Starting phenix.real_space_refine on Sat Mar 16 22:32:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l86_23223/03_2024/7l86_23223_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l86_23223/03_2024/7l86_23223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l86_23223/03_2024/7l86_23223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l86_23223/03_2024/7l86_23223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l86_23223/03_2024/7l86_23223_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l86_23223/03_2024/7l86_23223_updated.pdb" } resolution = 3.4 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 9831 2.51 5 N 2650 2.21 5 O 3222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 87": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 457": "OD1" <-> "OD2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15802 Number of models: 1 Model: "" Number of chains: 47 Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 595 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'TRANS': 118} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'UNK:plan-1': 119} Unresolved non-hydrogen planarities: 119 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: "E" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3442 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3488 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 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: 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: "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: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 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: 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: "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: "A" 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: "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 Time building chain proxies: 8.43, per 1000 atoms: 0.53 Number of scatterers: 15802 At special positions: 0 Unit cell: (141.11, 149.35, 119.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 3222 8.00 N 2650 7.00 C 9831 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 C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 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 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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 V 3 " - " MAN V 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA V 3 " - " MAN V 5 " " BMA f 3 " - " MAN f 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG 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 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 339 " " NAG C 604 " - " ASN C 448 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 137 " " NAG C 607 " - " ASN C 355 " " 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 339 " " NAG E 604 " - " ASN E 448 " " NAG E 605 " - " ASN E 88 " " NAG E 606 " - " ASN E 355 " " 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 392 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 234 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 295 " " NAG Y 1 " - " ASN C 301 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 392 " " NAG c 1 " - " ASN A 156 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 234 " " NAG f 1 " - " ASN A 262 " " NAG g 1 " - " ASN A 276 " " NAG h 1 " - " ASN A 295 " " NAG i 1 " - " ASN A 332 " " NAG j 1 " - " ASN A 386 " " NAG k 1 " - " ASN A 392 " " NAG l 1 " - " ASN A 448 " " NAG m 1 " - " ASN A 88 " " NAG n 1 " - " ASN A 462 " " NAG o 1 " - " ASN A 355 " Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 2.8 seconds 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3608 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 31 sheets defined 25.7% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 99 through 116 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 140 through 150 No H-bonds generated for 'chain 'E' and resid 140 through 150' Processing helix chain 'E' and resid 194 through 197 removed outlier: 4.476A 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: 4.049A 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 485 removed outlier: 3.606A pdb=" N SER E 481 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 543 removed outlier: 4.072A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 595 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 639 through 663 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 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.409A 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 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 387 through 391 Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 475 through 485 removed outlier: 5.056A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 543 removed outlier: 4.019A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 595 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 663 removed outlier: 5.045A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.438A 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 353 removed