Starting phenix.real_space_refine on Sun Feb 18 03:11:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn8_8717/02_2024/5vn8_8717.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn8_8717/02_2024/5vn8_8717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn8_8717/02_2024/5vn8_8717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn8_8717/02_2024/5vn8_8717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn8_8717/02_2024/5vn8_8717.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn8_8717/02_2024/5vn8_8717.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 120 5.16 5 C 12840 2.51 5 N 3444 2.21 5 O 4185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20589 Number of models: 1 Model: "" Number of chains: 51 Chain: "G" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3393 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1104 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3393 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1104 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "F" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "J" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3393 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1104 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.87, per 1000 atoms: 0.53 Number of scatterers: 20589 At special positions: 0 Unit cell: (179.47, 176.85, 117.9, 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 120 16.00 O 4185 8.00 N 3444 7.00 C 12840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.02 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS A 605 " distance=1.99 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS B 605 " distance=2.12 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS C 605 " distance=2.00 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA a 3 " - " MAN a 4 " " BMA l 3 " - " MAN l 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 616 " " NAG A 703 " - " ASN A 625 " " NAG A 704 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 616 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 616 " " NAG C 703 " - " ASN C 625 " " NAG C 704 " - " ASN C 637 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 160 " " NAG D 618 " - " ASN D 301 " " NAG D 621 " - " ASN D 339 " " NAG D 622 " - " ASN D 355 " " NAG D 629 " - " ASN D 392 " " NAG D 630 " - " ASN D 397 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 618 " - " ASN E 301 " " NAG E 621 " - " ASN E 339 " " NAG E 622 " - " ASN E 355 " " NAG E 629 " - " ASN E 392 " " NAG E 630 " - " ASN E 397 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 160 " " NAG G 618 " - " ASN G 301 " " NAG G 621 " - " ASN G 339 " " NAG G 622 " - " ASN G 355 " " NAG G 629 " - " ASN G 392 " " NAG G 630 " - " ASN G 397 " " NAG M 1 " - " ASN G 197 " " NAG N 1 " - " ASN G 234 " " NAG O 1 " - " ASN G 241 " " NAG P 1 " - " ASN G 262 " " NAG Q 1 " - " ASN G 276 " " NAG R 1 " - " ASN G 295 " " NAG S 1 " - " ASN G 332 " " NAG T 1 " - " ASN G 362 " " NAG U 1 " - " ASN G 386 " " NAG V 1 " - " ASN G 413 " " NAG W 1 " - " ASN G 448 " " NAG X 1 " - " ASN D 197 " " NAG Y 1 " - " ASN D 234 " " NAG Z 1 " - " ASN D 241 " " NAG a 1 " - " ASN D 262 " " NAG b 1 " - " ASN D 276 " " NAG c 1 " - " ASN D 295 " " NAG d 1 " - " ASN D 332 " " NAG e 1 " - " ASN D 362 " " NAG f 1 " - " ASN D 386 " " NAG g 1 " - " ASN D 413 " " NAG h 1 " - " ASN D 448 " " NAG i 1 " - " ASN E 197 " " NAG j 1 " - " ASN E 234 " " NAG k 1 " - " ASN E 241 " " NAG l 1 " - " ASN E 262 " " NAG m 1 " - " ASN E 276 " " NAG n 1 " - " ASN E 295 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 362 " " NAG q 1 " - " ASN E 386 " " NAG r 1 " - " ASN E 413 " " NAG s 1 " - " ASN E 448 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.07 Conformation dependent library (CDL) restraints added in 3.2 seconds 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 20.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 109 through 115 removed outlier: 3.520A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 185E through 186 removed outlier: 4.348A pdb=" N ASN G 185H" --> pdb=" O ASN G 185E" (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 353 removed outlier: 3.744A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU G 351 " --> pdb=" O ALA G 347 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.872A pdb=" N VAL G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR G 373 " --> pdb=" O PRO G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.975A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 546 removed outlier: 3.718A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.672A pdb=" N VAL A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 593 removed outlier: 3.522A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.523A pdb=" N TRP A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 633 Processing helix chain 'A' and resid 638 through 663 removed outlier: 4.033A pdb=" N THR A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.885A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.533A pdb=" N GLN H 64 " --> pdb=" O ALA H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.620A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.771A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.520A pdb=" N SER D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 185E through 186 removed outlier: 4.348A pdb=" N ASN D 185H" --> pdb=" O ASN D 185E" (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 353 removed outlier: 3.743A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.872A