Starting phenix.real_space_refine on Mon Mar 18 07:25:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpj_34194/03_2024/8gpj_34194.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpj_34194/03_2024/8gpj_34194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpj_34194/03_2024/8gpj_34194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpj_34194/03_2024/8gpj_34194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpj_34194/03_2024/8gpj_34194.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpj_34194/03_2024/8gpj_34194.pdb" } resolution = 3.5 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= 0.002 sd= 0.035 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 12653 2.51 5 N 3319 2.21 5 O 4167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "X PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20259 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "D" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "U" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "V" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "W" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "X" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 3 Chain: "Y" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 3 Chain: "Z" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 3 Chain: "B" 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: 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: "I" 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: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 10.75, per 1000 atoms: 0.53 Number of scatterers: 20259 At special positions: 0 Unit cell: (153.7, 149.46, 118.72, 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 4167 8.00 N 3319 7.00 C 12653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS U 598 " - pdb=" SG CYS U 604 " distance=2.03 Simple disulfide: pdb=" SG CYS U 605 " - pdb=" SG CYS Y 501 " distance=2.03 Simple disulfide: pdb=" SG CYS V 598 " - pdb=" SG CYS V 604 " distance=2.03 Simple disulfide: pdb=" SG CYS V 605 " - pdb=" SG CYS X 501 " distance=2.03 Simple disulfide: pdb=" SG CYS W 598 " - pdb=" SG CYS W 604 " distance=2.03 Simple disulfide: pdb=" SG CYS W 605 " - pdb=" SG CYS Z 501 " distance=2.03 Simple disulfide: pdb=" SG CYS X 54 " - pdb=" SG CYS X 74 " distance=2.03 Simple disulfide: pdb=" SG CYS X 119 " - pdb=" SG CYS X 205 " distance=2.04 Simple disulfide: pdb=" SG CYS X 126 " - pdb=" SG CYS X 196 " distance=2.03 Simple disulfide: pdb=" SG CYS X 131 " - pdb=" SG CYS X 157 " distance=2.03 Simple disulfide: pdb=" SG CYS X 218 " - pdb=" SG CYS X 247 " distance=2.02 Simple disulfide: pdb=" SG CYS X 228 " - pdb=" SG CYS X 239 " distance=2.03 Simple disulfide: pdb=" SG CYS X 296 " - pdb=" SG CYS X 331 " distance=2.05 Simple disulfide: pdb=" SG CYS X 378 " - pdb=" SG CYS X 445 " distance=2.03 Simple disulfide: pdb=" SG CYS X 385 " - pdb=" SG CYS X 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 54 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 119 " - pdb=" SG CYS Y 205 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 126 " - pdb=" SG CYS Y 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 131 " - pdb=" SG CYS Y 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 218 " - pdb=" SG CYS Y 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 228 " - pdb=" SG CYS Y 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 296 " - pdb=" SG CYS Y 331 " distance=2.05 Simple disulfide: pdb=" SG CYS Y 378 " - pdb=" SG CYS Y 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 385 " - pdb=" SG CYS Y 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 54 " - pdb=" SG CYS Z 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 119 " - pdb=" SG CYS Z 205 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 126 " - pdb=" SG CYS Z 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 131 " - pdb=" SG CYS Z 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 218 " - pdb=" SG CYS Z 247 " distance=2.05 Simple disulfide: pdb=" SG CYS Z 228 " - pdb=" SG CYS Z 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 296 " - pdb=" SG CYS Z 331 " distance=2.05 Simple disulfide: pdb=" SG CYS Z 378 " - pdb=" SG CYS Z 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 385 " - pdb=" SG CYS Z 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN j 8 " - " MAN j 9 " " MAN j 10 " - " MAN j 11 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 10 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 10 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 4 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 8 " " BMA N 3 " - " MAN N 5 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 8 " " BMA c 3 " - " MAN c 5 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 10 " " BMA l 3 " - " MAN l 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG B 1 " - " ASN U 637 " " NAG F 1 " - " ASN V 637 " " NAG G 1 " - " ASN W 637 " " NAG I 1 " - " ASN X 156 " " NAG J 1 " - " ASN X 197 " " NAG K 1 " - " ASN X 234 " " NAG M 1 " - " ASN X 241 " " NAG N 1 " - " ASN X 262 " " NAG O 1 " - " ASN X 276 " " NAG P 1 " - " ASN X 289 " " NAG Q 1 " - " ASN X 332 " " NAG R 1 " - " ASN X 386 " " NAG S 1 " - " ASN Y 156 " " NAG T 1 " - " ASN Y 197 " " NAG U 701 " - " ASN U 616 " " NAG U 702 " - " ASN U 625 " " NAG V 701 " - " ASN V 616 " " NAG W 701 " - " ASN W 616 " " NAG X 701 " - " ASN X 88 " " NAG X 702 " - " ASN X 160 " " NAG X 703 " - " ASN X 448 " " NAG X 704 " - " ASN X 301 " " NAG X 705 " - " ASN X 392 " " NAG X 706 " - " ASN X 442 " " NAG Y 701 " - " ASN Y 88 " " NAG Y 702 " - " ASN Y 160 " " NAG Y 703 " - " ASN Y 301 " " NAG Y 704 " - " ASN Y 392 " " NAG Y 705 " - " ASN Y 442 " " NAG Y 706 " - " ASN Y 448 " " NAG Z 701 " - " ASN Z 88 " " NAG Z 702 " - " ASN Z 160 " " NAG Z 703 " - " ASN Z 301 " " NAG Z 704 " - " ASN Z 392 " " NAG Z 705 " - " ASN Z 442 " " NAG Z 706 " - " ASN Z 448 " " NAG a 1 " - " ASN Y 234 " " NAG b 1 " - " ASN Y 241 " " NAG c 1 " - " ASN Y 262 " " NAG d 1 " - " ASN Y 276 " " NAG e 1 " - " ASN Y 289 " " NAG f 1 " - " ASN Y 332 " " NAG g 1 " - " ASN Y 386 " " NAG h 1 " - " ASN Z 156 " " NAG i 1 " - " ASN Z 197 " " NAG j 1 " - " ASN Z 234 " " NAG k 1 " - " ASN Z 241 " " NAG l 1 " - " ASN Z 262 " " NAG m 1 " - " ASN Z 276 " " NAG n 1 " - " ASN Z 289 " " NAG o 1 " - " ASN Z 332 " " NAG p 1 " - " ASN Z 386 " Time building additional restraints: 10.01 Conformation dependent library (CDL) restraints added in 3.4 seconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4410 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 45 sheets defined 18.9% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 60 through 63 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.695A pdb=" N THR A 93 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 63 removed outlier: 3.592A pdb=" N ARG D 63 " --> pdb=" O HIS D 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 89 through 93 removed outlier: 4.063A pdb=" N THR D 93 " --> pdb=" O SER D 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'H' and resid 89 through 93 removed outlier: 3.756A pdb=" N THR H 93 " --> pdb=" O SER H 90 " (cutoff:3.500A) Processing helix chain 