Starting phenix.real_space_refine on Fri Feb 16 09:14:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0r_20396/02_2024/6v0r_20396.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0r_20396/02_2024/6v0r_20396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0r_20396/02_2024/6v0r_20396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0r_20396/02_2024/6v0r_20396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0r_20396/02_2024/6v0r_20396.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0r_20396/02_2024/6v0r_20396.pdb" } resolution = 3.87 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= -0.001 sd= 0.086 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 108 5.16 5 C 9297 2.51 5 N 2454 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 91": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "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 PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B TYR 638": "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 PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 621": "OE1" <-> "OE2" Residue "E TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 621": "OE1" <-> "OE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3462 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3462 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "D" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3462 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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 Time building chain proxies: 7.97, per 1000 atoms: 0.53 Number of scatterers: 14910 At special positions: 0 Unit cell: (125.66, 128.75, 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 108 16.00 O 3051 8.00 N 2454 7.00 C 9297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.60 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.59 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.60 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS E 561 " distance=2.59 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.60 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS F 561 " distance=2.59 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN S 4 " - " MAN S 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA S 3 " - " MAN S 6 " " BMA b 3 " - " MAN b 6 " BETA1-4 " 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 J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 2 " " NAG V 1 " - " FUC V 3 " " NAG X 1 " - " FUC X 2 " " NAG e 1 " - " FUC e 3 " " NAG g 1 " - " FUC g 2 " NAG-ASN " NAG A 603 " - " ASN A 234 " " NAG A 606 " - " ASN A 392 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 295 " " NAG A 611 " - " ASN A 448 " " NAG A 618 " - " ASN A 301 " " NAG A 622 " - " ASN A 160 " " NAG A 623 " - " ASN A 197 " " NAG A 632 " - " ASN A 355 " " NAG B 703 " - " ASN B 618 " " NAG B 704 " - " ASN B 637 " " NAG C 603 " - " ASN C 234 " " NAG C 606 " - " ASN C 392 " " NAG C 609 " - " ASN C 339 " " NAG C 610 " - " ASN C 295 " " NAG C 611 " - " ASN C 448 " " NAG C 618 " - " ASN C 301 " " NAG C 622 " - " ASN C 160 " " NAG C 623 " - " ASN C 197 " " NAG C 632 " - " ASN C 355 " " NAG D 603 " - " ASN D 234 " " NAG D 606 " - " ASN D 392 " " NAG D 609 " - " ASN D 339 " " NAG D 610 " - " ASN D 295 " " NAG D 611 " - " ASN D 448 " " NAG D 618 " - " ASN D 301 " " NAG D 622 " - " ASN D 160 " " NAG D 623 " - " ASN D 197 " " NAG D 632 " - " ASN D 355 " " NAG E 703 " - " ASN E 618 " " NAG E 704 " - " ASN E 637 " " NAG F 703 " - " ASN F 618 " " NAG F 704 " - " ASN F 637 " " NAG G 1 " - " ASN A 88 " " NAG H 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 386 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 156 " " NAG L 1 " - " ASN A 133 " " NAG M 1 " - " ASN A 137 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN B 611 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 276 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 156 " " NAG U 1 " - " ASN C 133 " " NAG V 1 " - " ASN C 137 " " NAG W 1 " - " ASN C 332 " " NAG X 1 " - " ASN E 611 " " NAG Y 1 " - " ASN D 88 " " NAG Z 1 " - " ASN D 276 " " NAG a 1 " - " ASN D 386 " " NAG b 1 " - " ASN D 262 " " NAG c 1 " - " ASN D 156 " " NAG d 1 " - " ASN D 133 " " NAG e 1 " - " ASN D 137 " " NAG f 1 " - " ASN D 332 " " NAG g 1 " - " ASN F 611 " Time building additional restraints: 7.25 Conformation dependent library (CDL) restraints added in 2.7 seconds 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 