pdb=" N VAL D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.976A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 546 removed outlier: 3.717A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 removed outlier: 3.673A pdb=" N VAL B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 593 removed outlier: 3.522A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.524A pdb=" N TRP B 623 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 638 through 663 removed outlier: 4.033A pdb=" N THR B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.884A pdb=" N PHE F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.533A pdb=" N GLN F 64 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.620A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.771A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 106 Processing helix chain 'E' and resid 109 through 115 removed outlier: 3.519A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 185E through 186 removed outlier: 4.349A pdb=" N ASN E 185H" --> pdb=" O ASN E 185E" (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.744A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.872A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 373' Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.975A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 546 removed outlier: 3.718A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL C 539 " --> pdb=" O MET C 535 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 570 removed outlier: 3.673A pdb=" N VAL C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.523A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 582 " --> pdb=" O ALA C 578 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 591 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 596 No H-bonds generated for 'chain 'C' and resid 594 through 596' Processing helix chain 'C' and resid 619 through 626 removed outlier: 3.523A pdb=" N TRP C 623 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 624 " --> pdb=" O ASN C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 633 Processing helix chain 'C' and resid 638 through 663 removed outlier: 4.032A pdb=" N THR C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 660 " --> pdb=" O ASN C 656 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 662 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 663 " --> pdb=" O GLU C 659 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.885A pdb=" N PHE I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 64 removed outlier: 3.533A pdb=" N GLN I 64 " --> pdb=" O ALA I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.619A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.771A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.687A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 93 through 94 removed outlier: 3.511A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER G 447 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.590A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR G 357 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE G 468 " --> pdb=" O THR G 357 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE G 359 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 330 through 333 removed outlier: 3.656A pdb=" N LEU G 416 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE G 333 " --> pdb=" O ILE G 414 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE G 414 " --> pdb=" O ILE G 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AA8, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AA9, first strand: chain 'H' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.558A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L 73 " --> pdb=" O PHE L 21 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 35 through 38 removed outlier: 6.556A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 85 through 86 removed outlier: 3.632A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.688A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.511A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 447 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N LEU D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N LEU D 288 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 359 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 330 through 333 removed outlier: 3.656A pdb=" N LEU D 416 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 333 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 414 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 423 through 424 Processing sheet with id=AC3, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'F' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.558A pdb=" N THR J 5 " --> pdb=" O ARG J 24 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU J 73 " --> pdb=" O PHE J 21 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 35 through 38 removed outlier: 6.556A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 85 through 86 removed outlier: 3.631A pdb=" N TYR J 86 " --> pdb=" O THR J 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AD1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.688A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 93 through 94 removed outlier: 3.511A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 447 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.590A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE E 359 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 330 through 333 removed outlier: 3.656A pdb=" N LEU E 416 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 333 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE E 414 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD7, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AD8, first strand: chain 'I' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.558A pdb=" N THR K 5 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU K 73 " --> pdb=" O PHE K 21 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 35 through 38 removed outlier: 6.557A pdb=" N TRP K 35 " --> pdb=" O VAL K 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 85 through 86 removed outlier: 3.631A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1179 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: 6.59 Time building geometry restraints manager: 9.