'U' and resid 529 through 534 removed outlier: 3.565A pdb=" N SER U 534 " --> pdb=" O MET U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 536 through 543 removed outlier: 4.171A pdb=" N GLN U 540 " --> pdb=" O ALA U 536 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN U 543 " --> pdb=" O VAL U 539 " (cutoff:3.500A) Processing helix chain 'U' and resid 569 through 595 Processing helix chain 'U' and resid 618 through 626 removed outlier: 4.070A pdb=" N MET U 626 " --> pdb=" O ILE U 622 " (cutoff:3.500A) Processing helix chain 'U' and resid 627 through 635 Processing helix chain 'U' and resid 638 through 660 removed outlier: 3.649A pdb=" N LYS U 658 " --> pdb=" O GLU U 654 " (cutoff:3.500A) Processing helix chain 'V' and resid 529 through 534 Processing helix chain 'V' and resid 536 through 544 removed outlier: 4.658A pdb=" N GLN V 540 " --> pdb=" O ALA V 536 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU V 544 " --> pdb=" O GLN V 540 " (cutoff:3.500A) Processing helix chain 'V' and resid 569 through 596 removed outlier: 3.578A pdb=" N ILE V 573 " --> pdb=" O THR V 569 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP V 596 " --> pdb=" O LEU V 592 " (cutoff:3.500A) Processing helix chain 'V' and resid 618 through 625 Processing helix chain 'V' and resid 627 through 635 Processing helix chain 'V' and resid 638 through 660 Processing helix chain 'W' and resid 529 through 534 Processing helix chain 'W' and resid 536 through 544 removed outlier: 4.478A pdb=" N GLN W 540 " --> pdb=" O ALA W 536 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU W 544 " --> pdb=" O GLN W 540 " (cutoff:3.500A) Processing helix chain 'W' and resid 569 through 596 removed outlier: 3.555A pdb=" N TRP W 596 " --> pdb=" O LEU W 592 " (cutoff:3.500A) Processing helix chain 'W' and resid 618 through 625 Processing helix chain 'W' and resid 627 through 635 Processing helix chain 'W' and resid 638 through 660 Processing helix chain 'X' and resid 98 through 117 removed outlier: 4.208A pdb=" N ASN X 102 " --> pdb=" O ASN X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 195 through 197 No H-bonds generated for 'chain 'X' and resid 195 through 197' Processing helix chain 'X' and resid 335 through 353 removed outlier: 4.152A pdb=" N GLU X 351 " --> pdb=" O LYS X 347 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS X 352 " --> pdb=" O ASN X 348 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE X 353 " --> pdb=" O LEU X 349 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 373 Processing helix chain 'X' and resid 476 through 484 removed outlier: 4.237A pdb=" N SER X 481 " --> pdb=" O ASP X 477 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU X 482 " --> pdb=" O ASN X 478 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 97 removed outlier: 3.776A pdb=" N LYS Y 97 " --> pdb=" O ASN Y 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Y' and resid 98 through 117 removed outlier: 4.445A pdb=" N ASN Y 102 " --> pdb=" O ASN Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 126 Processing helix chain 'Y' and resid 335 through 350 Processing helix chain 'Y' and resid 368 through 373 Processing helix chain 'Y' and resid 474 through 479 Processing helix chain 'Z' and resid 67 through 73 Processing helix chain 'Z' and resid 94 through 97 removed outlier: 3.675A pdb=" N LYS Z 97 " --> pdb=" O ASN Z 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 94 through 97' Processing helix chain 'Z' and resid 98 through 117 removed outlier: 4.344A pdb=" N ASN Z 102 " --> pdb=" O ASN Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 336 through 353 removed outlier: 3.805A pdb=" N GLU Z 351 " --> pdb=" O LYS Z 347 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS Z 352 " --> pdb=" O ASN Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 368 through 373 Processing helix chain 'Z' and resid 476 through 481 removed outlier: 3.781A pdb=" N SER Z 481 " --> pdb=" O ASP Z 477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.684A pdb=" N GLU A 9 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 128 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N TYR A 32 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TRP A 52 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 34 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN A 50 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 40 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.684A pdb=" N GLU A 9 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 128 " --> pdb=" O GLU A 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.441A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.812A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 2 through 5 Processing sheet with id=AA9, first strand: chain 'D' and resid 55 through 58 Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 58 Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.253A pdb=" N VAL E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR E 49 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.810A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 2 through 6 removed outlier: 4.333A pdb=" N SER H 20 " --> pdb=" O SER H 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 55 through 58 removed outlier: 4.506A pdb=" N SER H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA H 40 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N TYR H 32 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 55 through 58 removed outlier: 4.506A pdb=" N SER H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA H 40 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N TYR H 32 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.749A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 603 through 609 removed outlier: 8.354A pdb=" N CYS U 604 " --> pdb=" O TYR Y 40 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR Y 40 " --> pdb=" O CYS U 604 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR U 606 " --> pdb=" O VAL Y 38 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL Y 38 " --> pdb=" O THR U 606 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL U 608 " --> pdb=" O VAL Y 36 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ILE Y 491 " --> pdb=" O PRO Y 43 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TRP Y 45 " --> pdb=" O VAL Y 489 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL Y 489 " --> pdb=" O TRP Y 45 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N GLU Y 47 " --> pdb=" O LYS Y 487 " (cutoff:3.500A) removed outlier: 11.182A pdb=" N LYS Y 487 " --> pdb=" O GLU Y 47 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL Y 242 " --> pdb=" O LEU Y 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 603 through 609 removed outlier: 8.386A pdb=" N CYS W 604 " --> pdb=" O TYR Z 40 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR Z 40 " --> pdb=" O CYS W 604 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR W 606 " --> pdb=" O VAL Z 38 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL Z 38 " --> pdb=" O THR W 606 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL W 608 " --> pdb=" O