27 sheets defined 30.5% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.847A pdb=" N THR A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.638A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 354 removed outlier: 5.125A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.935A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.464A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 571 through 596 removed outlier: 4.976A pdb=" N GLN B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.847A pdb=" N THR C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.638A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 354 removed outlier: 5.124A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.935A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.463A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 562 through 568 Processing helix chain 'E' and resid 571 through 596 removed outlier: 4.976A pdb=" N GLN E 577 " --> pdb=" O ILE E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 663 Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.847A pdb=" N THR D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 116 removed outlier: 3.638A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 334 through 354 removed outlier: 5.125A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.935A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 484 No H-bonds generated for 'chain 'D' and resid 482 through 484' Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.463A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 562 through 568 Processing helix chain 'F' and resid 571 through 596 removed outlier: 4.976A pdb=" N GLN F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 663 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.373A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.707A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.280A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.491A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 12.584A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.380A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.373A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.707A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.280A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.491A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 12.584A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.380A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.373A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.707A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.280A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.491A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N ILE D 453 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 10.451A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP D 457 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N ILE D 284 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 271 through 274 removed outlier: 12.584A pdb=" N ILE D 284 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP D 457 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 10.451A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N ILE D 453 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.380A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 7.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2963 1.32 - 1.44: 3799 1.44 - 1.57: 8256 1.57 - 1.70: 24 1.70 - 1.82: 144 Bond restraints: 15186 Sorted by residual: bond pdb=" CB TYR A 484 " pdb=" CG TYR A 484 " ideal model delta sigma weight residual 1.512 1.385 0.127 2.20e-02 2.07e+03 3.32e+01 bond pdb=" CB TYR C 484 " pdb=" CG TYR C 484 " ideal model delta sigma weight residual 1.512 1.385 0.127 2.20e-02 2.07e+03 3.31e+01 bond pdb=" CB TYR D 484 " pdb=" CG TYR D 484 " ideal model delta sigma weight residual 1.512 1.386 0.126 2.20e-02 2.07e+03 3.29e+01 bond pdb=" CB TYR C 217 " pdb=" CG TYR C 217 " ideal model delta sigma weight residual 1.512 1.410 0.102 2.20e-02 2.07e+03 2.16e+01 bond pdb=" CB TYR A 217 " pdb=" CG TYR A 217 " ideal model delta sigma weight residual 1.512 1.410 0.102 2.20e-02 2.07e+03 2.15e+01 ... (remaining 15181 not shown) Histogram of bond angle deviations from ideal: 91.79 - 100.28: 12 100.28 - 108.77: 2181 108.77 - 117.25: 9704 117.25 - 125.74: 8399 125.74 - 134.23: 320 Bond angle restraints: 20616 Sorted by residual: angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.01e+00 9.80e-01 6.19e+01 angle pdb=" C ARG D 298 " pdb=" N PRO D 299 " pdb=" CA PRO D 299 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.01e+00 9.80e-01 6.15e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.01e+00 9.80e-01 6.15e+01 angle pdb=" C4 FUC X 2 " pdb=" C5 FUC X 2 " pdb=" C6 FUC X 2 " ideal model delta sigma weight residual 113.23 91.79 21.44 3.00e+00 1.11e-01 5.11e+01 angle pdb=" C4 FUC O 2 " pdb=" C5 FUC O 2 " pdb=" C6 FUC O 2 " ideal model delta sigma weight residual 113.23 91.80 21.43 3.00e+00 1.11e-01 5.10e+01 ... (remaining 20611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 9945 21.81 - 43.62: 389 43.62 - 65.42: 112 65.42 - 87.23: 57 87.23 - 109.04: 36 Dihedral angle restraints: 10539 sinusoidal: 5619 harmonic: 4920 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.54 -60.54 1 1.00e+01 1.00e-02 4.88e+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 93.00 153.53 -60.53 1 1.00e+01 1.00e-02 4.88e+01 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 93.00 153.53 -60.53 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 10536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1960 0.114 - 0.229: 595 0.229 - 0.343: 82 0.343 - 0.457: 0 0.457 - 0.571: 12 Chirality restraints: 2649 Sorted by residual: chirality pdb=" C1 FUC X 2 " pdb=" O6 NAG X 1 " pdb=" C2 FUC X 2 " pdb=" O5 FUC X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.38e+02 chirality pdb=" C1 FUC g 2 " pdb=" O6 NAG g 1 " pdb=" C2 FUC g 2 " pdb=" O5 FUC g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 FUC O 2 " pdb=" O6 NAG O 1 " pdb=" C2 FUC O 2 " pdb=" O5 FUC O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.34e+02 ... (remaining 2646 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.052 2.00e-02 2.50e+03 5.46e-02 3.72e+01 pdb=" CG ASN F 611 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.085 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.052 2.00e-02 2.50e+03 5.46e-02 3.72e+01 pdb=" CG ASN B 611 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.085 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " -0.052 2.00e-02 2.50e+03 5.46e-02 3.72e+01 pdb=" CG ASN E 611 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " 0.085 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " -0.065 2.00e-02 2.50e+03 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3970 2.80 - 3.32: 13044 3.32 - 3.85: 24377 3.85 - 4.37: 28026 4.37 - 4.90: 46220 Nonbonded interactions: 115637 Sorted by model distance: nonbonded pdb=" OG1 THR D 37 " pdb=" OG1 THR D 499 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.270 2.440 nonbonded pdb=" O5 NAG H 1 " pdb=" O6 NAG H 1 " model vdw 2.383 2.432 nonbonded pdb=" O5 NAG Z 1 " pdb=" O6 NAG Z 1 " model vdw 2.383 2.432 ... (remaining 115632 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' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'b' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.440 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 42.040 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.020 0.127 15186 Z= 1.268 Angle : 1.800 21.437 20616 Z= 1.109 Chirality : 0.106 0.571 2649 Planarity : 0.009 0.049 2469 Dihedral : 14.988 109.037 7239 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 1.44 % Allowed : 4.32 % Favored : 94.24 % Rotamer: Outliers : 1.98 % Allowed : 1.19 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1668 helix: -0.30 (0.25), residues: 402 sheet: 0.77 (0.23), residues: 501 loop : 0.88 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.011 TRP A 479 HIS 0.006 0.002 HIS D 72 PHE 0.038 0.006 PHE A 383 TYR 0.048 0.008 TYR C 40 ARG 0.005 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 378 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8353 (ptm) cc_final: 0.8146 (ptp) REVERT: A 103 GLN cc_start: 0.8742 (tp40) cc_final: 0.8462 (tm-30) REVERT: A 199 SER cc_start: 0.9331 (p) cc_final: 0.9098 (m) REVERT: A 457 ASP cc_start: 0.7819 (t0) cc_final: 0.7561 (t0) REVERT: B 543 ASN cc_start: 0.8864 (m-40) cc_final: 0.8447 (m-40) REVERT: B 612 SER cc_start: 0.8439 (p) cc_final: 0.8161 (t) REVERT: B 647 GLU cc_start: 0.7662 (tt0) cc_final: 0.7431 (mt-10) REVERT: C 103 GLN cc_start: 0.8770 (tp40) cc_final: 0.8368 (tm-30) REVERT: C 107 ASP cc_start: 0.7888 (m-30) cc_final: 0.7672 (m-30) REVERT: C 109 ILE cc_start: 0.9178 (mt) cc_final: 0.8946 (tt) REVERT: C 199 SER cc_start: 0.9283 (p) cc_final: 0.9002 (m) REVERT: C 457 ASP cc_start: 0.7906 (t0) cc_final: 0.7704 (t0) REVERT: E 543 ASN cc_start: 0.8874 (m-40) cc_final: 0.8531 (m-40) REVERT: E 612 SER cc_start: 0.8532 (p) cc_final: 0.8271 (t) REVERT: E 623 TRP cc_start: 0.8897 (m100) cc_final: 0.8459 (m100) REVERT: D 103 GLN cc_start: 0.8771 (tp40) cc_final: 0.8464 (tm-30) REVERT: D 127 VAL cc_start: 0.9048 (m) cc_final: 0.8840 (p) REVERT: D 199 SER cc_start: 0.9291 (p) cc_final: 0.8980 (m) REVERT: D 457 ASP cc_start: 0.8032 (t0) cc_final: 0.7800 (t0) REVERT: D 486 TYR cc_start: 0.9108 (m-80) cc_final: 0.8893 (m-80) REVERT: F 530 MET cc_start: 0.8093 (mtp) cc_final: 0.7653 (mtp) REVERT: F 543 ASN cc_start: 0.8787 (m-40) cc_final: 0.8309 (m-40) REVERT: F 562 GLN cc_start: 0.6936 (mp10) cc_final: 0.6663 (mt0) REVERT: F 612 SER cc_start: 0.8402 (p) cc_final: 0.8069 (t) REVERT: F 615 SER cc_start: 0.9282 (t) cc_final: 0.9015 (t) REVERT: F 628 TRP cc_start: 0.8904 (m100) cc_final: 0.8702 (m100) outliers start: 30 outliers final: 12 residues processed: 399 average time/residue: 0.2696 time to fit residues: 156.1905 Evaluate side-chains 200 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain F residue 544 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN A 246 GLN A 425 ASN A 478 ASN B 575 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 478 ASN E 575 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN D 478 ASN F 575 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15186 Z= 0.255 Angle : 0.786 10.168 20616 Z= 0.402 Chirality : 0.047 0.196 2649 Planarity : 0.004 0.031 2469 Dihedral : 11.608 80.581 4034 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.74 % Favored : 95.02 % Rotamer: Outliers : 3.29 % Allowed : 9.68 % Favored : 87.02 % 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: 0.73 (0.21), residues: 1668 helix: 0.88 (0.28), residues: 387 sheet: 0.29 (0.24), residues: 465 loop : 0.61 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 571 HIS 0.005 0.001 HIS E 564 PHE 0.020 0.002 PHE C 383 TYR 0.020 0.002 TYR A 484 ARG 0.004 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 235 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8373 (tm-30) REVERT: A 199 SER cc_start: 0.9377 (p) cc_final: 0.9156 (m) REVERT: B 530 MET cc_start: 0.8073 (mtp) cc_final: 0.7620 (mtp) REVERT: B 543 ASN cc_start: 0.8792 (m-40) cc_final: 0.8409 (m-40) REVERT: B 612 SER cc_start: 0.7783 (p) cc_final: 0.7358 (t) REVERT: B 616 ASN cc_start: 0.8295 (t0) cc_final: 0.7574 (p0) REVERT: C 125 LEU cc_start: 0.9253 (tp) cc_final: 0.8681 (tp) REVERT: C 199 SER cc_start: 0.9390 (p) cc_final: 0.9091 (m) REVERT: E 543 ASN cc_start: 0.8758 (m-40) cc_final: 0.8549 (m110) REVERT: E 612 SER cc_start: 0.8187 (p) cc_final: 0.7828 (t) REVERT: E 616 ASN cc_start: 0.8155 (t0) cc_final: 0.7395 (p0) REVERT: D 199 SER cc_start: 0.9424 (p) cc_final: 0.9096 (m) REVERT: D 502 LYS cc_start: 0.8334 (tttm) cc_final: 0.8107 (tttt) REVERT: F 530 MET cc_start: 0.7891 (mtp) cc_final: 0.7356 (mtp) REVERT: F 543 ASN cc_start: 0.8679 (m-40) cc_final: 0.8458 (m-40) REVERT: F 612 SER cc_start: 0.8041 (p) cc_final: 0.7625 (t) REVERT: F 616 ASN cc_start: 0.8143 (t0) cc_final: 0.7330 (p0) REVERT: F 626 MET cc_start: 0.8229 (ttt) cc_final: 0.7825 (ttt) outliers start: 50 outliers final: 39 residues processed: 265 average time/residue: 0.2552 time to fit residues: 101.0778 Evaluate side-chains 212 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 133 optimal weight: 0.0970 chunk 148 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15186 Z= 0.216 Angle : 0.648 9.162 20616 Z= 0.330 Chirality : 0.045 0.221 2649 Planarity : 0.003 0.032 2469 Dihedral : 8.874 71.022 4026 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.10 % Favored : 94.54 % Rotamer: Outliers : 3.49 % Allowed : 11.59 % Favored : 84.91 % 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: 0.62 (0.21), residues: 1668 helix: 0.91 (0.27), residues: 405 sheet: 0.16 (0.23), residues: 474 loop : 0.50 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 623 HIS 0.007 0.001 HIS C 72 PHE 0.014 0.002 PHE D 176 TYR 0.015 0.001 TYR A 484 ARG 0.004 0.000 ARG D 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 203 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9393 (p) cc_final: 0.9073 (m) REVERT: A 502 LYS cc_start: 0.7890 (ttpp) cc_final: 0.7675 (mtpt) REVERT: B 530 MET cc_start: 0.7947 (mtp) cc_final: 0.7550 (mtp) REVERT: B 