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6435 1.34 - 1.46: 4944 1.46 - 1.58: 9444 1.58 - 1.70: 0 1.70 - 1.81: 168 Bond restraints: 20991 Sorted by residual: bond pdb=" C1 NAG D 630 " pdb=" O5 NAG D 630 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C1 NAG G 630 " pdb=" O5 NAG G 630 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C1 NAG E 630 " pdb=" O5 NAG E 630 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C1 NAG G 602 " pdb=" O5 NAG G 602 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" C THR D 123 " pdb=" N PRO D 124 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.80e+00 ... (remaining 20986 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.19: 563 106.19 - 113.22: 11900 113.22 - 120.25: 7278 120.25 - 127.28: 8481 127.28 - 134.31: 278 Bond angle restraints: 28500 Sorted by residual: angle pdb=" C LEU E 390 " pdb=" N PHE E 391 " pdb=" CA PHE E 391 " ideal model delta sigma weight residual 121.54 134.31 -12.77 1.91e+00 2.74e-01 4.47e+01 angle pdb=" C LEU D 390 " pdb=" N PHE D 391 " pdb=" CA PHE D 391 " ideal model delta sigma weight residual 121.54 134.30 -12.76 1.91e+00 2.74e-01 4.47e+01 angle pdb=" C LEU G 390 " pdb=" N PHE G 391 " pdb=" CA PHE G 391 " ideal model delta sigma weight residual 121.54 134.22 -12.68 1.91e+00 2.74e-01 4.40e+01 angle pdb=" C PHE D 391 " pdb=" N ASN D 392 " pdb=" CA ASN D 392 " ideal model delta sigma weight residual 121.54 131.45 -9.91 1.91e+00 2.74e-01 2.69e+01 angle pdb=" C PHE G 391 " pdb=" N ASN G 392 " pdb=" CA ASN G 392 " ideal model delta sigma weight residual 121.54 131.41 -9.87 1.91e+00 2.74e-01 2.67e+01 ... (remaining 28495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 13381 22.32 - 44.64: 401 44.64 - 66.96: 76 66.96 - 89.28: 71 89.28 - 111.61: 57 Dihedral angle restraints: 13986 sinusoidal: 7020 harmonic: 6966 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual 93.00 33.80 59.20 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS G 378 " pdb=" SG CYS G 378 " pdb=" SG CYS G 445 " pdb=" CB CYS G 445 " ideal model delta sinusoidal sigma weight residual 93.00 33.83 59.17 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual 93.00 33.85 59.15 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 13983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 3411 0.147 - 0.293: 74 0.293 - 0.440: 15 0.440 - 0.586: 1 0.586 - 0.733: 3 Chirality restraints: 3504 Sorted by residual: chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN D 386 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN E 386 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN G 386 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 3501 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 386 " -0.021 2.00e-02 2.50e+03 2.31e-02 6.68e+00 pdb=" CG ASN D 386 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN D 386 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN D 386 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 479 " -0.021 2.00e-02 2.50e+03 1.62e-02 6.55e+00 pdb=" CG TRP G 479 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP G 479 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP G 479 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 479 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 479 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 479 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 479 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 479 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 479 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 479 " 0.021 2.00e-02 2.50e+03 1.61e-02 6.49e+00 pdb=" CG TRP E 479 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP E 479 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP E 479 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 479 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 479 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 479 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 479 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 479 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 479 " 0.003 2.00e-02 2.50e+03 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3938 2.78 - 3.31: 17932 3.31 - 3.84: 32102 3.84 - 4.37: 36582 4.37 - 4.90: 62960 Nonbonded interactions: 153514 Sorted by model distance: nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR C 606 " model vdw 2.246 2.440 nonbonded pdb=" O VAL G 36 " pdb=" OG1 THR A 606 " model vdw 2.257 2.440 nonbonded pdb=" O VAL D 36 " pdb=" OG1 THR B 606 " model vdw 2.324 2.440 nonbonded pdb=" OG1 THR B 627 " pdb=" OE1 GLN B 630 " model vdw 2.342 2.440 nonbonded pdb=" OG1 THR C 627 " pdb=" OE1 GLN C 630 " model vdw 2.342 2.440 ... (remaining 