VAL Z 36 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL Z 38 " --> pdb=" O PRO Z 498 " (cutoff:3.500A) removed outlier: 9.680A pdb=" N TYR Z 40 " --> pdb=" O VAL Z 496 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N VAL Z 496 " --> pdb=" O TYR Z 40 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL Z 42 " --> pdb=" O LEU Z 494 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU Z 494 " --> pdb=" O VAL Z 42 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL Z 44 " --> pdb=" O LYS Z 492 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL Z 242 " --> pdb=" O LEU Z 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 35 through 47 removed outlier: 8.986A pdb=" N ILE X 491 " --> pdb=" O PRO X 43 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TRP X 45 " --> pdb=" O VAL X 489 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL X 489 " --> pdb=" O TRP X 45 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N GLU X 47 " --> pdb=" O LYS X 487 " (cutoff:3.500A) removed outlier: 11.455A pdb=" N LYS X 487 " --> pdb=" O GLU X 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 53 through 55 Processing sheet with id=AC5, first strand: chain 'X' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'X' and resid 130 through 132 Processing sheet with id=AC7, first strand: chain 'X' and resid 181 through 183 Processing sheet with id=AC8, first strand: chain 'X' and resid 200 through 203 removed outlier: 5.881A pdb=" N ALA X 200 " --> pdb=" O ALA X 433 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR X 435 " --> pdb=" O ALA X 200 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR X 202 " --> pdb=" O TYR X 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 260 through 261 removed outlier: 6.493A pdb=" N LEU X 260 " --> pdb=" O THR X 450 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY X 451 " --> pdb=" O LYS X 290 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N LYS X 290 " --> pdb=" O GLY X 451 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N LEU X 453 " --> pdb=" O LEU X 288 " (cutoff:3.500A) removed outlier: 11.986A pdb=" N LEU X 288 " --> pdb=" O LEU X 453 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N VAL X 455 " --> pdb=" O VAL X 286 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N VAL X 286 " --> pdb=" O VAL X 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 284 through 298 current: chain 'X' and resid 358 through 361 Processing sheet with id=AD1, first strand: chain 'X' and resid 271 through 273 removed outlier: 11.221A pdb=" N VAL X 286 " --> pdb=" O VAL X 455 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N VAL X 455 " --> pdb=" O VAL X 286 " (cutoff:3.500A) removed outlier: 11.986A pdb=" N LEU X 288 " --> pdb=" O LEU X 453 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N LEU X 453 " --> pdb=" O LEU X 288 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N LYS X 290 " --> pdb=" O GLY X 451 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY X 451 " --> pdb=" O LYS X 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 443 through 456 current: chain 'X' and resid 413 through 421 removed outlier: 4.085A pdb=" N PHE X 382 " --> pdb=" O LYS X 421 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 301 through 308 removed outlier: 7.208A pdb=" N ASN X 301 " --> pdb=" O ILE X 322 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE X 322 " --> pdb=" O ASN X 301 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR X 303 " --> pdb=" O GLY X 320A" (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 53 through 55 Processing sheet with id=AD4, first strand: chain 'Y' and resid 91 through 93 Processing sheet with id=AD5, first strand: chain 'Y' and resid 130 through 132 Processing sheet with id=AD6, first strand: chain 'Y' and resid 181 through 183 Processing sheet with id=AD7, first strand: chain 'Y' and resid 200 through 203 Processing sheet with id=AD8, first strand: chain 'Y' and resid 259 through 261 removed outlier: 7.017A pdb=" N GLY Y 451 " --> pdb=" O LYS Y 290 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N LYS Y 290 " --> pdb=" O GLY Y 451 " (cutoff:3.500A) removed outlier: 11.826A pdb=" N LEU Y 453 " --> pdb=" O LEU Y 288 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N LEU Y 288 " --> pdb=" O LEU Y 453 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N VAL Y 455 " --> pdb=" O VAL Y 286 " (cutoff:3.500A) removed outlier: 11.293A pdb=" N VAL Y 286 " --> pdb=" O VAL Y 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 284 through 298 current: chain 'Y' and resid 358 through 361 Processing sheet with id=AD9, first strand: chain 'Y' and resid 271 through 273 removed outlier: 11.293A pdb=" N VAL Y 286 " --> pdb=" O VAL Y 455 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N VAL Y 455 " --> pdb=" O VAL Y 286 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N LEU Y 288 " --> pdb=" O LEU Y 453 " (cutoff:3.500A) removed outlier: 11.826A pdb=" N LEU Y 453 " --> pdb=" O LEU Y 288 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N LYS Y 290 " --> pdb=" O GLY Y 451 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY Y 451 " --> pdb=" O LYS Y 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 443 through 456 current: chain 'Y' and resid 413 through 421 removed outlier: 3.512A pdb=" N LYS Y 421 " --> pdb=" O PHE Y 382 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE Y 382 " --> pdb=" O LYS Y 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 302 through 308 removed outlier: 4.810A pdb=" N THR Y 303 " --> pdb=" O GLY Y 320A" (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 53 through 55 Processing sheet with id=AE3, first strand: chain 'Z' and resid 91 through 93 Processing sheet with id=AE4, first strand: chain 'Z' and resid 130 through 133 Processing sheet with id=AE5, first strand: chain 'Z' and resid 181 through 183 Processing sheet with id=AE6, first strand: chain 'Z' and resid 200 through 203 removed outlier: 6.141A pdb=" N ALA Z 200 " --> pdb=" O ALA Z 433 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR Z 435 " --> pdb=" O ALA Z 200 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR Z 202 " --> pdb=" O TYR Z 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 259 through 261 removed outlier: 6.540A pdb=" N LEU Z 260 " --> pdb=" O THR Z 450 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE Z 443 " --> pdb=" O ARG Z 298 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY Z 451 " --> pdb=" O LYS Z 290 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N LYS Z 290 " --> pdb=" O GLY Z 451 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N LEU Z 453 " --> pdb=" O LEU Z 288 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU Z 288 " --> pdb=" O LEU Z 453 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N VAL Z 455 " --> pdb=" O VAL Z 286 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N VAL Z 286 " --> pdb=" O VAL Z 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 284 through 298 current: chain 'Z' and resid 358 through 361 Processing sheet with id=AE8, first strand: chain 'Z' and resid 271 through 273 removed outlier: 10.514A pdb=" N VAL Z 286 " --> pdb=" O VAL Z 455 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N VAL Z 455 " --> pdb=" O VAL Z 286 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU Z 288 " --> pdb=" O LEU Z 453 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N LEU Z 453 " --> pdb=" O LEU Z 288 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N LYS Z 290 " --> pdb=" O GLY Z 451 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY Z 451 " --> pdb=" O LYS Z 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE Z 443 " --> pdb=" O ARG Z 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 443 through 456 current: chain 'Z' and resid 413 through 421 removed outlier: 4.018A pdb=" N PHE Z 382 " --> pdb=" O LYS Z 421 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 304 through 308 737 hydrogen bonds defined for protein. 