Starting phenix.real_space_refine on Sat Mar 16 21:31:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8a_23227/03_2024/7l8a_23227_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8a_23227/03_2024/7l8a_23227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8a_23227/03_2024/7l8a_23227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8a_23227/03_2024/7l8a_23227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8a_23227/03_2024/7l8a_23227_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8a_23227/03_2024/7l8a_23227_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 99 5.16 5 C 9783 2.51 5 N 2635 2.21 5 O 3211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15728 Number of models: 1 Model: "" Number of chains: 47 Chain: "E" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3460 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 948 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3480 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 3 Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3455 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 Time building chain proxies: 8.77, per 1000 atoms: 0.56 Number of scatterers: 15728 At special positions: 0 Unit cell: (151.41, 126.69, 118.45, 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 99 16.00 O 3211 8.00 N 2635 7.00 C 9783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.07 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.08 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.07 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.11 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA W 3 " - " MAN W 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA W 3 " - " MAN W 5 " " BMA h 3 " - " MAN h 5 " BETA1-4 " NAG G 1 " - " NAG G 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG 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 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 h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " 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-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 137 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 398 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 295 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 137 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 392 " " NAG E 604 " - " ASN E 137 " " NAG E 605 " - " ASN E 339 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN E 156 " " NAG I 1 " - " ASN E 197 " " NAG J 1 " - " ASN E 234 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 276 " " NAG N 1 " - " ASN E 295 " " NAG O 1 " - " ASN E 301 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN E 386 " " NAG R 1 " - " ASN E 448 " " NAG S 1 " - " ASN E 88 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 276 " " NAG Y 1 " - " ASN A 295 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN A 448 " " NAG d 1 " - " ASN A 88 " " NAG e 1 " - " ASN C 156 " " NAG f 1 " - " ASN C 197 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 262 " " NAG i 1 " - " ASN C 276 " " NAG j 1 " - " ASN C 301 " " NAG k 1 " - " ASN C 332 " " NAG l 1 " - " ASN C 386 " " NAG m 1 " - " ASN C 392 " " NAG n 1 " - " ASN C 448 " " NAG o 1 " - " ASN C 88 " Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 2.2 seconds 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 36 sheets defined 24.6% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.697A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 125 Processing helix chain 'E' and resid 194 through 197 removed outlier: 4.350A pdb=" N ASN E 197 " --> pdb=" O ILE E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.968A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.715A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 535 removed outlier: 4.376A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 removed outlier: 4.156A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 595 Processing helix chain 'F' and resid 619 through 621 No H-bonds generated for 'chain 'F' and resid 619 through 621' Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 636 through 662 removed outlier: 4.705A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE F 642 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR F 643 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 68 removed outlier: 5.551A pdb=" N UNK H 67 " --> pdb=" O UNK H 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.713A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.319A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.607A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.790A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 