153509 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'P' selection = chain 'a' selection = chain 'l' } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.850 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 52.730 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.007 0.104 20991 Z= 0.457 Angle : 1.177 12.769 28500 Z= 0.618 Chirality : 0.070 0.733 3504 Planarity : 0.007 0.061 3510 Dihedral : 14.586 111.605 9390 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.63 % Allowed : 12.42 % Favored : 86.95 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -4.89 (0.14), residues: 2367 helix: -4.80 (0.07), residues: 378 sheet: -2.62 (0.17), residues: 657 loop : -3.17 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP G 479 HIS 0.010 0.002 HIS F 35 PHE 0.035 0.004 PHE E 233 TYR 0.020 0.003 TYR J 96 ARG 0.005 0.001 ARG G 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 571 time to evaluate : 2.296 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: G 217 TYR cc_start: 0.8808 (m-10) cc_final: 0.8157 (m-10) REVERT: A 542 ARG cc_start: 0.8365 (mtt90) cc_final: 0.7988 (mtt90) REVERT: A 599 SER cc_start: 0.9080 (t) cc_final: 0.8829 (p) REVERT: H 52 ASN cc_start: 0.8573 (t0) cc_final: 0.8368 (t0) REVERT: H 53 TYR cc_start: 0.8879 (t80) cc_final: 0.8560 (t80) REVERT: H 107 THR cc_start: 0.5861 (t) cc_final: 0.5454 (t) REVERT: L 4 LEU cc_start: 0.8682 (mt) cc_final: 0.8170 (mp) REVERT: L 6 GLN cc_start: 0.6739 (mt0) cc_final: 0.6339 (mt0) REVERT: L 83 PHE cc_start: 0.7430 (m-10) cc_final: 0.6757 (m-80) REVERT: D 104 MET cc_start: 0.8196 (ttm) cc_final: 0.7985 (ttt) REVERT: D 383 PHE cc_start: 0.7579 (m-10) cc_final: 0.7349 (m-80) REVERT: B 629 MET cc_start: 0.8736 (mmm) cc_final: 0.8393 (mmm) REVERT: F 52 ASN cc_start: 0.8762 (t0) cc_final: 0.8190 (t0) REVERT: F 82 LEU cc_start: 0.7513 (mt) cc_final: 0.7296 (tp) REVERT: F 107 THR cc_start: 0.6553 (t) cc_final: 0.6293 (t) REVERT: J 4 LEU cc_start: 0.8272 (mt) cc_final: 0.7974 (mp) REVERT: J 6 GLN cc_start: 0.6866 (mt0) cc_final: 0.6559 (mt0) REVERT: J 104 LEU cc_start: 0.6787 (tp) cc_final: 0.6528 (tp) REVERT: E 80 ASN cc_start: 0.8276 (m-40) cc_final: 0.7953 (m-40) REVERT: E 376 PHE cc_start: 0.7786 (m-80) cc_final: 0.7513 (m-80) REVERT: C 599 SER cc_start: 0.9263 (t) cc_final: 0.8821 (p) REVERT: C 629 MET cc_start: 0.8610 (mmm) cc_final: 0.8352 (mmp) REVERT: K 4 LEU cc_start: 0.8556 (mt) cc_final: 0.8270 (mp) REVERT: K 83 PHE cc_start: 0.7417 (m-10) cc_final: 0.6772 (m-80) REVERT: K 97 THR cc_start: 0.7320 (t) cc_final: 0.6955 (p) outliers start: 0 outliers final: 0 residues processed: 571 average time/residue: 0.3716 time to fit residues: 306.4385 Evaluate side-chains 307 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 136 optimal weight: 0.3980 chunk 212 optimal weight: 6.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 72 HIS G 99 ASN G 229 ASN G 302 ASN G 363 HIS G 462 GLN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS D 229 ASN D 302 ASN D 377 ASN ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 564 HIS B 653 GLN B 658 GLN F 1 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS E 229 ASN E 302 ASN E 462 GLN ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN I 39 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS K 49 HIS K 53 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 20991 Z= 0.190 Angle : 0.728 13.498 28500 Z= 0.368 Chirality : 0.049 0.310 3504 Planarity : 0.006 0.068 3510 Dihedral : 13.730 105.348 4968 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.58 % Favored : 91.09 % Rotamer: Outliers : 2.20 % Allowed : 9.46 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -4.03 (0.14), residues: 2367 helix: -2.60 (0.21), residues: 375 sheet: -2.26 (0.18), residues: 645 loop : -2.99 (0.14), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 479 HIS 0.015 0.001 HIS G 363 PHE 0.028 0.002 PHE G 391 TYR 0.020 0.001 TYR I 98 ARG 0.005 0.000 ARG G 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 346 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 217 TYR cc_start: 0.8796 (m-10) cc_final: 0.8173 (m-10) REVERT: G 447 SER cc_start: 0.8935 (t) cc_final: 0.8705 (m) REVERT: L 81 GLU cc_start: 0.7488 (mp0) cc_final: 0.7062 (pp20) REVERT: L 83 PHE cc_start: 0.7206 (m-10) cc_final: 0.6600 (m-80) REVERT: D 203 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.6212 (pm20) REVERT: D 270 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7945 (mp) REVERT: D 383 PHE cc_start: 0.7376 (m-10) cc_final: 0.7135 (m-80) REVERT: D 426 MET cc_start: 0.7035 (ttp) cc_final: 0.6622 (ttp) REVERT: D 486 TYR cc_start: 0.6630 (p90) cc_final: 0.5563 (p90) REVERT: B 621 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7515 (tt0) REVERT: B 629 MET cc_start: 0.8891 (mmm) cc_final: 0.8363 (mmm) REVERT: B 659 GLU cc_start: 0.7707 (pp20) cc_final: 0.7342 (tm-30) REVERT: F 1 GLN cc_start: 0.8053 (mm110) cc_final: 0.7616 (pt0) REVERT: J 6 GLN cc_start: 0.7125 (mt0) cc_final: 0.6304 (mt0) REVERT: J 83 PHE cc_start: 0.7510 (m-10) cc_final: 0.7275 (m-80) REVERT: J 106 ARG cc_start: 0.6608 (ptt-90) cc_final: 0.6222 (mtm110) REVERT: E 376 PHE cc_start: 0.7647 (m-80) cc_final: 0.7183 (m-10) REVERT: E 461 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: C 599 SER cc_start: 0.9275 (t) cc_final: 0.8849 (p) REVERT: C 656 ASN cc_start: 0.7763 (m-40) cc_final: 0.7525 (m-40) REVERT: K 83 PHE cc_start: 0.7215 (m-10) cc_final: 0.6734 (m-80) outliers start: 46 outliers final: 21 residues processed: 372 average time/residue: 0.3650 time to