543 ASN cc_start: 0.8814 (m-40) cc_final: 0.8454 (m-40) REVERT: B 612 SER cc_start: 0.8111 (p) cc_final: 0.7720 (t) REVERT: B 616 ASN cc_start: 0.8288 (t0) cc_final: 0.7582 (p0) REVERT: C 103 GLN cc_start: 0.8730 (tp40) cc_final: 0.8334 (tm-30) REVERT: C 199 SER cc_start: 0.9410 (p) cc_final: 0.8919 (m) REVERT: E 612 SER cc_start: 0.8289 (p) cc_final: 0.7989 (t) REVERT: E 616 ASN cc_start: 0.8229 (t0) cc_final: 0.7534 (p0) REVERT: D 199 SER cc_start: 0.9462 (p) cc_final: 0.8971 (m) REVERT: F 543 ASN cc_start: 0.8699 (m-40) cc_final: 0.8322 (m-40) REVERT: F 612 SER cc_start: 0.8195 (p) cc_final: 0.7947 (m) REVERT: F 616 ASN cc_start: 0.8249 (t0) cc_final: 0.7405 (p0) REVERT: F 623 TRP cc_start: 0.8908 (m100) cc_final: 0.8233 (m-10) REVERT: F 634 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7844 (tp30) outliers start: 53 outliers final: 40 residues processed: 235 average time/residue: 0.2428 time to fit residues: 87.3638 Evaluate side-chains 222 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15186 Z= 0.284 Angle : 0.645 8.258 20616 Z= 0.325 Chirality : 0.044 0.228 2649 Planarity : 0.004 0.041 2469 Dihedral : 8.154 64.856 4025 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.28 % Favored : 94.36 % Rotamer: Outliers : 4.55 % Allowed : 11.53 % Favored : 83.93 % 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: 0.36 (0.20), residues: 1668 helix: 0.87 (0.27), residues: 426 sheet: 0.10 (0.24), residues: 432 loop : 0.12 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 623 HIS 0.005 0.001 HIS E 564 PHE 0.015 0.002 PHE A 383 TYR 0.012 0.001 TYR A 484 ARG 0.006 0.000 ARG D 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 188 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9452 (p) cc_final: 0.9032 (m) REVERT: B 612 SER cc_start: 0.8418 (p) cc_final: 0.8110 (t) REVERT: B 616 ASN cc_start: 0.8400 (t0) cc_final: 0.7703 (p0) REVERT: C 103 GLN cc_start: 0.8706 (tp40) cc_final: 0.8445 (tm-30) REVERT: C 199 SER cc_start: 0.9408 (p) cc_final: 0.8955 (m) REVERT: E 616 ASN cc_start: 0.8307 (t0) cc_final: 0.7450 (p0) REVERT: D 114 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8344 (tm-30) REVERT: D 195 ASN cc_start: 0.8027 (p0) cc_final: 0.7808 (p0) REVERT: D 199 SER cc_start: 0.9484 (p) cc_final: 0.8981 (m) REVERT: F 543 ASN cc_start: 0.8754 (m-40) cc_final: 0.8341 (m-40) REVERT: F 612 SER cc_start: 0.8414 (p) cc_final: 0.8199 (m) REVERT: F 616 ASN cc_start: 0.8402 (t0) cc_final: 0.7549 (p0) REVERT: F 634 GLU cc_start: 0.8213 (mm-30) cc_final: 0.8002 (tp30) outliers start: 69 outliers final: 52 residues processed: 232 average time/residue: 0.2454 time to fit residues: 87.8647 Evaluate side-chains 228 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 570 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 0.0870 chunk 65 optimal weight: 0.0270 chunk 136 optimal weight: 0.9980 chunk 110 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN C 246 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15186 Z= 0.185 Angle : 0.588 7.121 20616 Z= 0.296 Chirality : 0.043 0.234 2649 Planarity : 0.003 0.036 2469 Dihedral : 7.477 58.201 4025 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.86 % Favored : 94.78 % Rotamer: Outliers : 3.95 % Allowed : 12.58 % Favored : 83.47 % 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: 0.29 (0.21), residues: 1668 helix: 0.90 (0.27), residues: 429 sheet: -0.12 (0.24), residues: 420 loop : 0.14 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 623 HIS 0.004 0.001 HIS B 564 PHE 0.010 0.001 PHE D 383 TYR 0.009 0.001 TYR A 484 ARG 0.005 0.000 ARG D 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 194 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8580 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 199 SER cc_start: 0.9442 (p) cc_final: 0.9141 (m) REVERT: B 612 SER cc_start: 0.8426 (p) cc_final: 0.8140 (t) REVERT: B 616 ASN cc_start: 0.8381 (t0) cc_final: 0.7696 (p0) REVERT: C 69 TRP cc_start: 0.8851 (m-90) cc_final: 0.8528 (m-90) REVERT: C 125 LEU cc_start: 0.9206 (tp) cc_final: 0.8619 (tp) REVERT: C 199 SER cc_start: 0.9411 (p) cc_final: 0.8988 (m) REVERT: C 467 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8290 (p) REVERT: E 596 TRP cc_start: 0.8884 (m-10) cc_final: 0.8670 (m-10) REVERT: E 616 ASN cc_start: 0.8252 (t0) cc_final: 0.7448 (p0) REVERT: D 103 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8207 (tm-30) REVERT: D 114 