1950 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: 6.90 Time building geometry restraints manager: 10.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6277 1.35 - 1.49: 5706 1.49 - 1.62: 8525 1.62 - 1.76: 3 1.76 - 1.89: 159 Bond restraints: 20670 Sorted by residual: bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" CB CYS Z 218 " pdb=" SG CYS Z 218 " ideal model delta sigma weight residual 1.808 1.894 -0.086 3.30e-02 9.18e+02 6.80e+00 bond pdb=" CB CYS X 331 " pdb=" SG CYS X 331 " ideal model delta sigma weight residual 1.808 1.882 -0.074 3.30e-02 9.18e+02 4.96e+00 bond pdb=" CB CYS Y 331 " pdb=" SG CYS Y 331 " ideal model delta sigma weight residual 1.808 1.881 -0.073 3.30e-02 9.18e+02 4.84e+00 bond pdb=" CB CYS Z 331 " pdb=" SG CYS Z 331 " ideal model delta sigma weight residual 1.808 1.876 -0.068 3.30e-02 9.18e+02 4.25e+00 ... (remaining 20665 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.52: 365 105.52 - 112.69: 11971 112.69 - 119.87: 6461 119.87 - 127.04: 9016 127.04 - 134.22: 280 Bond angle restraints: 28093 Sorted by residual: angle pdb=" CA CYS Z 296 " pdb=" CB CYS Z 296 " pdb=" SG CYS Z 296 " ideal model delta sigma weight residual 114.40 127.95 -13.55 2.30e+00 1.89e-01 3.47e+01 angle pdb=" CA CYS Y 296 " pdb=" CB CYS Y 296 " pdb=" SG CYS Y 296 " ideal model delta sigma weight residual 114.40 127.91 -13.51 2.30e+00 1.89e-01 3.45e+01 angle pdb=" CA CYS X 296 " pdb=" CB CYS X 296 " pdb=" SG CYS X 296 " ideal model delta sigma weight residual 114.40 126.60 -12.20 2.30e+00 1.89e-01 2.81e+01 angle pdb=" CA GLN W 577 " pdb=" CB GLN W 577 " pdb=" CG GLN W 577 " ideal model delta sigma weight residual 114.10 124.63 -10.53 2.00e+00 2.50e-01 2.77e+01 angle pdb=" N CYS Z 119 " pdb=" CA CYS Z 119 " pdb=" C CYS Z 119 " ideal model delta sigma weight residual 107.73 112.99 -5.26 1.34e+00 5.57e-01 1.54e+01 ... (remaining 28088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.35: 12954 23.35 - 46.69: 732 46.69 - 70.04: 89 70.04 - 93.38: 106 93.38 - 116.73: 56 Dihedral angle restraints: 13937 sinusoidal: 7091 harmonic: 6846 Sorted by residual: dihedral pdb=" CB CYS Y 119 " pdb=" SG CYS Y 119 " pdb=" SG CYS Y 205 " pdb=" CB CYS Y 205 " ideal model delta sinusoidal sigma weight residual -86.00 -167.61 81.61 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS X 119 " pdb=" SG CYS X 119 " pdb=" SG CYS X 205 " pdb=" CB CYS X 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.20 75.20 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS X 378 " pdb=" SG CYS X 378 " pdb=" SG CYS X 445 " pdb=" CB CYS X 445 " ideal model delta sinusoidal sigma weight residual -86.00 -155.64 69.64 1 1.00e+01 1.00e-02 6.26e+01 ... (remaining 13934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3171 0.088 - 0.176: 347 0.176 - 0.265: 19 0.265 - 0.353: 7 0.353 - 0.441: 2 Chirality restraints: 3546 Sorted by residual: chirality pdb=" CB ILE Z 270 " pdb=" CA ILE Z 270 " pdb=" CG1 ILE Z 270 " pdb=" CG2 ILE Z 270 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN Z 197 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" C1 NAG Z 705 " pdb=" ND2 ASN Z 442 " pdb=" C2 NAG Z 705 " pdb=" O5 NAG Z 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3543 not shown) Planarity restraints: 3431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS X 117 " -0.083 5.00e-02 4.00e+02 1.30e-01 2.69e+01 pdb=" N PRO X 118 " 0.224 5.00e-02 4.00e+02 pdb=" CA PRO X 118 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO X 118 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 614 " 0.029 2.00e-02 2.50e+03 2.31e-02 1.33e+01 pdb=" CG TRP U 614 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP U 614 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP U 614 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP U 614 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP U 614 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP U 614 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 614 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 614 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP U 614 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS Z 117 " 0.047 5.00e-02 4.00e+02 7.41e-02 8.80e+00 pdb=" N PRO Z 118 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO Z 118 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Z 118 " 0.041 5.00e-02 4.00e+02 ... (remaining 3428 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1010 2.72 - 3.27: 19438 3.27 - 3.81: 32250 3.81 - 4.36: 37503 4.36 - 4.90: 65330 Nonbonded interactions: 155531 Sorted by model distance: nonbonded pdb=" OG SER D 69 " pdb=" OG SER D 82 " model vdw 2.176 2.440 nonbonded pdb=" NE1 TRP H 36 " pdb=" OG SER H 81 " model vdw 2.183 2.520 nonbonded pdb=" OG SER A 69 " pdb=" OG SER A 82 " model vdw 2.190 2.440 nonbonded pdb=" O GLN D 43 " pdb=" OH TYR E 87 " model vdw 2.215 2.440 nonbonded pdb=" OH TYR C 49 " pdb=" O7 NAG G 2 " model vdw 2.230 2.440 ... (remaining 155526 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 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = (chain 'K' and (resid 1 or resid 4 through 10)) selection = (chain 'a' and (resid 1 or resid 4 through 10)) selection = (chain 'j' and (resid 2 or resid 5 through 11)) } ncs_group { reference = chain 'N' selection = chain 'c' selection = chain 'l' } ncs_group { reference = chain 'O' selection = chain 'd' selection = chain 'm' } ncs_group { reference = (chain 'U' and (resid 520 through 660 or resid 701)) selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 1.940 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: 5.670 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 54.450 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.350 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:2.760 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.006 0.086 20670 Z= 0.361 Angle : 0.850 13.549 28093 Z= 0.396 Chirality : 0.054 0.441 3546 Planarity : 0.005 0.130 3379 Dihedral : 16.936 116.730 9413 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.48 (0.18), residues: 2340 helix: 1.30 (0.28), residues: 363 sheet: 0.24 (0.19), residues: 786 loop : -1.23 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP U 614 HIS 0.007 0.001 HIS X 374 PHE 0.040 0.002 PHE X 53 TYR 0.035 0.002 TYR