fit residues: 200.4613 Evaluate side-chains 297 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 272 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain J residue 29 ARG Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain I residue 59 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 189 optimal weight: 0.0770 chunk 211 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20991 Z= 0.250 Angle : 0.740 16.224 28500 Z= 0.367 Chirality : 0.052 0.824 3504 Planarity : 0.005 0.056 3510 Dihedral : 10.931 100.044 4968 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.10 % Favored : 89.78 % Rotamer: Outliers : 3.25 % Allowed : 10.65 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.57 (0.15), residues: 2367 helix: -1.59 (0.24), residues: 378 sheet: -2.04 (0.18), residues: 681 loop : -2.86 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 479 HIS 0.005 0.001 HIS F 35 PHE 0.032 0.002 PHE G 391 TYR 0.033 0.002 TYR I 98 ARG 0.008 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 283 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 217 TYR cc_start: 0.8907 (m-10) cc_final: 0.8468 (m-10) REVERT: G 447 SER cc_start: 0.9012 (t) cc_final: 0.8795 (m) REVERT: A 518 PHE cc_start: 0.8314 (m-10) cc_final: 0.8106 (m-10) REVERT: A 566 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8287 (tp) REVERT: H 53 TYR cc_start: 0.8901 (t80) cc_final: 0.8451 (t80) REVERT: L 83 PHE cc_start: 0.7450 (m-10) cc_final: 0.6722 (m-80) REVERT: D 203 GLN cc_start: 0.6436 (OUTLIER) cc_final: 0.6043 (pm20) REVERT: B 566 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8266 (tp) REVERT: B 629 MET cc_start: 0.8795 (mmm) cc_final: 0.8233 (mmm) REVERT: B 645 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8551 (mm) REVERT: F 1 GLN cc_start: 0.8078 (mm110) cc_final: 0.7875 (mm110) REVERT: J 83 PHE cc_start: 0.7804 (m-10) cc_final: 0.7148 (m-10) REVERT: J 106 ARG cc_start: 0.6753 (ptt-90) cc_final: 0.6169 (mtm110) REVERT: E 270 ILE cc_start: 0.8355 (mt) cc_final: 0.8131 (mt) REVERT: E 461 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: C 599 SER cc_start: 0.9326 (t) cc_final: 0.8988 (p) REVERT: C 629 MET cc_start: 0.8541 (mmm) cc_final: 0.8305 (mtp) REVERT: I 13 LYS cc_start: 0.7197 (mmtt) cc_final: 0.6919 (tppt) REVERT: K 83 PHE cc_start: 0.7480 (m-10) cc_final: 0.6813 (m-80) outliers start: 68 outliers final: 32 residues processed: 332 average time/residue: 0.3484 time to fit residues: 172.8336 Evaluate side-chains 287 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 250 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain K residue 22 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 377 ASN ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN F 3 GLN ** J 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 20991 Z= 0.465 Angle : 0.872 14.885 28500 Z= 0.436 Chirality : 0.055 0.749 3504 Planarity : 0.006 0.076 3510 Dihedral : 9.282 92.082 4968 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.34 % Favored : 87.45 % Rotamer: Outliers : 4.35 % Allowed : 13.09 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.46 (0.16), residues: 2367 helix: -1.42 (0.24), residues: 387 sheet: -1.93 (0.20), residues: 618 loop : -2.84 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 479 HIS 0.009 0.002 HIS D 374 PHE 0.035 0.003 PHE E 391 TYR 0.037 0.003 TYR I 98 ARG 0.008 0.001 ARG J 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 272 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8646 (tp) REVERT: H 44 ARG cc_start: 0.6669 (mtt180) cc_final: 0.6090 (mtt180) REVERT: H 46 GLU cc_start: 0.7785 (mp0) cc_final: 0.7445 (mp0) REVERT: H 53 TYR cc_start: 0.8884 (t80) cc_final: 0.8371 (t80) REVERT: D 108 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8418 (tt) REVERT: D 182 VAL cc_start: 0.7415 (t) cc_final: 0.7087 (m) REVERT: D 426 MET cc_start: 0.7606 (ttp) cc_final: 0.7333 (ttp) REVERT: B 564 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.6588 (t-90) REVERT: B 626 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7980 (mtm) REVERT: B 629 MET cc_start: 0.8780 (mmm) cc_final: 0.8297 (mmm) REVERT: B 634 GLU cc_start: 0.8657 (tp30) cc_final: 0.8390 (tt0) REVERT: B 645 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8665 (mm) REVERT: B 654 GLU cc_start: 0.8010 (tt0) cc_final: 0.7715 (tt0) REVERT: F 98 TYR cc_start: 0.8832 (t80) cc_final: 0.8530 (t80) REVERT: E 317 PHE cc_start: 0.7023 (t80) cc_final: 0.6699 (t80) REVERT: E 486 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6229 (p90) REVERT: C 619 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8094 (mt) REVERT: I 13 LYS cc_start: 0.7478 (mmtt) cc_final: 0.7210 (tppt) REVERT: I 46 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7789 (pt0) REVERT: I 54 ASN cc_start: 0.8911 (p0) cc_final: 0.8697 (p0) outliers start: 91 outliers final: 53 residues processed: 342 average time/residue: 0.3494 time to fit residues: 177.6697 Evaluate side-chains 312 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 251 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 203 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 377 ASN H 6 GLN H 43 GLN L 6 GLN L 49 HIS ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 100 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20991 Z= 0.192 Angle : 0.696 10.846 28500 Z= 0.345 Chirality : 0.050 0.650 3504 Planarity : 0.004 0.060 3510 Dihedral : 8.211 87.717 4968 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.34 % Rotamer: Outliers : 3.25 % Allowed : 14.71 