536 removed outlier: 5.188A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 542 No H-bonds generated for 'chain 'B' and resid 539 through 542' Processing helix chain 'B' and resid 571 through 595 Processing helix chain 'B' and resid 619 through 623 removed outlier: 4.230A pdb=" N TRP B 623 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 662 removed outlier: 5.345A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.688A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.516A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.517A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.758A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 543 removed outlier: 3.953A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.885A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 662 removed outlier: 4.464A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.852A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.702A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 443 through 449 removed outlier: 7.451A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 465 through 469 removed outlier: 6.318A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 301 through 308 removed outlier: 3.818A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.992A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 3 through 8 Processing sheet with id= L, first strand: chain 'H' and resid 111 through 113 removed outlier: 5.939A pdb=" N UNK H 39 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N UNK H 48 " --> pdb=" O UNK H 39 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.213A pdb=" N UNK L 22 " --> pdb=" O UNK L 7 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.301A pdb=" N UNK L 103 " --> pdb=" O UNK L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'L' and resid 85 through 90 removed outlier: 5.918A pdb=" N UNK L 37 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N UNK L 46 " --> pdb=" O UNK L 37 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= Q, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.777A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= S, first strand: chain 'A' and resid 91 through 93 Processing sheet with id= T, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= U, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= V, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.850A pdb=" N ALA A 433 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.167A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.066A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 98 through 100 removed outlier: 3.710A pdb=" N UNK H 106 " --> pdb=" O UNK H 99 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 302 through 308 removed outlier: 6.004A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= AB, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.900A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= AD, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= AE, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= AF, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= AG, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= AH, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.308A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.969A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 302 through 308 removed outlier: 6.036A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1332 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: 5.27 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3338 1.32 - 1.46: 5023 1.46 - 1.59: 7482 1.59 - 1.73: 24 1.73 - 1.87: 129 Bond restraints: 15996 Sorted by residual: bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.632 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" CB HIS A 352 " pdb=" CG HIS A 352 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" CB ASN A 478 " pdb=" CG ASN A 478 " ideal model delta sigma weight residual 1.516 1.396 0.120 2.50e-02 1.60e+03 2.31e+01 bond pdb=" NE1 TRP E 427 " pdb=" CE2 TRP E 427 " ideal model delta sigma weight residual 1.370 1.319 0.051 1.10e-02 8.26e+03 2.17e+01 bond pdb=" NE1 TRP B 623 " pdb=" CE2 TRP B 623 " ideal model delta sigma weight residual 1.370 1.319 0.051 1.10e-02 8.26e+03 2.17e+01 ... (remaining 15991 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.16: 492 106.16 - 113.21: 8905 113.21 - 120.26: 6347 120.26 - 127.30: 5821 127.30 - 134.35: 