U 638 ARG 0.009 0.001 ARG Z 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 666 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 THR cc_start: 0.7590 (p) cc_final: 0.7316 (p) REVERT: H 99 THR cc_start: 0.8406 (p) cc_final: 0.8174 (p) REVERT: H 110 LEU cc_start: 0.8987 (tt) cc_final: 0.8784 (tt) REVERT: U 522 PHE cc_start: 0.8669 (t80) cc_final: 0.8418 (t80) REVERT: U 577 GLN cc_start: 0.7641 (mt0) cc_final: 0.7142 (mt0) REVERT: U 647 GLU cc_start: 0.7276 (pt0) cc_final: 0.6976 (pt0) REVERT: V 625 ASN cc_start: 0.8268 (t0) cc_final: 0.7744 (t0) REVERT: W 647 GLU cc_start: 0.7156 (tt0) cc_final: 0.6948 (tt0) REVERT: X 83 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6571 (tm-30) REVERT: X 84 MET cc_start: 0.7082 (tmm) cc_final: 0.6145 (tmm) REVERT: X 244 THR cc_start: 0.8492 (t) cc_final: 0.8137 (t) REVERT: X 275 GLU cc_start: 0.7221 (tt0) cc_final: 0.6792 (tt0) REVERT: X 315 GLN cc_start: 0.8306 (mp10) cc_final: 0.7938 (mp10) REVERT: X 347 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7844 (tmmt) REVERT: X 370 GLU cc_start: 0.7512 (mp0) cc_final: 0.7210 (mp0) REVERT: X 424 ILE cc_start: 0.8387 (mm) cc_final: 0.8178 (mm) REVERT: X 428 GLN cc_start: 0.7884 (mp10) cc_final: 0.7504 (mp10) REVERT: X 467 ILE cc_start: 0.8166 (pt) cc_final: 0.7696 (pt) REVERT: X 482 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6816 (mm-30) REVERT: Y 190 GLU cc_start: 0.7253 (tt0) cc_final: 0.7010 (tt0) REVERT: Y 359 ILE cc_start: 0.8327 (mm) cc_final: 0.8125 (mm) REVERT: Y 415 THR cc_start: 0.8039 (p) cc_final: 0.7762 (m) REVERT: Y 434 MET cc_start: 0.8066 (ttp) cc_final: 0.7695 (ttp) REVERT: Y 467 ILE cc_start: 0.8309 (mm) cc_final: 0.7812 (mm) REVERT: Y 485 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7839 (ptpp) REVERT: Z 39 TYR cc_start: 0.8520 (m-80) cc_final: 0.7996 (m-80) REVERT: Z 97 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8249 (mtmt) REVERT: Z 175 LEU cc_start: 0.8580 (mt) cc_final: 0.8371 (mt) REVERT: Z 199 SER cc_start: 0.8431 (m) cc_final: 0.8179 (t) REVERT: Z 388 SER cc_start: 0.8387 (t) cc_final: 0.8134 (t) REVERT: Z 448 ASN cc_start: 0.8449 (m-40) cc_final: 0.8240 (m-40) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.3426 time to fit residues: 336.3099 Evaluate side-chains 638 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 638 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 93 optimal weight: 0.0170 chunk 181 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN D 111 HIS ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 624 ASN W 630 GLN ** X 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 203 GLN X 302 ASN X 425 ASN Y 94 ASN Y 203 GLN Z 33 ASN Z 348 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20670 Z= 0.233 Angle : 0.636 10.426 28093 Z= 0.318 Chirality : 0.047 0.323 3546 Planarity : 0.004 0.068 3379 Dihedral : 12.253 86.178 5096 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.49 % Allowed : 12.31 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2340 helix: 1.97 (0.28), residues: 360 sheet: 0.29 (0.19), residues: 798 loop : -1.29 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP U 614 HIS 0.005 0.001 HIS X 374 PHE 0.029 0.002 PHE Y 53 TYR 0.031 0.002 TYR U 638 ARG 0.006 0.000 ARG W 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 649 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7876 (mmpt) REVERT: C 4 THR cc_start: 0.7514 (p) cc_final: 0.7285 (p) REVERT: D 22 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8130 (mtpp) REVERT: H 110 LEU cc_start: 0.9004 (tt) cc_final: 0.8764 (tt) REVERT: L 32 TRP cc_start: 0.8495 (m100) cc_final: 0.7834 (m100) REVERT: U 522 PHE cc_start: 0.8804 (t80) cc_final: 0.8565 (t80) REVERT: U 577 GLN cc_start: 0.7692 (mt0) cc_final: 0.7239 (mt0) REVERT: U 647 GLU cc_start: 0.7239 (pt0) cc_final: 0.6946 (pt0) REVERT: V 542 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7959 (ttm110) REVERT: V 579 ARG cc_start: 0.7798 (ptp-170) cc_final: 0.7282 (mtp180) REVERT: V 625 ASN cc_start: 0.8171 (t0) cc_final: 0.7830 (t0) REVERT: W 579 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7690 (mtm110) REVERT: W 647 GLU cc_start: 0.7202 (tt0) cc_final: 0.6624 (tt0) REVERT: X 68 VAL cc_start: 0.8507 (m) cc_final: 0.8203 (p) REVERT: X 83 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6665 (tm-30) REVERT: X 84 MET cc_start: 0.7278 (tmm) cc_final: 0.6551 (tmm) REVERT: X 97 LYS cc_start: 0.8348 (ptpp) cc_final: 0.8127 (ptpp) REVERT: X 121 LYS cc_start: 0.8343 (ttmm) cc_final: 0.8132 (ttmm) REVERT: X 275 GLU cc_start: 0.7171 (tt0) cc_final: 0.6748 (tt0) REVERT: X 315 GLN cc_start: 0.8294 (mp10) cc_final: 0.7977 (mp10) REVERT: X 428 GLN cc_start: 0.7942 (mp10) cc_final: 0.7520 (mp10) REVERT: X 434 MET cc_start: 0.7858 (ptp) cc_final: 0.7617 (ptm) REVERT: X 466 GLU cc_start: 0.7771 (tp30) cc_final: 0.7459 (mm-30) REVERT: X 482 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6753 (mm-30) REVERT: X 485 LYS cc_start: 0.8318 (mttm) cc_final: 0.7884 (mtmm) REVERT: Y 190 GLU cc_start: 0.7216 (tt0) cc_final: 0.6954 (tt0) REVERT: Y 293 GLU cc_start: 0.6810 (tt0) cc_final: 0.6602 (tt0) REVERT: Y 415 THR cc_start: 0.8025 (p) cc_final: 0.7810 (m) REVERT: Y 426 MET cc_start: 0.7710 (mtm) cc_final: 0.7114 (mtt) REVERT: Y 434 MET cc_start: 0.8083 (ttp) cc_final: 0.7725 (ttp) REVERT: Y 485 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7725 (ptpp) REVERT: Z 39 TYR cc_start: 0.8564 (m-80) cc_final: 0.7984 (m-80) REVERT: Z 66 HIS cc_start: 0.6845 (t-90) cc_final: 0.6585 (t70) REVERT: Z 97 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8136 (mtmt) REVERT: Z 173 TYR cc_start: 0.8463 (p90) cc_final: 0.8241 (p90) REVERT: Z 175 LEU cc_start: 0.8615 (mt) cc_final: 0.8336 (mt) REVERT: Z 199 SER cc_start: 0.8397 (m) cc_final: 0.8153 (t) REVERT: Z 388 SER cc_start: 0.8357 (t) cc_final: 0.8108 (t) outliers start: 31 outliers final: 20 residues processed: 655 average time/residue: 0.3457 time to fit residues: 333.9398 Evaluate side-chains 655 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 635 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 203 GLN Chi-restraints excluded: chain Y residue 232 ARG Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 295 VAL Chi-restraints excluded: chain Y residue 388 SER Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.0770 chunk 65 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 142 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN D 111 HIS ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 94 ASN X 103 GLN X 203 GLN X 302 ASN ** Y 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 ASN ** Z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 203 GLN Z 348 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20670 Z= 0.207 Angle : 0.599 9.233 28093 Z= 0.300 Chirality : 0.046 0.327 3546 Planarity : 0.004 0.040 3379 Dihedral : 10.548 83.521 5096 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.74 % Allowed : 15.15 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2340 helix: 2.14 (0.28), residues: 360 sheet: 0.23 (0.19), residues: 807 loop : -1.21 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP U 614 HIS 0.005 0.001 HIS X 374 PHE 0.028 0.002 PHE Y 53 TYR 0.025 0.001 TYR Y 173 ARG 0.008 0.000 ARG W 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 630 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8262 (mmpt) cc_final: 0.7855 (mmpt) REVERT: C 4 THR cc_start: 0.7478 (p) cc_final: 0.7270 (p) REVERT: C 73 LEU cc_start: 0.8366 (tp) cc_final: 0.8154 (tp) REVERT: D 22 LYS cc_start: 0.8342 (mtpp) cc_final: 0.7994 (mtpp) REVERT: D 50 GLN cc_start: 0.8176 (pt0) cc_final: 0.7957 (pt0) REVERT: H 54 TRP cc_start: 0.8261 (m100) cc_final: 0.7936 (m100) REVERT: H 110 LEU cc_start: 0.9034 (tt) cc_final: 0.8781 (tt) REVERT: L 32 TRP cc_start: 0.8478 (m100) cc_final: 0.7856 (m100) REVERT: U 522 PHE cc_start: 0.8807 (t80) cc_final: 0.8554 (t80) REVERT: U 577 GLN cc_start: 0.7708 (mt0) cc_final: 0.7210 (mt0) REVERT: U 647 GLU cc_start: 0.7257 (pt0) cc_final: 0.6947 (pt0) REVERT: V 579 ARG cc_start: 0.7804 (ptp-170) cc_final: 0.7304 (mtp180) REVERT: V 650 GLN cc_start: 0.8524 (tp40) cc_final: 0.8270 (tp40) REVERT: W 579 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7680 (mtm180) REVERT: W 647 GLU cc_start: 0.7211 (tt0) cc_final: 0.6833 (tt0) REVERT: X 45 TRP cc_start: 0.8602 (p90) cc_final: 0.8183 (p90) REVERT: X 68 VAL cc_start: 0.8514 (m) cc_final: 0.8211 (p) REVERT: X 83 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6688 (tm-30) REVERT: X 84 MET cc_start: 0.7404 (tmm) cc_final: 0.6977 (tmm) REVERT: X 103 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6965 (tm130) REVERT: X 275 GLU cc_start: 0.7147 (tt0) cc_final: 0.6732 (tt0) REVERT: X 315 GLN cc_start: 0.8302 (mp10) cc_final: 0.7964 (mp10) REVERT: X 466 GLU cc_start: 0.7817 (tp30) cc_final: 0.7257 (mm-30) REVERT: X 482 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6642 (mm-30) REVERT: Y 46 LYS cc_start: 0.8379 (mmtm) cc_final: 0.8145 (mmtm) REVERT: Y 190 GLU cc_start: 0.7191 (tt0) cc_final: 0.6924 (tt0) REVERT: Y 335 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8230 (ttm-80) REVERT: Y 415 THR cc_start: 0.8029 (p) cc_final: 0.7825 (m) REVERT: Y 426 MET cc_start: 0.7627 (mtm) cc_final: 0.7199 (mtt) REVERT: Y 434 MET cc_start: 0.8098 (ttp) cc_final: 0.7701 (ttp) REVERT: Y 485 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7661 (ptpp) REVERT: Z 97 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8013 (mtmt) REVERT: Z 173 TYR cc_start: 0.8466 (p90) cc_final: 0.8256 (p90) REVERT: Z 175 LEU cc_start: 0.8564 (mt) cc_final: 0.8244 (mt) REVERT: Z 208 VAL cc_start: 0.8659 (m) cc_final: 0.8258 (m) REVERT: Z 388 SER cc_start: 0.8365 (t) cc_final: 0.8122 (t) REVERT: Z 390 LEU cc_start: 0.8821 (mt) cc_final: 0.8549 (mt) REVERT: Z 474 ASP cc_start: 0.5776 (t0) cc_final: 0.5328 (t0) REVERT: Z 484 TYR cc_start: 0.8886 (p90) cc_final: 0.8677 (p90) outliers start: 57 outliers final: 35 residues processed: 646 average time/residue: 0.3346 time to fit residues: 321.4887 Evaluate side-chains 661 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 625 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 588 LYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 103 GLN Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 477 ASP Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 232 ARG Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 180 ASP Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 429 GLU Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 0.0370 chunk 223 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 630 GLN ** W 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN Y 425 ASN Z 33 ASN ** Z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 203 GLN Z 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20670 Z= 0.295 Angle : 0.621 8.726 28093 Z= 0.312 Chirality : 0.046 0.324 3546 Planarity : 0.004 0.043 3379 Dihedral : 9.626 78.911 5096 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.37 % Allowed : 16.59 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2340 helix: 2.04 (0.28), residues: 366 sheet: 0.26 (0.19), residues: 762 loop : -1.22 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP U 614 HIS 0.007 0.001 HIS X 374 PHE 0.029 0.002 PHE Y 53 TYR 0.027 0.002 TYR Y 173 ARG 0.009 0.001 ARG W 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 632 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8290 (mmpt) cc_final: 0.7869 (mmpt) REVERT: C 4 THR cc_start: 0.7507 (p) cc_final: 0.7304 (p) REVERT: C 73 LEU cc_start: 0.8395 (tp) cc_final: 0.8140 (tp) REVERT: D 22 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8005 (mtpp) REVERT: D 50 GLN cc_start: 0.8246 (pt0) cc_final: 0.7988 (pt0) REVERT: H 54 TRP cc_start: 0.8297 (m100) cc_final: 0.8071 (m100) REVERT: H 110 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8822 (tt) REVERT: L 32 TRP cc_start: 0.8503 (m100) cc_final: 0.7882 (m100) REVERT: U 522 PHE cc_start: 0.8846 (t80) cc_final: 0.8592 (t80) REVERT: U 577 GLN cc_start: 0.7730 (mt0) cc_final: 0.7235 (mt0) REVERT: U 647 GLU cc_start: 0.7266 (pt0) cc_final: 0.6967 (pt0) REVERT: V 579 ARG cc_start: 0.7829 (ptp-170) cc_final: 0.7309 (mtp180) REVERT: V 647 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6354 (mt-10) REVERT: V 650 GLN cc_start: 0.8554 (tp40) cc_final: 0.8262 (tp40) REVERT: W 579 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7554 (mtm180) REVERT: W 647 GLU cc_start: 0.7214 (tt0) cc_final: 0.6840 (tt0) REVERT: X 45 TRP cc_start: 0.8618 (p90) cc_final: 0.8272 (p90) REVERT: X 68 VAL cc_start: 0.8530 (m) cc_final: 0.8241 (p) REVERT: X 83 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6833 (tm-30) REVERT: X 84 MET cc_start: 0.7442 (tmm) cc_final: 0.7026 (tmm) REVERT: X 103 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: X 104 MET cc_start: 0.8088 (ttt) cc_final: 0.7858 (ttp) REVERT: X 275 GLU cc_start: 0.7120 (tt0) cc_final: 0.6725 (tt0) REVERT: X 315 GLN cc_start: 0.8294 (mp10) cc_final: 0.7884 (mp10) REVERT: X 466 GLU cc_start: 0.7743 (tp30) cc_final: 0.7390 (mm-30) REVERT: X 482 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6666 (mm-30) REVERT: Y 112 TRP cc_start: 0.8214 (m100) cc_final: 0.8005 (m100) REVERT: Y 190 GLU cc_start: 0.7290 (tt0) cc_final: 0.7013 (tt0) REVERT: Y 335 ARG cc_start: 0.8579 (tpp80) cc_final: 0.8360 (ttm-80) REVERT: Y 434 MET cc_start: 0.8203 (ttp) cc_final: 0.7943 (ttp) REVERT: Y 439 ILE cc_start: 0.8486 (mp) cc_final: 0.8123 (tp) REVERT: Y 485 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7629 (ptpp) REVERT: Z 39 TYR cc_start: 0.8569 (m-80) cc_final: 0.7699 (m-80) REVERT: Z 66 HIS cc_start: 0.6976 (t-90) cc_final: 0.6661 (t70) REVERT: Z 97 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8288 (mttt) REVERT: Z 175 LEU cc_start: 0.8583 (mt) cc_final: 0.8245 (mt) REVERT: Z 208 VAL cc_start: 0.8642 (m) cc_final: 0.8393 (m) REVERT: Z 388 SER cc_start: 0.8376 (t) cc_final: 0.8147 (t) REVERT: Z 474 ASP cc_start: 0.5842 (t0) cc_final: 0.5398 (t0) outliers start: 70 outliers final: 44 residues processed: 655 average time/residue: 0.3345 time to fit residues: 325.8119 Evaluate side-chains 674 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 628 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 