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.06 (0.16), residues: 2367 helix: -0.91 (0.25), residues: 387 sheet: -1.52 (0.21), residues: 591 loop : -2.72 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 50 HIS 0.005 0.001 HIS B 641 PHE 0.031 0.002 PHE D 391 TYR 0.029 0.001 TYR I 98 ARG 0.008 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 263 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7634 (m-80) cc_final: 0.7338 (m-80) REVERT: A 566 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8455 (tp) REVERT: H 46 GLU cc_start: 0.7780 (mp0) cc_final: 0.7450 (mp0) REVERT: H 53 TYR cc_start: 0.8760 (t80) cc_final: 0.8255 (t80) REVERT: H 80 MET cc_start: 0.7286 (ppp) cc_final: 0.6783 (tmm) REVERT: D 318 TYR cc_start: 0.7253 (m-80) cc_final: 0.6658 (m-80) REVERT: B 564 HIS cc_start: 0.6707 (OUTLIER) cc_final: 0.6434 (t-90) REVERT: B 566 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8127 (tp) REVERT: B 626 MET cc_start: 0.8281 (mtm) cc_final: 0.8008 (mtm) REVERT: B 629 MET cc_start: 0.8777 (mmm) cc_final: 0.8245 (mmm) REVERT: B 634 GLU cc_start: 0.8564 (tp30) cc_final: 0.8163 (tt0) REVERT: B 645 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8811 (mm) REVERT: B 654 GLU cc_start: 0.7962 (tt0) cc_final: 0.7683 (tt0) REVERT: F 1 GLN cc_start: 0.7966 (mm110) cc_final: 0.7457 (pt0) REVERT: F 54 ASN cc_start: 0.9053 (p0) cc_final: 0.8754 (p0) REVERT: F 80 MET cc_start: 0.8147 (tmm) cc_final: 0.7896 (tmm) REVERT: F 98 TYR cc_start: 0.8606 (t80) cc_final: 0.8185 (t80) REVERT: E 317 PHE cc_start: 0.6840 (t80) cc_final: 0.6516 (t80) REVERT: E 318 TYR cc_start: 0.7646 (m-80) cc_final: 0.7153 (m-80) REVERT: C 599 SER cc_start: 0.9198 (t) cc_final: 0.8941 (p) REVERT: C 619 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7601 (mt) REVERT: I 46 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: K 31 ARG cc_start: 0.7037 (ttp80) cc_final: 0.6827 (ttp80) outliers start: 68 outliers final: 45 residues processed: 315 average time/residue: 0.3495 time to fit residues: 166.4815 Evaluate side-chains 296 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 245 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 29 ARG Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 226 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 18 optimal weight: 0.0870 chunk 74 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20991 Z= 0.205 Angle : 0.669 11.710 28500 Z= 0.333 Chirality : 0.048 0.614 3504 Planarity : 0.004 0.059 3510 Dihedral : 7.543 82.493 4968 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.67 % Favored : 90.20 % Rotamer: Outliers : 3.49 % Allowed : 14.52 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.91 (0.16), residues: 2367 helix: -0.62 (0.25), residues: 387 sheet: -1.53 (0.20), residues: 627 loop : -2.63 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 47 HIS 0.004 0.001 HIS B 641 PHE 0.030 0.002 PHE D 391 TYR 0.031 0.001 TYR I 98 ARG 0.008 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 263 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 149 MET cc_start: 0.7062 (mmm) cc_final: 0.6692 (mmm) REVERT: G 318 TYR cc_start: 0.7714 (m-80) cc_final: 0.7405 (m-80) REVERT: G 486 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.5866 (p90) REVERT: A 566 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8489 (tp) REVERT: H 46 GLU cc_start: 0.7759 (mp0) cc_final: 0.7411 (mp0) REVERT: H 53 TYR cc_start: 0.8729 (t80) cc_final: 0.8246 (t80) REVERT: H 80 MET cc_start: 0.7363 (ppp) cc_final: 0.6971 (tmm) REVERT: L 106 ARG cc_start: 0.6343 (ptt-90) cc_final: 0.5753 (ptt-90) REVERT: D 318 TYR cc_start: 0.7205 (m-80) cc_final: 0.6662 (m-80) REVERT: D 486 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.5815 (p90) REVERT: B 566 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8199 (tp) REVERT: B 626 MET cc_start: 0.8198 (mtm) cc_final: 0.7906 (mtm) REVERT: B 629 MET cc_start: 0.8791 (mmm) cc_final: 0.8292 (mmm) REVERT: B 634 GLU cc_start: 0.8501 (tp30) cc_final: 0.8136 (tt0) REVERT: B 645 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8813 (mm) REVERT: B 654 GLU cc_start: 0.7954 (tt0) cc_final: 0.7670 (tt0) REVERT: F 1 GLN cc_start: 0.8086 (mm110) cc_final: 0.7670 (pt0) REVERT: F 52 ASN cc_start: 0.9020 (t0) cc_final: 0.8625 (t0) REVERT: F 54 ASN cc_start: 0.9069 (p0) cc_final: 0.8726 (p0) REVERT: F 80 MET cc_start: 0.8164 (tmm) cc_final: 0.7902 (tmm) REVERT: F 98 TYR cc_start: 0.8634 (t80) cc_final: 0.8274 (t80) REVERT: E 317 PHE cc_start: 0.6807 (t80) cc_final: 0.6435 (t80) REVERT: E 318 TYR cc_start: 0.7695 (m-80) cc_final: 0.7133 (m-80) REVERT: E 486 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.5894 (p90) REVERT: C 599 SER cc_start: 0.9258 (t) cc_final: 0.8996 (p) REVERT: C 619 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7547 (mt) REVERT: I 46 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7951 (pt0) outliers start: 73 outliers final: 55 residues processed: 315 average time/residue: 0.3460 time to fit residues: 165.4354 Evaluate side-chains 317 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 254 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 486 TYR Chi-restraints excluded: chain A residue 564 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 HIS ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20991 Z= 0.355 Angle : 0.739 12.096 28500 Z= 0.367 Chirality : 0.050 0.592 3504 Planarity : 0.005 0.065 3510 Dihedral : 7.590 78.756 4968 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.20 % Favored : 88.68 % Rotamer: Outliers : 3.63 % Allowed : 