199 Bond angle restraints: 21764 Sorted by residual: angle pdb=" C CYS E 239 " pdb=" N PRO E 240 " pdb=" CA PRO E 240 " ideal model delta sigma weight residual 119.56 127.56 -8.00 1.02e+00 9.61e-01 6.16e+01 angle pdb=" N LEU B 544 " pdb=" CA LEU B 544 " pdb=" C LEU B 544 " ideal model delta sigma weight residual 110.48 99.27 11.21 1.48e+00 4.57e-01 5.74e+01 angle pdb=" N THR A 461 " pdb=" CA THR A 461 " pdb=" C THR A 461 " ideal model delta sigma weight residual 114.56 105.04 9.52 1.27e+00 6.20e-01 5.62e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 126.87 -7.31 1.01e+00 9.80e-01 5.24e+01 angle pdb=" N GLU E 87 " pdb=" CA GLU E 87 " pdb=" C GLU E 87 " ideal model delta sigma weight residual 111.28 119.11 -7.83 1.09e+00 8.42e-01 5.16e+01 ... (remaining 21759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 10579 21.86 - 43.72: 208 43.72 - 65.58: 56 65.58 - 87.43: 30 87.43 - 109.29: 14 Dihedral angle restraints: 10887 sinusoidal: 5357 harmonic: 5530 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.69 -66.69 1 1.00e+01 1.00e-02 5.80e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.20 -59.20 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -127.81 41.81 1 1.00e+01 1.00e-02 2.44e+01 ... (remaining 10884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1764 0.099 - 0.198: 548 0.198 - 0.298: 277 0.298 - 0.397: 123 0.397 - 0.496: 82 Chirality restraints: 2794 Sorted by residual: chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.60e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.53e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.50e+02 ... (remaining 2791 not shown) Planarity restraints: 2720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " -0.286 2.00e-02 2.50e+03 2.46e-01 7.55e+02 pdb=" C7 NAG d 1 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " 0.007 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " 0.419 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 702 " -0.182 2.00e-02 2.50e+03 1.54e-01 2.98e+02 pdb=" C7 NAG D 702 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG D 702 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG D 702 " 0.250 2.00e-02 2.50e+03 pdb=" O7 NAG D 702 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 702 " -0.156 2.00e-02 2.50e+03 1.29e-01 2.08e+02 pdb=" C7 NAG F 702 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG F 702 " -0.115 2.00e-02 2.50e+03 pdb=" N2 NAG F 702 " 0.209 2.00e-02 2.50e+03 pdb=" O7 NAG F 702 " 0.019 2.00e-02 2.50e+03 ... (remaining 2717 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1993 2.74 - 3.28: 14363 3.28 - 3.82: 23963 3.82 - 4.36: 31132 4.36 - 4.90: 49775 Nonbonded interactions: 121226 Sorted by model distance: nonbonded pdb=" OG SER D 528 " pdb=" O7 NAG o 1 " model vdw 2.195 2.440 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.378 2.520 nonbonded pdb=" N LEU B 544 " pdb=" O LEU B 544 " model vdw 2.398 2.496 nonbonded pdb=" N UNK L 50 " pdb=" O UNK L 50 " model vdw 2.401 2.496 nonbonded pdb=" N THR A 461 " pdb=" N ASN A 462 " model vdw 2.408 2.560 ... (remaining 121221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 66 through 397 or resid 410 through \ 503 or resid 601 through 605)) selection = (chain 'C' and (resid 33 through 184 or resid 189 through 503 or resid 601 throu \ gh 605)) selection = (chain 'E' and (resid 33 through 57 or resid 66 through 184 or resid 189 through \ 503 or resid 601 through 605)) } ncs_group { reference = (chain 'B' and (resid 519 through 546 or resid 572 through 663 or resid 701 thro \ ugh 702)) selection = (chain 'D' and (resid 519 through 546 or resid 572 through 663 or resid 701 thro \ ugh 702)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } ncs_group { reference = (chain 'H' and resid 11 through 115) selection = chain 'L' } ncs_group { reference = chain 'W' selection = chain 'h' } 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: 2.350 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: 10.830 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 43.670 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.280 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.023 0.148 15996 Z= 1.457 Angle : 1.692 11.209 21764 Z= 1.081 Chirality : 0.150 0.496 2794 Planarity : 0.010 0.246 2664 Dihedral : 10.984 109.293 7190 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 1651 helix: -0.18 (0.23), residues: 418 sheet: 1.18 (0.23), residues: 432 loop : 0.57 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.009 TRP C 69 HIS 0.017 0.002 HIS E 374 PHE 0.028 