588 LYS Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 595 ILE Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 103 GLN Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 180 ASP Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 232 ARG Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 295 VAL Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 180 ASP Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 429 GLU Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 0.2980 chunk 126 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 630 GLN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 425 ASN Z 33 ASN ** Z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20670 Z= 0.260 Angle : 0.614 9.386 28093 Z= 0.310 Chirality : 0.047 0.325 3546 Planarity : 0.004 0.046 3379 Dihedral : 9.081 77.117 5096 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.56 % Allowed : 17.94 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2340 helix: 2.06 (0.28), residues: 366 sheet: 0.23 (0.19), residues: 768 loop : -1.25 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP U 614 HIS 0.006 0.001 HIS X 374 PHE 0.033 0.002 PHE Y 53 TYR 0.027 0.002 TYR U 638 ARG 0.008 0.001 ARG X 469 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 627 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8294 (mmpt) cc_final: 0.7839 (mmpt) REVERT: C 73 LEU cc_start: 0.8417 (tp) cc_final: 0.8146 (tp) REVERT: D 22 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8003 (mtpp) REVERT: D 50 GLN cc_start: 0.8252 (pt0) cc_final: 0.7974 (pt0) REVERT: H 54 TRP cc_start: 0.8281 (m100) cc_final: 0.8056 (m100) REVERT: H 110 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8829 (tt) REVERT: L 32 TRP cc_start: 0.8517 (m100) cc_final: 0.7846 (m100) REVERT: U 522 PHE cc_start: 0.8848 (t80) cc_final: 0.8577 (t80) REVERT: U 577 GLN cc_start: 0.7770 (mt0) cc_final: 0.7157 (mt0) REVERT: U 647 GLU cc_start: 0.7280 (pt0) cc_final: 0.6992 (pt0) REVERT: V 579 ARG cc_start: 0.7820 (ptp-170) cc_final: 0.7315 (mtp180) REVERT: V 647 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6350 (mt-10) REVERT: V 650 GLN cc_start: 0.8554 (tp40) cc_final: 0.8303 (tp-100) REVERT: W 581 LEU cc_start: 0.8173 (tp) cc_final: 0.7923 (tp) REVERT: W 647 GLU cc_start: 0.7201 (tt0) cc_final: 0.6813 (tt0) REVERT: X 45 TRP cc_start: 0.8622 (p90) cc_final: 0.8281 (p90) REVERT: X 68 VAL cc_start: 0.8536 (m) cc_final: 0.8228 (p) REVERT: X 84 MET cc_start: 0.7444 (tmm) cc_final: 0.7072 (tmm) REVERT: X 97 LYS cc_start: 0.8145 (ptpp) cc_final: 0.7903 (mtmm) REVERT: X 107 ASP cc_start: 0.7336 (m-30) cc_final: 0.6921 (t0) REVERT: X 275 GLU cc_start: 0.7098 (tt0) cc_final: 0.6699 (tt0) REVERT: X 315 GLN cc_start: 0.8312 (mp10) cc_final: 0.7901 (mp10) REVERT: X 466 GLU cc_start: 0.7792 (tp30) cc_final: 0.7303 (mm-30) REVERT: X 482 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6739 (mm-30) REVERT: Y 190 GLU cc_start: 0.7275 (tt0) cc_final: 0.7000 (tt0) REVERT: Y 335 ARG cc_start: 0.8633 (tpp80) cc_final: 0.8403 (ttm-80) REVERT: Y 381 GLU cc_start: 0.6966 (tp30) cc_final: 0.6675 (tp30) REVERT: Y 426 MET cc_start: 0.7464 (mtm) cc_final: 0.6848 (mtt) REVERT: Y 439 ILE cc_start: 0.8520 (mp) cc_final: 0.8132 (tp) REVERT: Z 39 TYR cc_start: 0.8587 (m-80) cc_final: 0.7721 (m-80) REVERT: Z 56 SER cc_start: 0.8340 (t) cc_final: 0.8078 (p) REVERT: Z 66 HIS cc_start: 0.6973 (t-90) cc_final: 0.6670 (t70) REVERT: Z 97 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8163 (mtmt) REVERT: Z 175 LEU cc_start: 0.8622 (mt) cc_final: 0.8267 (mt) REVERT: Z 208 VAL cc_start: 0.8659 (m) cc_final: 0.8421 (m) REVERT: Z 231 LYS cc_start: 0.7680 (mmmt) cc_final: 0.7377 (mmmm) REVERT: Z 330 HIS cc_start: 0.8301 (p-80) cc_final: 0.8074 (p-80) REVERT: Z 474 ASP cc_start: 0.5853 (t0) cc_final: 0.5382 (t0) outliers start: 74 outliers final: 56 residues processed: 654 average time/residue: 0.3355 time to fit residues: 327.4082 Evaluate side-chains 676 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 619 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 588 LYS Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain V residue 595 ILE Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 413 THR Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 180 ASP Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 295 VAL Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 337 ASP Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Y residue 490 GLU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 228 CYS Chi-restraints excluded: chain Z residue 229 ASN Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 429 GLU Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 chunk 185 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 630 GLN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN Z 33 ASN ** Z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20670 Z= 0.217 Angle : 0.597 8.419 28093 Z= 0.302 Chirality : 0.046 0.327 3546 Planarity : 0.004 0.041 3379 Dihedral : 8.689 75.135 5096 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.66 % Allowed : 19.05 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.30 (0.17), residues: 2340 helix: 2.09 (0.28), residues: 366 sheet: 0.21 (0.19), residues: 762 loop : -1.22 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP Y 112 HIS 0.005 0.001 HIS X 374 PHE 0.031 0.002 PHE Y 53 TYR 0.027 0.002 TYR U 638 ARG 0.008 0.000 ARG X 469 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 616 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8296 (mmpt) cc_final: 0.7827 (mmpt) REVERT: D 22 LYS cc_start: 0.8398 (mtpp) cc_final: 0.7968 (mtpp) REVERT: D 50 GLN cc_start: 0.8129 (pt0) cc_final: 0.7848 (pt0) REVERT: H 54 TRP cc_start: 0.8241 (m100) cc_final: 0.8022 (m100) REVERT: H 110 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8835 (tt) REVERT: L 32 TRP cc_start: 0.8493 (m100) cc_final: 0.7831 (m100) REVERT: U 522 PHE cc_start: 0.8846 (t80) cc_final: 0.8560 (t80) REVERT: U 577 GLN cc_start: 0.7759 (mt0) cc_final: 0.7235 (mt0) REVERT: U 647 GLU cc_start: 0.7295 (pt0) cc_final: 0.6974 (pt0) REVERT: V 579 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.7284 (mtp180) REVERT: V 647 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6368 (mt-10) REVERT: V 650 GLN cc_start: 0.8570 (tp40) cc_final: 0.8298 (tp-100) REVERT: W 581 LEU cc_start: 0.8160 (tp) cc_final: 0.7923 (tp) REVERT: W 647 GLU cc_start: 0.7194 (tt0) cc_final: 0.6801 (tt0) REVERT: X 45 TRP cc_start: 0.8617 (p90) cc_final: 0.8251 (p90) REVERT: X 68 VAL cc_start: 0.8527 (m) cc_final: 0.8221 (p) REVERT: X 107 ASP cc_start: 0.7338 (m-30) cc_final: 0.6894 (t0) REVERT: X 275 GLU cc_start: 0.7083 (tt0) cc_final: 0.6693 (tt0) REVERT: X 315 GLN cc_start: 0.8297 (mp10) cc_final: 0.7890 (mp10) REVERT: X 466 GLU cc_start: 0.7770 (tp30) cc_final: 0.7274 (mm-30) REVERT: X 482 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6738 (mm-30) REVERT: Y 190 GLU cc_start: 0.7179 (tt0) cc_final: 0.6906 (tt0) REVERT: Y 293 GLU cc_start: 0.7055 (tt0) cc_final: 0.6847 (tt0) REVERT: Y 335 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8376 