14.76 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.90 (0.16), residues: 2367 helix: -0.58 (0.25), residues: 390 sheet: -1.52 (0.20), residues: 639 loop : -2.64 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 47 HIS 0.005 0.001 HIS L 27 PHE 0.031 0.002 PHE D 391 TYR 0.029 0.002 TYR I 98 ARG 0.013 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 249 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7889 (m-80) cc_final: 0.7504 (m-80) REVERT: G 486 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.5780 (p90) REVERT: A 566 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8571 (tp) REVERT: H 53 TYR cc_start: 0.8760 (t80) cc_final: 0.8271 (t80) REVERT: H 80 MET cc_start: 0.7461 (ppp) cc_final: 0.7056 (tmm) REVERT: L 106 ARG cc_start: 0.6290 (ptt-90) cc_final: 0.5912 (ptt-90) REVERT: D 318 TYR cc_start: 0.7440 (m-80) cc_final: 0.6901 (m-80) REVERT: D 486 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.5825 (p90) REVERT: B 629 MET cc_start: 0.8819 (mmm) cc_final: 0.8263 (mmm) REVERT: B 634 GLU cc_start: 0.8471 (tp30) cc_final: 0.8035 (tt0) REVERT: B 645 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8827 (mm) REVERT: B 654 GLU cc_start: 0.7982 (tt0) cc_final: 0.7691 (tt0) REVERT: F 1 GLN cc_start: 0.8094 (mm110) cc_final: 0.7677 (pt0) REVERT: F 52 ASN cc_start: 0.9077 (t0) cc_final: 0.8672 (t0) REVERT: F 54 ASN cc_start: 0.9113 (p0) cc_final: 0.8762 (p0) REVERT: F 80 MET cc_start: 0.8177 (tmm) cc_final: 0.7824 (tmm) REVERT: F 98 TYR cc_start: 0.8685 (t80) cc_final: 0.8271 (t80) REVERT: E 318 TYR cc_start: 0.7450 (m-80) cc_final: 0.6940 (m-80) REVERT: E 486 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6387 (p90) REVERT: C 599 SER cc_start: 0.9236 (t) cc_final: 0.8987 (p) REVERT: C 619 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7636 (mt) REVERT: I 47 TRP cc_start: 0.8229 (t60) cc_final: 0.7802 (t60) outliers start: 76 outliers final: 57 residues processed: 302 average time/residue: 0.3381 time to fit residues: 153.4168 Evaluate side-chains 304 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 241 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 486 TYR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.1980 chunk 134 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20991 Z= 0.178 Angle : 0.661 11.621 28500 Z= 0.329 Chirality : 0.047 0.583 3504 Planarity : 0.004 0.065 3510 Dihedral : 6.953 72.862 4968 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.20 % Favored : 91.68 % Rotamer: Outliers : 3.25 % Allowed : 15.14 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.57 (0.16), residues: 2367 helix: -0.10 (0.27), residues: 372 sheet: -1.16 (0.21), residues: 585 loop : -2.52 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP H 47 HIS 0.004 0.001 HIS B 641 PHE 0.030 0.002 PHE D 391 TYR 0.028 0.001 TYR I 98 ARG 0.009 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 258 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 217 TYR cc_start: 0.8919 (m-80) cc_final: 0.8342 (m-80) REVERT: G 428 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.6149 (tt0) REVERT: G 486 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.5833 (p90) REVERT: A 566 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8486 (tp) REVERT: H 53 TYR cc_start: 0.8710 (t80) cc_final: 0.8381 (t80) REVERT: H 80 MET cc_start: 0.7340 (ppp) cc_final: 0.6987 (tmm) REVERT: L 106 ARG cc_start: 0.6238 (ptt-90) cc_final: 0.5910 (ptt-90) REVERT: D 318 TYR cc_start: 0.7135 (m-80) cc_final: 0.6673 (m-80) REVERT: D 486 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6249 (p90) REVERT: B 566 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8127 (tp) REVERT: B 629 MET cc_start: 0.8762 (mmm) cc_final: 0.8340 (mmm) REVERT: B 634 GLU cc_start: 0.8433 (tp30) cc_final: 0.8094 (tt0) REVERT: B 645 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8744 (mm) REVERT: B 654 GLU cc_start: 0.7994 (tt0) cc_final: 0.7648 (tt0) REVERT: F 1 GLN cc_start: 0.8099 (mm110) cc_final: 0.7694 (pt0) REVERT: F 52 ASN cc_start: 0.9026 (t0) cc_final: 0.8641 (t0) REVERT: F 54 ASN cc_start: 0.9065 (p0) cc_final: 0.8672 (p0) REVERT: F 80 MET cc_start: 0.8029 (tmm) cc_final: 0.7687 (tmm) REVERT: E 318 TYR cc_start: 0.7431 (m-80) cc_final: 0.6985 (m-80) REVERT: E 486 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6042 (p90) REVERT: C 599 SER cc_start: 0.9240 (t) cc_final: 0.8977 (p) REVERT: I 47 TRP cc_start: 0.8102 (t60) cc_final: 0.7674 (t60) outliers start: 68 outliers final: 55 residues processed: 303 average time/residue: 0.3468 time to fit residues: 157.5120 Evaluate side-chains 301 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 239 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 428 GLN Chi-restraints excluded: chain G residue 486 TYR Chi-restraints excluded: chain A residue 564 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20991 Z= 0.318 Angle : 0.722 11.853 28500 Z= 0.363 Chirality : 0.049 0.559 3504 Planarity : 0.005 0.063 3510 Dihedral : 6.923 58.883 4968 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.53 % Favored : 88.34 % Rotamer: Outliers : 3.58 % Allowed : 15.19 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.62 (0.16), residues: 2367 helix: -0.30 (0.26), residues: 393 sheet: -1.32 (0.21), residues: 612 loop : -2.48 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP H 47 HIS 0.005 0.001 HIS B 641 PHE 0.031 0.002 PHE D 391 TYR 0.033 0.002 TYR I 98 ARG 0.010 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 244 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 