average time/residue: 0.1668 time to fit residues: 55.3345 Evaluate side-chains 223 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 8 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111710 restraints weight = 24277.989| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.22 r_work: 0.2836 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20202 Z= 0.129 Angle : 0.628 18.261 27623 Z= 0.296 Chirality : 0.045 0.342 3375 Planarity : 0.004 0.081 3338 Dihedral : 6.981 58.583 4478 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.59 % Allowed : 12.05 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.18), residues: 2290 helix: 0.76 (0.29), residues: 390 sheet: 0.34 (0.20), residues: 735 loop : -1.16 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 542 TYR 0.014 0.001 TYR C 165 PHE 0.018 0.001 PHE E 53 TRP 0.010 0.001 TRP C 427 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00306 (20075) covalent geometry : angle 0.56321 (27274) SS BOND : bond 0.01063 ( 32) SS BOND : angle 3.58014 ( 64) hydrogen bonds : bond 0.03327 ( 640) hydrogen bonds : angle 4.57363 ( 1875) link_BETA1-4 : bond 0.00471 ( 39) link_BETA1-4 : angle 1.79542 ( 117) link_NAG-ASN : bond 0.00426 ( 56) link_NAG-ASN : angle 2.48333 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7651 (mttt) cc_final: 0.7451 (mtpt) REVERT: A 272 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8455 (mp) REVERT: A 323 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8770 (mp) REVERT: B 536 THR cc_start: 0.8937 (t) cc_final: 0.8712 (p) REVERT: B 588 ARG cc_start: 0.8396 (ttm110) cc_final: 0.7650 (mtt180) REVERT: B 626 MET cc_start: 0.8704 (ttm) cc_final: 0.8226 (ttm) REVERT: B 640 GLN cc_start: 0.8323 (tp40) cc_final: 0.8090 (tp40) REVERT: D 542 ARG cc_start: 0.8406 (ptp-110) cc_final: 0.7865 (ptp-110) REVERT: E 46 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8550 (mmtt) REVERT: E 195 ASN cc_start: 0.8259 (p0) cc_final: 0.7942 (p0) REVERT: E 271 MET cc_start: 0.9209 (mmm) cc_final: 0.8983 (mmp) REVERT: H 171 GLN cc_start: 0.8009 (mt0) cc_final: 0.7517 (mt0) outliers start: 33 outliers final: 25 residues processed: 219 average time/residue: 0.1580 time to fit residues: 52.5339 Evaluate side-chains 220 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 164 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 chunk 209 optimal weight: 0.2980 chunk 223 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN E 188 ASN H 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.128940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.097558 restraints weight = 25151.462| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.61 r_work: 0.2770 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20202 Z= 0.142 Angle : 0.641 19.114 27623 Z= 0.303 Chirality : 0.046 0.345 3375 Planarity : 0.004 0.073 3338 Dihedral : 7.026 59.392 4478 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.40 % Allowed : 12.44 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.18), residues: 2290 helix: 0.77 (0.29), residues: 389 sheet: 0.35 (0.20), residues: 733 loop : -1.14 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.014 0.001 TYR J 50 PHE 0.017 0.001 PHE I 49 TRP 0.007 0.001 TRP A 112 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00339 (20075) covalent geometry : angle 0.57568 (27274) SS BOND : bond 0.01084 ( 32) SS BOND : angle 3.63313 ( 64) hydrogen bonds : bond 0.03446 ( 640) hydrogen bonds : angle 4.59382 ( 1875) link_BETA1-4 : bond 0.00463 ( 39) link_BETA1-4 : angle 1.79132 ( 117) link_NAG-ASN : bond 0.00428 ( 56) link_NAG-ASN : angle 2.54182 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7682 (mttt) cc_final: 0.7464 (mtpt) REVERT: A 272 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8470 (mp) REVERT: A 323 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8740 (mp) REVERT: B 588 ARG cc_start: 0.8512 (ttm110) cc_final: 0.7761 (mtt180) REVERT: B 626 MET cc_start: 0.8738 (ttm) cc_final: 0.8271 (ttm) REVERT: B 633 LYS cc_start: 0.8623 (mptt) cc_final: 0.8258 (mmtm) REVERT: B 640 GLN cc_start: 0.8451 (tp40) cc_final: 0.8234 (tp40) REVERT: D 542 ARG cc_start: 0.8554 (ptp-110) cc_final: 0.7960 (ptp-110) REVERT: E 46 LYS cc_start: 0.8799 (mmtm) cc_final: 0.8577 (mmtt) REVERT: E 271 MET cc_start: 0.9228 (mmm) cc_final: 0.9018 (mmp) REVERT: H 171 GLN cc_start: 0.8040 (mt0) cc_final: 0.7716 (mt0) REVERT: I 165 SER cc_start: 0.8262 (m) cc_final: 0.7902 (t) outliers start: 29 outliers final: 25 residues processed: 211 average time/residue: 0.1613 time to fit residues: 51.1190 Evaluate side-chains 216 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 190 optimal weight: 0.4980 chunk 200 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 89 optimal weight: 0.0970 chunk 161 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN E 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.099057 restraints weight = 25128.279| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.63 r_work: 0.2794 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20202 Z= 0.110 Angle : 0.612 17.824 27623 Z= 0.288 Chirality : 0.045 0.333 3375 Planarity : 0.004 0.067 3338 Dihedral : 6.842 58.729 4478 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.59 % Allowed : 12.49 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.18), residues: 2290 helix: 0.85 (0.29), residues: 390 sheet: 0.41 (0.20), residues: 730 loop : -1.10 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.013 0.001 TYR C 165 PHE 0.018 0.001 PHE E 53 TRP 0.008 0.001 TRP A 112 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00256 (20075) covalent geometry : angle 0.54857 (27274) SS BOND : bond 0.00962 ( 32) SS BOND : angle 3.47752 ( 64) hydrogen bonds : bond 0.03146 ( 640) hydrogen bonds : angle 4.49957 ( 1875) link_BETA1-4 : bond 0.00487 ( 39) link_BETA1-4 : angle 1.73332 ( 117) link_NAG-ASN : bond 0.00435 ( 56) link_NAG-ASN : angle 2.44649 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5006.59 seconds wall clock time: 86 minutes 32.84 seconds (5192.84 seconds total)