outlier: 3.985A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (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 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'B' and resid 530 through 543 removed outlier: 4.719A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 595 removed outlier: 3.831A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 622 No H-bonds generated for 'chain 'B' and resid 619 through 622' Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 663 removed outlier: 4.143A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 656 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 657 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'H' and resid 116 through 118 removed outlier: 5.799A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N UNK H 40 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N UNK H 45 " --> pdb=" O UNK H 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 32 through 37 Processing sheet with id= D, first strand: chain 'L' and resid 61 through 64 removed outlier: 3.683A pdb=" N UNK L 74 " --> pdb=" O UNK L 62 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= F, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.826A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= H, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= I, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= J, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= K, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.362A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.298A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 301 through 308 removed outlier: 4.073A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.933A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= O, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= P, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= Q, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= R, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= S, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= T, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.254A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.329A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 301 through 308 removed outlier: 4.130A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= X, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.792A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= Z, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= AA, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= AB, first strand: chain 'A' and resid 200 through 203 Processing sheet with id= AC, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.119A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.995A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 301 through 308 removed outlier: 4.293A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.932A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1344 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: 5.49 Time building geometry restraints manager: 7.59 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: 3830 1.32 - 1.46: 5006 1.46 - 1.60: 7100 1.60 - 1.74: 13 1.74 - 1.88: 122 Bond restraints: 16071 Sorted by residual: bond pdb=" CB ASN E 289 " pdb=" CG ASN E 289 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.93e+01 bond pdb=" CB LEU E 125 " pdb=" CG LEU E 125 " ideal model delta sigma weight residual 1.530 1.424 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CB ASN E 195 " pdb=" CG ASN E 195 " ideal model delta sigma weight residual 1.516 1.386 0.130 2.50e-02 1.60e+03 2.70e+01 bond pdb=" CB ILE E 201 " pdb=" CG1 ILE E 201 " ideal model delta sigma weight residual 1.530 1.426 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CB HIS C 66 " pdb=" CG HIS C 66 " ideal model delta sigma weight residual 1.497 1.567 -0.070 1.40e-02 5.10e+03 2.52e+01 ... (remaining 16066 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.13: 499 106.13 - 113.18: 8900 113.18 - 120.22: 6390 120.22 - 127.27: 5876 127.27 - 134.31: 198 Bond angle restraints: 21863 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 119.56 127.86 -8.30 1.02e+00 9.61e-01 6.62e+01 angle pdb=" CA ASN E 195 " pdb=" CB ASN E 195 " pdb=" CG ASN E 195 " ideal model delta sigma weight residual 112.60 104.63 7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.39 -7.83 1.02e+00 9.61e-01 5.89e+01 angle pdb=" C CYS C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.56 126.92 -7.36 1.02e+00 9.61e-01 5.21e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 126.86 -7.30 1.02e+00 9.61e-01 5.12e+01 ... (remaining 21858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 10630 21.26 - 42.52: 227 42.52 - 63.77: 58 63.77 - 85.03: 28 85.03 - 106.29: 13 Dihedral angle restraints: 10956 sinusoidal: 5415 harmonic: 5541 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.57 -63.57 1 1.00e+01 1.00e-02 5.33e+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 93.00 149.26 -56.26 1 1.00e+01 1.00e-02 4.27e+01 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 93.00 