486 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.5687 (p90) REVERT: A 566 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8568 (tp) REVERT: H 46 GLU cc_start: 0.7674 (mp0) cc_final: 0.7425 (mp0) REVERT: H 53 TYR cc_start: 0.8733 (t80) cc_final: 0.8245 (t80) REVERT: H 80 MET cc_start: 0.7411 (ppp) cc_final: 0.7042 (tmm) REVERT: L 106 ARG cc_start: 0.6259 (ptt-90) cc_final: 0.5906 (ptt-90) REVERT: D 233 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6736 (m-80) REVERT: D 318 TYR cc_start: 0.7232 (m-80) cc_final: 0.6761 (m-80) REVERT: D 486 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.5956 (p90) REVERT: B 629 MET cc_start: 0.8816 (mmm) cc_final: 0.8214 (mmm) REVERT: B 634 GLU cc_start: 0.8443 (tp30) cc_final: 0.8015 (tt0) REVERT: B 645 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8830 (mm) REVERT: B 654 GLU cc_start: 0.8039 (tt0) cc_final: 0.7708 (tt0) REVERT: F 1 GLN cc_start: 0.8145 (mm110) cc_final: 0.7710 (pt0) REVERT: F 52 ASN cc_start: 0.9076 (t0) cc_final: 0.8659 (t0) REVERT: F 80 MET cc_start: 0.7962 (tmm) cc_final: 0.7584 (tmm) REVERT: E 318 TYR cc_start: 0.7570 (m-80) cc_final: 0.7002 (m-80) REVERT: E 486 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.6538 (p90) REVERT: C 599 SER cc_start: 0.9220 (t) cc_final: 0.8971 (p) REVERT: I 47 TRP cc_start: 0.8253 (t60) cc_final: 0.7367 (t60) outliers start: 75 outliers final: 60 residues processed: 295 average time/residue: 0.3452 time to fit residues: 152.8874 Evaluate side-chains 306 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 240 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 486 TYR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 29 ARG Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 214 optimal weight: 0.2980 chunk 185 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20991 Z= 0.338 Angle : 0.731 10.589 28500 Z= 0.369 Chirality : 0.049 0.547 3504 Planarity : 0.005 0.065 3510 Dihedral : 7.014 56.719 4968 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.01 % Favored : 89.86 % Rotamer: Outliers : 3.39 % Allowed : 15.38 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.63 (0.16), residues: 2367 helix: -0.35 (0.25), residues: 393 sheet: -1.32 (0.21), residues: 618 loop : -2.48 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.032 0.002 PHE D 391 TYR 0.032 0.002 TYR I 98 ARG 0.016 0.001 ARG K 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 244 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 182 VAL cc_start: 0.7867 (t) cc_final: 0.7580 (m) REVERT: G 486 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.5670 (p90) REVERT: A 566 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8434 (tp) REVERT: H 53 TYR cc_start: 0.8735 (t80) cc_final: 0.8257 (t80) REVERT: H 80 MET cc_start: 0.7357 (ppp) cc_final: 0.6951 (tmm) REVERT: L 106 ARG cc_start: 0.6271 (ptt-90) cc_final: 0.5916 (ptt-90) REVERT: D 57 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7022 (t0) REVERT: D 233 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: D 318 TYR cc_start: 0.7214 (m-80) cc_final: 0.6778 (m-80) REVERT: D 486 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.5940 (p90) REVERT: B 566 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8161 (tp) REVERT: B 629 MET cc_start: 0.8787 (mmm) cc_final: 0.8216 (mmm) REVERT: B 634 GLU cc_start: 0.8493 (tp30) cc_final: 0.8046 (tt0) REVERT: B 645 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8815 (mm) REVERT: B 654 GLU cc_start: 0.8028 (tt0) cc_final: 0.7697 (tt0) REVERT: F 1 GLN cc_start: 0.8126 (mm110) cc_final: 0.7705 (pt0) REVERT: F 52 ASN cc_start: 0.9057 (t0) cc_final: 0.8662 (t0) REVERT: F 54 ASN cc_start: 0.9114 (p0) cc_final: 0.8760 (p0) REVERT: F 80 MET cc_start: 0.8000 (tmm) cc_final: 0.7611 (tmm) REVERT: E 318 TYR cc_start: 0.7567 (m-80) cc_final: 0.6999 (m-80) REVERT: E 486 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.6643 (p90) REVERT: C 599 SER cc_start: 0.9226 (t) cc_final: 0.8972 (p) REVERT: I 80 MET cc_start: 0.8227 (tmm) cc_final: 0.7905 (tmm) outliers start: 71 outliers final: 59 residues processed: 294 average time/residue: 0.3516 time to fit residues: 155.9057 Evaluate side-chains 304 residues out of total 2097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 237 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 486 TYR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 171 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 190 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.122883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095481 restraints weight = 41507.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095956 restraints weight = 32760.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.096634 restraints weight = 37290.229| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20991 Z= 0.173 Angle : 0.649 10.578 28500 Z= 0.328 Chirality : 0.047 0.541 3504 Planarity : 0.004 0.061 3510 Dihedral : 6.412 55.534 4968 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.87 % Favored : 91.00 % Rotamer: Outliers : 2.87 % Allowed : 16.09 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.38 (0.17), residues: 2367 helix: 0.06 (0.26), residues: 393 sheet: -1.10 (0.21), residues: 612 loop : -2.41 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H 47 HIS 0.004 0.001 HIS B 641 PHE 0.029 0.002 PHE D 391 TYR 0.028 0.001 TYR I 98 ARG 0.009 0.000 ARG J 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4000.65 seconds wall clock time: 74 minutes 4.40 seconds (4444.40 seconds total)