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8386 (tm-30) REVERT: D 125 LEU cc_start: 0.9081 (tp) cc_final: 0.8462 (tp) REVERT: D 199 SER cc_start: 0.9500 (p) cc_final: 0.9172 (m) REVERT: D 486 TYR cc_start: 0.8742 (m-80) cc_final: 0.8505 (m-10) REVERT: F 543 ASN cc_start: 0.8704 (m-40) cc_final: 0.8329 (m-40) REVERT: F 616 ASN cc_start: 0.8429 (t0) cc_final: 0.7582 (p0) outliers start: 60 outliers final: 50 residues processed: 233 average time/residue: 0.2338 time to fit residues: 83.9717 Evaluate side-chains 233 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 182 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 HIS D 105 HIS D 246 GLN F 577 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15186 Z= 0.338 Angle : 0.665 7.145 20616 Z= 0.333 Chirality : 0.045 0.231 2649 Planarity : 0.004 0.043 2469 Dihedral : 7.358 53.228 4023 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.88 % Favored : 93.76 % Rotamer: Outliers : 4.02 % Allowed : 13.64 % Favored : 82.35 % 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 (0.21), residues: 1668 helix: 0.91 (0.27), residues: 432 sheet: -0.29 (0.24), residues: 420 loop : -0.04 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 112 HIS 0.003 0.001 HIS D 105 PHE 0.016 0.002 PHE D 383 TYR 0.011 0.001 TYR A 484 ARG 0.005 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 190 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 199 SER cc_start: 0.9534 (p) cc_final: 0.9242 (m) REVERT: A 207 LYS cc_start: 0.8874 (tppt) cc_final: 0.8559 (mttp) REVERT: A 486 TYR cc_start: 0.8832 (m-80) cc_final: 0.8492 (m-10) REVERT: B 542 ARG cc_start: 0.8623 (ttp-170) cc_final: 0.8386 (ttp-170) REVERT: B 612 SER cc_start: 0.8664 (p) cc_final: 0.8456 (t) REVERT: B 616 ASN cc_start: 0.8510 (t0) cc_final: 0.7809 (p0) REVERT: C 125 LEU cc_start: 0.9260 (tp) cc_final: 0.8736 (tp) REVERT: C 199 SER cc_start: 0.9495 (p) cc_final: 0.9104 (m) REVERT: C 207 LYS cc_start: 0.8866 (tppt) cc_final: 0.7918 (tmtt) REVERT: C 467 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8428 (p) REVERT: E 612 SER cc_start: 0.8614 (m) cc_final: 0.8227 (t) REVERT: E 616 ASN cc_start: 0.8445 (t0) cc_final: 0.7808 (p0) REVERT: E 653 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8774 (tm-30) REVERT: D 103 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8322 (tm-30) REVERT: D 114 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8444 (tm-30) REVERT: D 125 LEU cc_start: 0.9156 (tp) cc_final: 0.8579 (tp) REVERT: D 199 SER cc_start: 0.9514 (p) cc_final: 0.9214 (m) REVERT: D 209 SER cc_start: 0.8839 (t) cc_final: 0.8427 (p) REVERT: F 616 ASN cc_start: 0.8604 (t0) cc_final: 0.7755 (p0) outliers start: 61 outliers final: 52 residues processed: 231 average time/residue: 0.2527 time to fit residues: 88.5940 Evaluate side-chains 238 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 184 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 663 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15186 Z= 0.191 Angle : 0.583 6.670 20616 Z= 0.294 Chirality : 0.043 0.199 2649 Planarity : 0.003 0.036 2469 Dihedral : 6.860 56.303 4021 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.62 % Favored : 95.02 % Rotamer: Outliers : 3.75 % Allowed : 14.16 % Favored : 82.08 % 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: 0.15 (0.20), residues: 1668 helix: 0.97 (0.27), residues: 432 sheet: -0.09 (0.25), residues: 384 loop : -0.15 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 112 HIS 0.003 0.001 HIS E 564 PHE 0.011 0.001 PHE A 383 TYR 0.007 0.001 TYR A 484 ARG 0.006 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 197 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 199 SER cc_start: 0.9540 (p) cc_final: 0.9254 (m) REVERT: A 209 SER cc_start: 0.8711 (t) cc_final: 0.8397 (p) REVERT: A 271 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7726 (mtp) REVERT: B 612 SER cc_start: 0.8641 (p) cc_final: 0.8402 (t) REVERT: B 616 ASN cc_start: 0.8520 (t0) cc_final: 0.7848 (p0) REVERT: C 107 ASP cc_start: 0.8508 (m-30) cc_final: 0.8270 (t0) REVERT: C 125 LEU cc_start: 0.9250 (tp) cc_final: 0.8748 (tp) REVERT: C 199 SER cc_start: 0.9491 (p) cc_final: 0.9163 (m) REVERT: C 207 LYS cc_start: 0.8747 (tppt) cc_final: 0.7915 (tmtt) REVERT: C 209 SER cc_start: 0.8764 (t) cc_final: 0.8358 (p) REVERT: C 467 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8258 (p) REVERT: E 612 SER cc_start: 0.8614 (m) cc_final: 