0.005 PHE A 383 TYR 0.049 0.007 TYR A 191 ARG 0.007 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 1.764 Fit side-chains REVERT: E 142 MET cc_start: 0.8659 (mmm) cc_final: 0.8398 (mmm) REVERT: E 232 LYS cc_start: 0.7902 (mttt) cc_final: 0.7562 (mtmm) REVERT: A 142 MET cc_start: 0.8690 (mmm) cc_final: 0.8307 (mmm) REVERT: A 173 TYR cc_start: 0.7778 (p90) cc_final: 0.7519 (m-80) REVERT: B 542 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.8248 (mtt90) REVERT: B 579 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8571 (mtp180) REVERT: B 627 THR cc_start: 0.9065 (p) cc_final: 0.8765 (p) REVERT: C 95 MET cc_start: 0.9158 (ptm) cc_final: 0.8937 (ptp) REVERT: D 624 ASP cc_start: 0.8492 (m-30) cc_final: 0.8283 (m-30) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.3362 time to fit residues: 159.1483 Evaluate side-chains 164 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN E 246 GLN A 246 GLN B 570 HIS B 607 ASN C 99 ASN D 543 ASN D 591 GLN D 607 ASN D 625 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 15996 Z= 0.229 Angle : 0.641 7.634 21764 Z= 0.332 Chirality : 0.046 0.316 2794 Planarity : 0.005 0.049 2664 Dihedral : 8.182 83.588 4022 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.47 % Allowed : 6.47 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1651 helix: 0.62 (0.26), residues: 401 sheet: 1.00 (0.23), residues: 456 loop : 0.13 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 571 HIS 0.003 0.001 HIS E 105 PHE 0.017 0.002 PHE F 522 TYR 0.015 0.001 TYR E 177 ARG 0.004 0.001 ARG E 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 230 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 268 GLU cc_start: 0.7464 (pm20) cc_final: 0.7209 (mt-10) REVERT: F 634 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 142 MET cc_start: 0.8403 (mmm) cc_final: 0.7783 (mmm) REVERT: A 173 TYR cc_start: 0.7949 (p90) cc_final: 0.7540 (m-80) REVERT: A 191 TYR cc_start: 0.8862 (m-80) cc_final: 0.8570 (m-80) REVERT: B 542 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.8180 (mtt90) REVERT: B 634 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: B 660 LEU cc_start: 0.8933 (mp) cc_final: 0.8636 (mt) REVERT: C 95 MET cc_start: 0.9108 (ptm) cc_final: 0.8906 (ptp) outliers start: 22 outliers final: 11 residues processed: 243 average time/residue: 0.2769 time to fit residues: 99.0371 Evaluate side-chains 183 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 616 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 0.0570 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 152 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN F 607 ASN A 440 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15996 Z= 0.319 Angle : 0.641 12.195 21764 Z= 0.327 Chirality : 0.047 0.300 2794 Planarity : 0.004 0.042 2664 Dihedral : 7.434 74.712 4022 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.33 % Allowed : 7.87 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1651 helix: 0.28 (0.26), residues: 415 sheet: 0.94 (0.24), residues: 442 loop : -0.28 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 571 HIS 0.006 0.001 HIS E 72 PHE 0.015 0.002 PHE A 176 TYR 0.012 0.001 TYR A 191 ARG 0.004 0.001 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 268 GLU cc_start: 0.7588 (pm20) cc_final: 0.7256 (mt-10) REVERT: F 634 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 142 MET cc_start: 0.8374 (mmm) cc_final: 0.7843 (mmm) REVERT: B 542 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8172 (mtt90) outliers start: 35 outliers final: 27 residues processed: 193 average time/residue: 0.2770 time to fit residues: 79.5310 Evaluate side-chains 184 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 636 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15996 Z= 0.188 Angle : 0.533 9.411 21764 Z= 0.272 Chirality : 0.043 0.261 2794 Planarity : 0.004 0.042 2664 Dihedral : 6.715 67.355 4022 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.80 % Allowed : 10.07 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1651 helix: 0.29 (0.27), residues: 418 sheet: 0.87 (0.24), residues: 442 loop : -0.32 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 571 HIS 0.003 0.001 HIS C 374 PHE 0.011 0.001 PHE A 176 TYR 0.008 0.001 TYR C 484 ARG 0.002 0.000 ARG E 503 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: F 634 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 142 MET cc_start: 0.8326 (mmm) cc_final: 0.7857 (mmm) REVERT: B 542 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8140 (mtt90) REVERT: D 530 MET cc_start: 0.9065 (mtp) cc_final: 0.8790 (mtp) outliers start: 27 outliers final: 21 residues processed: 186 average time/residue: 0.2831 time to fit residues: 78.0099 Evaluate side-chains 181 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 660 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 15996 Z= 0.434 Angle : 0.693 9.754 21764 Z= 0.345 Chirality : 0.049 0.305 2794 Planarity : 0.005 0.046 2664 Dihedral : 6.963 59.759 4022 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.94 % Allowed : 9.61 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1651 helix: 0.06 (0.27), residues: 409 sheet: 0.54 (0.25), residues: 409 loop : -0.57 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 571 HIS 0.005 0.001 HIS C 374 PHE 0.018 0.003 PHE E 383 TYR 0.012 0.002 TYR A 217 ARG 0.006 0.001 ARG E 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 155 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: F 634 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 142 MET cc_start: 0.8365 (mmm) cc_final: 0.8111 (mmm) REVERT: B 542 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8220 (mtt90) REVERT: C 205 CYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6456 (m) outliers start: 44 outliers final: 33 residues processed: 183 average time/residue: 0.2747 time to fit residues: 75.1322 Evaluate side-chains 184 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 95 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15996 Z= 0.162 Angle : 0.513 7.949 21764 Z= 0.261 Chirality : 0.043 0.238 2794 Planarity : 0.004 0.042 2664 Dihedral : 6.070 54.270 4022 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.80 % Allowed : 11.41 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1651 helix: 0.39 (0.28), residues: 406 sheet: 0.63 (0.25), residues: 396 loop : -0.52 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 571 HIS 0.003 0.001 HIS C 374 PHE 0.011 0.001 PHE C 176 TYR 0.008 0.001 TYR E 191 ARG 0.003 0.000 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.780 Fit side-chains revert: symmetry clash REVERT: E 153 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7893 (mm-30) REVERT: F 542 ARG cc_start: 0.8542 (ptp90) cc_final: 0.8276 (ptp90) REVERT: F 634 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 142 MET cc_start: 0.8261 (mmm) cc_final: 0.7422 (mmm) REVERT: A 191 TYR cc_start: 0.9073 (m-80) cc_final: 0.8639 (m-80) REVERT: B 542 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8173 (mtm-85) REVERT: C 205 CYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6134 (m) REVERT: D 530 MET cc_start: 0.9080 (mtp) cc_final: 0.8798 (mtp) outliers start: 27 outliers final: 18 residues processed: 179 average time/residue: 0.2895 time to fit residues: 76.2367 Evaluate side-chains 178 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 chunk 181 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15996 Z= 0.162 Angle : 0.500 7.775 21764 Z= 0.254 Chirality : 0.042 0.309 2794 Planarity : 0.004 0.041 2664 Dihedral : 5.323 54.288 4022 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.73 % Allowed : 11.74 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1651 helix: 0.48 (0.28), residues: 408 sheet: 0.83 (0.25), residues: 406 loop : -0.61 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 96 HIS 0.003 0.001 HIS C 374 PHE 0.009 0.001 PHE E 383 TYR 0.008 0.001 TYR E 191 ARG 0.004 0.000 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: E 153 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7902 (mm-30) REVERT: F 542 ARG cc_start: 0.8537 (ptp90) cc_final: 0.8284 (ptp90) REVERT: F 634 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 142 MET cc_start: 0.8290 (mmm) cc_final: 0.7996 (mmm) REVERT: A 191 TYR cc_start: 0.9048 (m-80) cc_final: 0.8617 (m-80) REVERT: B 542 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8192 (mtm-85) REVERT: C 205 CYS cc_start: 0.6323 (OUTLIER) cc_final: 0.5923 (m) REVERT: D 530 MET cc_start: 0.9079 (mtp) cc_final: 0.8813 (mtp) outliers start: 26 outliers final: 21 residues processed: 184 average time/residue: 0.2924 time to fit residues: 78.6912 Evaluate side-chains 182 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15996 Z= 0.222 Angle : 0.525 8.245 21764 Z= 0.267 Chirality : 0.043 0.264 2794 Planarity : 0.004 0.041 2664 Dihedral : 5.200 54.243 4022 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.13 % Allowed : 11.54 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1651 helix: 0.43 (0.28), residues: 408 sheet: 0.75 (0.25), residues: 382 loop : -0.63 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 96 HIS 0.004 0.001 HIS C 374 PHE 0.011 0.001 PHE E 383 TYR 0.007 0.001 TYR A 191 ARG 0.004 0.000 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 1.720 Fit side-chains revert: symmetry clash REVERT: E 358 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7898 (mt) REVERT: F 542 ARG cc_start: 0.8549 (ptp90) cc_final: 0.8307 (ptp90) REVERT: F 634 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 142 MET cc_start: 0.8317 (mmm) cc_final: 0.7518 (mmm) REVERT: B 542 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8184 (mtm-85) REVERT: C 205 CYS cc_start: 0.6478 (OUTLIER) cc_final: 0.6029 (m) REVERT: D 530 MET cc_start: 0.9060 (mtp) cc_final: 0.8782 (mtp) outliers start: 32 outliers final: 30 residues processed: 176 average time/residue: 0.2987 time to fit residues: 77.6921 Evaluate side-chains 187 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15996 Z= 0.200 Angle : 0.510 7.587 21764 Z= 0.260 Chirality : 0.042 0.246 2794 Planarity : 0.004 0.040 2664 Dihedral : 5.122 54.373 4022 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.20 % Allowed : 11.74 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1651 helix: 0.45 (0.27), residues: 408 sheet: 0.78 (0.25), residues: 392 loop : -0.66 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 96 HIS 0.004 0.001 HIS C 374 PHE 0.010 0.001 PHE E 383 TYR 0.008 0.001 TYR A 191 ARG 0.003 0.000 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 1.854 Fit side-chains revert: symmetry clash REVERT: E 358 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7895 (mt) REVERT: F 542 ARG cc_start: 0.8567 (ptp90) cc_final: 0.8318 (ptp90) REVERT: F 634 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 142 MET cc_start: 0.8308 (mmm) cc_final: 0.8064 (mmm) REVERT: B 542 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8205 (mtm-85) REVERT: C 205 CYS cc_start: 0.6470 (OUTLIER) cc_final: 0.6057 (m) REVERT: D 530 MET cc_start: 0.9070 (mtp) cc_final: 0.8807 (mtp) outliers start: 33 outliers final: 30 residues processed: 180 average time/residue: 0.2927 time to fit residues: 77.9668 Evaluate side-chains 187 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 149 optimal weight: 0.1980 chunk 15 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15996 Z= 0.254 Angle : 0.547 8.592 21764 Z= 0.276 Chirality : 0.044 0.239 2794 Planarity : 0.004 0.041 2664 Dihedral : 5.272 54.628 4022 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.40 % Allowed : 11.67 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1651 helix: 0.39 (0.27), residues: 408 sheet: 0.65 (0.26), residues: 375 loop : -0.68 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 571 HIS 0.004 0.001 HIS C 374 PHE 0.013 0.002 PHE E 383 TYR 0.008 0.001 TYR C 484 ARG 0.004 0.000 ARG E 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 1.723 Fit side-chains revert: symmetry clash REVERT: E 358 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7879 (mt) REVERT: F 542 ARG cc_start: 0.8566 (ptp90) cc_final: 0.8326 (ptp90) REVERT: F 634 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8277 (tm-30) REVERT: A 142 MET cc_start: 0.8311 (mmm) cc_final: 0.7561 (mmm) REVERT: B 542 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8223 (mtm-85) REVERT: C 205 CYS cc_start: 0.6519 (OUTLIER) cc_final: 0.6089 (m) REVERT: D 530 MET cc_start: 0.9057 (mtp) cc_final: 0.8777 (mtp) outliers start: 36 outliers final: 32 residues processed: 184 average time/residue: 0.2890 time to fit residues: 78.4515 Evaluate side-chains 190 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 27 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.120817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098834 restraints weight = 23972.955| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.73 r_work: 0.2951 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15996 Z= 0.222 Angle : 0.528 7.890 21764 Z= 0.269 Chirality : 0.043 0.236 2794 Planarity : 0.004 0.040 2664 Dihedral : 5.227 54.455 4022 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.47 % Allowed : 11.94 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1651 helix: 0.43 (0.27), residues: 408 sheet: 0.57 (0.25), residues: 396 loop : -0.71 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 571 HIS 0.004 0.001 HIS C 374 PHE 0.011 0.001 PHE E 383 TYR 0.010 0.001 TYR A 191 ARG 0.004 0.000 ARG E 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3179.34 seconds wall clock time: 58 minutes 39.11 seconds (3519.11 seconds total)