147.47 -54.47 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 10953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1798 0.101 - 0.202: 608 0.202 - 0.302: 224 0.302 - 0.403: 119 0.403 - 0.504: 59 Chirality restraints: 2808 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.63e+02 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 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 a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 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 ... (remaining 2805 not shown) Planarity restraints: 2730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG o 2 " -0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG o 2 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG o 2 " -0.083 2.00e-02 2.50e+03 pdb=" N2 NAG o 2 " 0.528 2.00e-02 2.50e+03 pdb=" O7 NAG o 2 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG n 2 " 0.344 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG n 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG n 2 " 0.159 2.00e-02 2.50e+03 pdb=" N2 NAG n 2 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG n 2 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG n 1 " -0.323 2.00e-02 2.50e+03 2.76e-01 9.53e+02 pdb=" C7 NAG n 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG n 1 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG n 1 " 0.485 2.00e-02 2.50e+03 pdb=" O7 NAG n 1 " -0.070 2.00e-02 2.50e+03 ... (remaining 2727 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5315 2.87 - 3.38: 14113 3.38 - 3.88: 25420 3.88 - 4.39: 29750 4.39 - 4.90: 47111 Nonbonded interactions: 121709 Sorted by model distance: nonbonded pdb=" N UNK H 67 " pdb=" N UNK H 68 " model vdw 2.361 2.560 nonbonded pdb=" OD1 ASP C 107 " pdb=" NZ LYS D 574 " model vdw 2.389 2.520 nonbonded pdb=" NZ LYS C 490 " pdb=" OE2 GLU C 492 " model vdw 2.397 2.520 nonbonded pdb=" N VAL A 75 " pdb=" O VAL A 75 " model vdw 2.424 2.496 nonbonded pdb=" N THR C 139 " pdb=" O THR C 139 " model vdw 2.430 2.496 ... (remaining 121704 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 397 or resid 412 through 458 or resid 463 throu \ gh 505 or resid 601 through 605)) selection = (chain 'C' and (resid 33 through 397 or resid 412 through 505 or resid 601 throu \ gh 605)) selection = (chain 'E' and (resid 33 through 57 or resid 66 through 397 or resid 412 through \ 505 or resid 601 through 605)) } ncs_group { reference = chain 'B' selection = chain 'D' 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 'W' 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 'g' selection = chain 'h' 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 16 through 120) selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'V' selection = chain 'f' } 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.930 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 45.030 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.300 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 0.140 16071 Z= 1.444 Angle : 1.697 9.957 21863 Z= 1.083 Chirality : 0.144 0.504 2808 Planarity : 0.015 0.298 2673 Dihedral : 10.850 106.288 7249 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 0.96 (0.19), residues: 1646 helix: 0.51 (0.24), residues: 407 sheet: 1.06 (0.24), residues: 396 loop : 0.67 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.009 TRP E 69 HIS 0.009 0.002 HIS E 374 PHE 0.029 0.006 PHE A 383 TYR 0.049 0.008 TYR C 486 ARG 0.007 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 195 ASN cc_start: 0.8419 (p0) cc_final: 0.8084 (p0) REVERT: F 617 ARG cc_start: 0.8639 (mtt-85) cc_final: 0.8213 (mtp85) REVERT: C 51 THR cc_start: 0.9397 (m) cc_final: 0.8988 (p) REVERT: C 150 MET cc_start: 0.8771 (mmm) cc_final: 0.8537 (mmt) REVERT: C 482 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8063 (mm-30) REVERT: B 636 SER cc_start: 0.8916 (t) cc_final: 0.8693 (t) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.3182 time to fit residues: 156.3588 Evaluate side-chains 170 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN E 66 HIS E 246 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 428 GLN C 280 ASN D 590 GLN A 67 ASN A 85 HIS A 280 ASN B 618 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16071 Z= 0.234 Angle : 0.663 14.401 21863 Z= 0.338 Chirality : 0.046 0.279 2808 Planarity : 0.005 0.067 2673 Dihedral : 8.529 82.897 4066 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.93 % Allowed : 6.93 % Favored : 91.14 % 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: 1.11 (0.20), residues: 1646 helix: 1.21 (0.26), residues: 404 sheet: 0.97 (0.24), residues: 426 loop : 0.50 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 112 HIS 0.005 0.001 HIS C 249 PHE 0.017 0.002 PHE A 353 TYR 0.010 0.001 TYR C 173 ARG 0.007 0.001 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 222 time to evaluate : 1.783 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9048 (mt) cc_final: 0.8820 (tp) REVERT: C 482 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8176 (mm-30) REVERT: D 654 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: A 325 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8217 (t0) outliers start: 29 outliers final: 14 residues processed: 242 average time/residue: 0.2641 time to fit residues: 95.6885 Evaluate side-chains 191 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 606 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 46 optimal weight: 0.4980 chunk 170 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 168 optimal weight: 0.0070 chunk 57 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN E 66 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN C 422 GLN A 422 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16071 Z= 0.325 Angle : 0.642 11.569 21863 Z= 0.326 Chirality : 0.046 0.229 2808 Planarity : 0.005 0.043 2673 Dihedral : 7.730 70.607 4066 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.53 % Allowed : 9.19 % Favored : 88.27 % 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: 0.71 (0.20), residues: 1646 helix: 0.88 (0.25), residues: 410 sheet: 0.90 (0.24), residues: 431 loop : 0.12 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 45 HIS 0.006 0.001 HIS C 249 PHE 0.020 0.002 PHE F 522 TYR 0.022 0.002 TYR E 173 ARG 0.005 0.001 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.638 Fit side-chains REVERT: C 482 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8186 (mm-30) REVERT: A 106 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7880 (mt-10) outliers start: 38 outliers final: 29 residues processed: 201 average time/residue: 0.2791 time to fit residues: 82.7866 Evaluate side-chains 191 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.0060 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN A 195 ASN B 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16071 Z= 0.300 Angle : 0.602 8.784 21863 Z= 0.303 Chirality : 0.045 0.239 2808 Planarity : 0.004 0.045 2673 Dihedral : 7.209 61.663 4066 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.40 % Allowed : 10.46 % Favored : 87.14 % 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: 0.51 (0.20), residues: 1646 helix: 0.80 (0.26), residues: 410 sheet: 0.80 (0.24), residues: 436 loop : -0.07 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 45 HIS 0.004 0.001 HIS C 105 PHE 0.013 0.002 PHE C 53 TYR 0.022 0.002 TYR E 173 ARG 0.007 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.804 Fit side-chains revert: symmetry clash REVERT: E 201 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8526 (mt) REVERT: C 103 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: C 482 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8162 (mm-30) outliers start: 36 outliers final: 25 residues processed: 188 average time/residue: 0.2760 time to fit residues: 77.3963 Evaluate side-chains 188 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 606 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 124 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS E 103 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16071 Z= 0.276 Angle : 0.584 9.636 21863 Z= 0.291 Chirality : 0.044 0.272 2808 Planarity : 0.004 0.044 2673 Dihedral : 6.862 54.100 4066 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.80 % Allowed : 9.93 % Favored : 87.28 % 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: 0.44 (0.20), residues: 1646 helix: 0.89 (0.26), residues: 403 sheet: 0.77 (0.25), residues: 418 loop : -0.17 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.004 0.001 HIS C 105 PHE 0.012 0.002 PHE C 53 TYR 0.024 0.002 TYR E 173 ARG 0.006 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 201 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8542 (mt) REVERT: C 103 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7659 (tm-30) outliers start: 42 outliers final: 30 residues processed: 190 average time/residue: 0.2723 time to fit residues: 77.5501 Evaluate side-chains 196 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16071 Z= 0.296 Angle : 0.592 7.723 21863 Z= 0.294 Chirality : 0.044 0.234 2808 Planarity : 0.004 0.046 2673 Dihedral : 6.670 54.370 4066 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.00 % Allowed : 10.06 % Favored : 86.94 % 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: 0.35 (0.20), residues: 1646 helix: 0.85 (0.26), residues: 405 sheet: 0.67 (0.25), residues: 423 loop : -0.24 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 96 HIS 0.004 0.001 HIS C 105 PHE 0.013 0.002 PHE C 53 TYR 0.025 0.002 TYR E 173 ARG 0.005 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 2.136 Fit side-chains revert: symmetry clash REVERT: E 201 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8597 (mt) REVERT: C 103 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: C 112 TRP cc_start: 0.8748 (t-100) cc_final: 0.8463 (t-100) REVERT: B 607 ASN cc_start: 0.9232 (m-40) cc_final: 0.8932 (t0) outliers start: 45 outliers final: 33 residues processed: 200 average time/residue: 0.2822 time to fit residues: 83.8366 Evaluate side-chains 199 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN E 66 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN B 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 16071 Z= 0.424 Angle : 0.684 9.545 21863 Z= 0.336 Chirality : 0.047 0.248 2808 Planarity : 0.005 0.053 2673 Dihedral : 7.238 56.468 4066 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.13 % Allowed : 11.06 % Favored : 85.81 % 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: 0.02 (0.20), residues: 1646 helix: 0.60 (0.26), residues: 409 sheet: 0.45 (0.25), residues: 430 loop : -0.46 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 96 HIS 0.005 0.001 HIS C 105 PHE 0.022 0.002 PHE C 53 TYR 0.022 0.002 TYR E 173 ARG 0.004 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 201 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8614 (mt) REVERT: F 626 MET cc_start: 0.8499 (mtm) cc_final: 0.8290 (mtm) REVERT: C 103 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7662 (tm-30) outliers start: 47 outliers final: 37 residues processed: 190 average time/residue: 0.2818 time to fit residues: 78.5259 Evaluate side-chains 196 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 606 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 16 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16071 Z= 0.287 Angle : 0.607 8.726 21863 Z= 0.300 Chirality : 0.045 0.433 2808 Planarity : 0.004 0.049 2673 Dihedral : 6.997 59.923 4066 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.66 % Allowed : 11.73 % Favored : 85.61 % 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: 0.11 (0.20), residues: 1646 helix: 0.80 (0.26), residues: 402 sheet: 0.47 (0.25), residues: 428 loop : -0.45 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 96 HIS 0.003 0.001 HIS C 105 PHE 0.011 0.002 PHE C 53 TYR 0.021 0.001 TYR E 173 ARG 0.007 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 201 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8620 (mt) REVERT: C 103 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7676 (tm-30) outliers start: 40 outliers final: 32 residues processed: 190 average time/residue: 0.2807 time to fit residues: 78.2417 Evaluate side-chains 194 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16071 Z= 0.227 Angle : 0.558 8.353 21863 Z= 0.276 Chirality : 0.044 0.332 2808 Planarity : 0.004 0.045 2673 Dihedral : 6.548 55.807 4066 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.20 % Allowed : 11.99 % Favored : 85.81 % 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: 0.23 (0.20), residues: 1646 helix: 0.96 (0.26), residues: 404 sheet: 0.43 (0.25), residues: 424 loop : -0.33 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS C 105 PHE 0.010 0.001 PHE A 353 TYR 0.025 0.001 TYR E 173 ARG 0.004 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 201 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8655 (mt) REVERT: C 103 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: C 112 TRP cc_start: 0.8750 (t-100) cc_final: 0.8407 (t-100) REVERT: A 69 TRP cc_start: 0.7535 (m100) cc_final: 0.7129 (m100) outliers start: 33 outliers final: 28 residues processed: 192 average time/residue: 0.2879 time to fit residues: 81.4979 Evaluate side-chains 199 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 543 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 16071 Z= 0.456 Angle : 0.706 10.264 21863 Z= 0.345 Chirality : 0.048 0.405 2808 Planarity : 0.005 0.051 2673 Dihedral : 7.154 57.968 4066 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.13 % Allowed : 11.86 % Favored : 86.01 % 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: -0.09 (0.20), residues: 1646 helix: 0.60 (0.26), residues: 411 sheet: 0.36 (0.25), residues: 416 loop : -0.55 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 96 HIS 0.005 0.001 HIS C 105 PHE 0.016 0.002 PHE C 53 TYR 0.025 0.002 TYR E 173 ARG 0.005 0.001 ARG B 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 201 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8675 (mt) REVERT: C 103 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7672 (tm-30) outliers start: 32 outliers final: 24 residues processed: 181 average time/residue: 0.2904 time to fit residues: 77.6270 Evaluate side-chains 187 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 148 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.092920 restraints weight = 29431.942| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.79 r_work: 0.2988 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16071 Z= 0.164 Angle : 0.537 9.176 21863 Z= 0.268 Chirality : 0.043 0.309 2808 Planarity : 0.004 0.042 2673 Dihedral : 6.391 56.006 4066 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.27 % Allowed : 12.92 % Favored : 85.81 % 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: 0.28 (0.21), residues: 1646 helix: 1.06 (0.26), residues: 401 sheet: 0.48 (0.26), residues: 399 loop : -0.32 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.003 0.000 HIS C 105 PHE 0.008 0.001 PHE A 353 TYR 0.023 0.001 TYR E 173 ARG 0.003 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.22 seconds wall clock time: 57 minutes 3.51 seconds (3423.51 seconds total)