0.8225 (t) REVERT: E 616 ASN cc_start: 0.8511 (t0) cc_final: 0.7887 (p0) REVERT: E 653 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8800 (tm-30) REVERT: D 103 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8384 (tm-30) REVERT: D 114 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8458 (tm-30) REVERT: D 125 LEU cc_start: 0.9116 (tp) cc_final: 0.8553 (tp) REVERT: D 199 SER cc_start: 0.9474 (p) cc_final: 0.9206 (m) REVERT: D 209 SER cc_start: 0.8763 (t) cc_final: 0.8378 (p) REVERT: D 466 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8119 (pm20) REVERT: F 616 ASN cc_start: 0.8593 (t0) cc_final: 0.7699 (p0) outliers start: 57 outliers final: 48 residues processed: 236 average time/residue: 0.2480 time to fit residues: 88.9624 Evaluate side-chains 238 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 186 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15186 Z= 0.229 Angle : 0.601 6.960 20616 Z= 0.301 Chirality : 0.044 0.335 2649 Planarity : 0.003 0.039 2469 Dihedral : 6.606 59.805 4021 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.70 % Favored : 93.94 % Rotamer: Outliers : 4.22 % Allowed : 14.03 % Favored : 81.75 % 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: 0.06 (0.20), residues: 1668 helix: 1.03 (0.27), residues: 432 sheet: -0.22 (0.25), residues: 390 loop : -0.25 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 614 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.002 PHE D 383 TYR 0.009 0.001 TYR A 484 ARG 0.005 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 200 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 199 SER cc_start: 0.9564 (p) cc_final: 0.9127 (m) REVERT: A 207 LYS cc_start: 0.8707 (tppt) cc_final: 0.8102 (tmtt) REVERT: A 209 SER cc_start: 0.8723 (t) cc_final: 0.8451 (p) REVERT: A 271 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7741 (mtp) REVERT: B 612 SER cc_start: 0.8651 (p) cc_final: 0.8449 (t) REVERT: B 616 ASN cc_start: 0.8543 (t0) cc_final: 0.7857 (p0) REVERT: B 620 SER cc_start: 0.8857 (m) cc_final: 0.8641 (t) REVERT: C 107 ASP cc_start: 0.8540 (m-30) cc_final: 0.8316 (t0) REVERT: C 125 LEU cc_start: 0.9278 (tp) cc_final: 0.8811 (tp) REVERT: C 199 SER cc_start: 0.9507 (p) cc_final: 0.9203 (m) REVERT: C 207 LYS cc_start: 0.8811 (tppt) cc_final: 0.7885 (tmtt) REVERT: C 209 SER cc_start: 0.8816 (t) cc_final: 0.8448 (p) REVERT: E 612 SER cc_start: 0.8682 (m) cc_final: 0.8292 (t) REVERT: E 616 ASN cc_start: 0.8536 (t0) cc_final: 0.7928 (p0) REVERT: D 103 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8454 (tm-30) REVERT: D 125 LEU cc_start: 0.9172 (tp) cc_final: 0.8636 (tp) REVERT: D 199 SER cc_start: 0.9533 (p) cc_final: 0.9273 (m) REVERT: D 209 SER cc_start: 0.8785 (t) cc_final: 0.8399 (p) REVERT: D 466 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: D 486 TYR cc_start: 0.8727 (m-80) cc_final: 0.8187 (m-80) REVERT: F 571 TRP cc_start: 0.5427 (t60) cc_final: 0.5171 (t60) REVERT: F 616 ASN cc_start: 0.8635 (t0) cc_final: 0.7700 (p0) outliers start: 64 outliers final: 55 residues processed: 240 average time/residue: 0.2520 time to fit residues: 93.2955 Evaluate side-chains 247 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 190 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15186 Z= 0.226 Angle : 0.610 8.877 20616 Z= 0.307 Chirality : 0.044 0.390 2649 Planarity : 0.003 0.039 2469 Dihedral : 6.360 51.315 4021 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.64 % Favored : 94.00 % Rotamer: Outliers : 4.02 % Allowed : 14.82 % Favored : 81.16 % 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: 0.05 (0.20), residues: 1668 helix: 1.12 (0.27), residues: 435 sheet: -0.22 (0.25), residues: 390 loop : -0.32 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 69 HIS 0.002 0.001 HIS F 564 PHE 0.012 0.002 PHE D 383 TYR 0.008 0.001 TYR A 484 ARG 0.006 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 193 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9534 (p) cc_final: 0.9165 (m) REVERT: A 207 LYS cc_start: 0.8658 (tppt) cc_final: 0.8094 (tmtt) REVERT: A 209 SER cc_start: 0.8712 (t) cc_final: 0.8447 (p) REVERT: A 271 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7752 (mtp) REVERT: B 616 ASN cc_start: 0.8579 (t0) cc_final: 0.7884 (p0) REVERT: B 620 SER cc_start: 0.8784 (m) cc_final: 0.8567 (t) REVERT: C 112 TRP cc_start: 0.8945 (t-100) cc_final: 0.8664 (t-100) REVERT: C 125 LEU cc_start: 0.9290 (tp) cc_final: 0.8826 (tp) REVERT: C 199 SER cc_start: 0.9519 (p) cc_final: 0.9233 (m) REVERT: C 207 LYS cc_start: 0.8763 (tppt) cc_final: 0.7953 (tmtt) REVERT: C 209 SER cc_start: 0.8849 (t) cc_final: 0.8493 (p) REVERT: E 612 SER cc_start: 0.8737 (m) cc_final: 0.8334 (t) REVERT: E 616 ASN cc_start: 0.8541 (t0) cc_final: 0.7892 (p0) REVERT: D 103 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8475 (tm-30) REVERT: D 125 LEU cc_start: 0.9158 (tp) cc_final: 0.8619 (tp) REVERT: D 199 SER cc_start: 0.9530 (p) cc_final: 0.9267 (m) REVERT: D 209 SER cc_start: 0.8744 (t) cc_final: 0.8386 (p) REVERT: D 213 ILE cc_start: 0.8474 (tp) cc_final: 0.8077 (pt) REVERT: D 271 MET cc_start: 0.8297 (mpp) cc_final: 0.8055 (mmm) REVERT: D 466 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8177 (pm20) REVERT: F 571 TRP cc_start: 0.5391 (t60) cc_final: 0.5154 (t60) outliers start: 61 outliers final: 51 residues processed: 234 average time/residue: 0.2686 time to fit residues: 96.9150 Evaluate side-chains 239 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 186 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN D 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15186 Z= 0.198 Angle : 0.588 6.160 20616 Z= 0.298 Chirality : 0.044 0.289 2649 Planarity : 0.003 0.037 2469 Dihedral : 6.103 45.599 4021 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.46 % Favored : 94.18 % Rotamer: Outliers : 3.29 % Allowed : 15.09 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1668 helix: 1.16 (0.27), residues: 435 sheet: -0.20 (0.25), residues: 390 loop : -0.33 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 112 HIS 0.002 0.001 HIS F 564 PHE 0.013 0.001 PHE C 53 TYR 0.010 0.001 TYR C 217 ARG 0.007 0.000 ARG D 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 195 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8537 (m-30) cc_final: 0.8229 (t0) REVERT: A 207 LYS cc_start: 0.8606 (tppt) cc_final: 0.7977 (tmtt) REVERT: A 209 SER cc_start: 0.8748 (t) cc_final: 0.8525 (p) REVERT: A 271 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7644 (mtp) REVERT: B 616 ASN cc_start: 0.8610 (t0) cc_final: 0.7846 (p0) REVERT: B 620 SER cc_start: 0.8702 (m) cc_final: 0.8490 (t) REVERT: C 112 TRP cc_start: 0.8966 (t-100) cc_final: 0.8730 (t-100) REVERT: C 125 LEU cc_start: 0.9280 (tp) cc_final: 0.8846 (tp) REVERT: C 207 LYS cc_start: 0.8763 (tppt) cc_final: 0.7929 (tmtt) REVERT: C 209 SER cc_start: 0.8882 (t) cc_final: 0.8584 (p) REVERT: E 612 SER cc_start: 0.8725 (m) cc_final: 0.8330 (t) REVERT: E 616 ASN cc_start: 0.8624 (t0) cc_final: 0.8011 (p0) REVERT: D 103 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8397 (tm-30) REVERT: D 125 LEU cc_start: 0.9149 (tp) cc_final: 0.8611 (tp) REVERT: D 209 SER cc_start: 0.8698 (t) cc_final: 0.8379 (p) REVERT: D 213 ILE cc_start: 0.8610 (tp) cc_final: 0.8231 (pt) REVERT: D 271 MET cc_start: 0.8402 (mpp) cc_final: 0.8087 (mmm) REVERT: D 466 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8148 (pm20) REVERT: D 486 TYR cc_start: 0.8732 (m-80) cc_final: 0.8165 (m-80) REVERT: F 571 TRP cc_start: 0.5261 (t60) cc_final: 0.5047 (t60) outliers start: 50 outliers final: 45 residues processed: 226 average time/residue: 0.2749 time to fit residues: 94.6930 Evaluate side-chains 231 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 184 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 0.0010 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110289 restraints weight = 23780.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113429 restraints weight = 15206.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115563 restraints weight = 11352.599| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15186 Z= 0.178 Angle : 0.579 6.278 20616 Z= 0.293 Chirality : 0.043 0.308 2649 Planarity : 0.003 0.035 2469 Dihedral : 5.873 43.822 4019 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.34 % Favored : 94.30 % Rotamer: Outliers : 3.16 % Allowed : 15.42 % Favored : 81.42 % 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: 0.10 (0.20), residues: 1668 helix: 1.16 (0.27), residues: 435 sheet: 0.11 (0.23), residues: 438 loop : -0.50 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 112 HIS 0.002 0.001 HIS B 564 PHE 0.010 0.001 PHE A 383 TYR 0.012 0.001 TYR C 217 ARG 0.007 0.000 ARG D 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.93 seconds wall clock time: 52 minutes 52.23 seconds (3172.23 seconds total)