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7035 (tp30) cc_final: 0.6655 (tp30) REVERT: Z 39 TYR cc_start: 0.8578 (m-80) cc_final: 0.7715 (m-80) REVERT: Z 56 SER cc_start: 0.8298 (t) cc_final: 0.8024 (p) REVERT: Z 66 HIS cc_start: 0.6976 (t-90) cc_final: 0.6666 (t70) REVERT: Z 107 ASP cc_start: 0.7384 (m-30) cc_final: 0.7014 (t0) REVERT: Z 175 LEU cc_start: 0.8632 (mt) cc_final: 0.8257 (mt) REVERT: Z 208 VAL cc_start: 0.8657 (m) cc_final: 0.8380 (m) REVERT: Z 474 ASP cc_start: 0.5852 (t0) cc_final: 0.5405 (t0) outliers start: 76 outliers final: 57 residues processed: 640 average time/residue: 0.3380 time to fit residues: 321.7338 Evaluate side-chains 666 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 608 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 588 LYS Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 95 MET Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 217 TYR Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 371 ILE Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 180 ASP Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 337 ASP Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 434 MET Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Y residue 490 GLU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 229 ASN Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 188 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 222 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 630 GLN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 360 GLN Z 33 ASN ** Z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 229 ASN ** Z 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20670 Z= 0.212 Angle : 0.607 12.268 28093 Z= 0.304 Chirality : 0.046 0.327 3546 Planarity : 0.004 0.051 3379 Dihedral : 8.382 73.154 5096 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.46 % Allowed : 20.01 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2340 helix: 2.13 (0.28), residues: 366 sheet: 0.21 (0.19), residues: 792 loop : -1.20 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP Y 112 HIS 0.005 0.001 HIS X 374 PHE 0.033 0.002 PHE Y 53 TYR 0.027 0.001 TYR U 638 ARG 0.008 0.000 ARG X 469 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 605 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8356 (m100) cc_final: 0.7950 (m100) REVERT: A 55 LYS cc_start: 0.8300 (mmpt) cc_final: 0.7806 (mmpt) REVERT: C 73 LEU cc_start: 0.8372 (tp) cc_final: 0.8120 (tp) REVERT: D 22 LYS cc_start: 0.8397 (mtpp) cc_final: 0.7956 (mtpp) REVERT: D 50 GLN cc_start: 0.8119 (pt0) cc_final: 0.7870 (pt0) REVERT: E 4 THR cc_start: 0.8141 (m) cc_final: 0.7562 (p) REVERT: H 54 TRP cc_start: 0.8236 (m100) cc_final: 0.8030 (m100) REVERT: H 110 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8828 (tt) REVERT: L 32 TRP cc_start: 0.8491 (m100) cc_final: 0.7803 (m100) REVERT: U 522 PHE cc_start: 0.8835 (t80) cc_final: 0.8533 (t80) REVERT: U 577 GLN cc_start: 0.7789 (mt0) cc_final: 0.7453 (mt0) REVERT: U 647 GLU cc_start: 0.7287 (pt0) cc_final: 0.6994 (pt0) REVERT: V 579 ARG cc_start: 0.7796 (ptp-170) cc_final: 0.7281 (mtp180) REVERT: V 647 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6463 (mt-10) REVERT: V 650 GLN cc_start: 0.8567 (tp40) cc_final: 0.8294 (tp-100) REVERT: W 581 LEU cc_start: 0.8165 (tp) cc_final: 0.7947 (tp) REVERT: W 647 GLU cc_start: 0.7197 (tt0) cc_final: 0.6790 (tt0) REVERT: X 45 TRP cc_start: 0.8612 (p90) cc_final: 0.8232 (p90) REVERT: X 68 VAL cc_start: 0.8524 (m) cc_final: 0.8228 (p) REVERT: X 167 ASP cc_start: 0.7823 (t0) cc_final: 0.7614 (t0) REVERT: X 275 GLU cc_start: 0.7081 (tt0) cc_final: 0.6677 (tt0) REVERT: X 315 GLN cc_start: 0.8305 (mp10) cc_final: 0.7906 (mp10) REVERT: X 466 GLU cc_start: 0.7804 (tp30) cc_final: 0.7358 (mm-30) REVERT: X 482 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6731 (mm-30) REVERT: Y 190 GLU cc_start: 0.7175 (tt0) cc_final: 0.6886 (tt0) REVERT: Y 293 GLU cc_start: 0.7088 (tt0) cc_final: 0.6866 (tt0) REVERT: Y 335 ARG cc_start: 0.8589 (tpp80) cc_final: 0.8361 (ttm-80) REVERT: Y 360 GLN cc_start: 0.7599 (tp-100) cc_final: 0.7386 (tp40) REVERT: Y 381 GLU cc_start: 0.7037 (tp30) cc_final: 0.6659 (tp30) REVERT: Z 39 TYR cc_start: 0.8575 (m-80) cc_final: 0.7719 (m-80) REVERT: Z 56 SER cc_start: 0.8310 (t) cc_final: 0.8047 (p) REVERT: Z 66 HIS cc_start: 0.7048 (t-90) cc_final: 0.6747 (t70) REVERT: Z 107 ASP cc_start: 0.7371 (m-30) cc_final: 0.7003 (t0) REVERT: Z 175 LEU cc_start: 0.8637 (mt) cc_final: 0.8339 (mt) REVERT: Z 208 VAL cc_start: 0.8642 (m) cc_final: 0.8384 (m) REVERT: Z 282 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8212 (mmtm) REVERT: Z 388 SER cc_start: 0.8320 (t) cc_final: 0.8095 (t) REVERT: Z 474 ASP cc_start: 0.5863 (t0) cc_final: 0.5412 (t0) outliers start: 72 outliers final: 59 residues processed: 631 average time/residue: 0.3303 time to fit residues: 309.4855 Evaluate side-chains 657 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 597 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 588 LYS Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 523 LEU Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 203 GLN Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 360 GLN Chi-restraints excluded: chain X residue 371 ILE Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 429 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 180 ASP Chi-restraints excluded: chain Y residue 201 ILE Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 337 ASP Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 452 LEU Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Y residue 490 GLU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 347 LYS Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 0.0470 chunk 88 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 630 GLN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 328 GLN X 425 ASN Y 302 ASN Z 33 ASN ** Z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20670 Z= 0.204 Angle : 0.606 12.394 28093 Z= 0.304 Chirality : 0.046 0.327 3546 Planarity : 0.004 0.047 3379 Dihedral : 8.185 71.638 5096 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.51 % Allowed : 20.78 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.33 (0.17), residues: 2340 helix: 2.11 (0.28), residues: 366 sheet: 0.15 (0.20), residues: 738 loop : -1.20 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP Y 112 HIS 0.004 0.001 HIS X 374 PHE 0.034 0.002 PHE Y 53 TYR 0.027 0.001 TYR Y 173 ARG 0.009 0.000 ARG X 469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 604 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8360 (m100) cc_final: 0.7956 (m100) REVERT: A 55 LYS cc_start: 0.8332 (mmpt) cc_final: 0.7861 (mmpt) REVERT: C 73 LEU cc_start: 0.8372 (tp) cc_final: 0.8127 (tp) REVERT: D 22 LYS cc_start: 0.8397 (mtpp) cc_final: 0.7949 (mtpp) REVERT: D 50 GLN cc_start: 0.8090 (pt0) cc_final: 0.7837 (pt0) REVERT: E 4 THR cc_start: 0.8148 (m) cc_final: 0.7580 (p) REVERT: H 92 ASP cc_start: 0.8010 (m-30) cc_final: 0.7626 (m-30) REVERT: H 110 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8823 (tt) REVERT: L 32 TRP cc_start: 0.8491 (m100) cc_final: 0.7705 (m100) REVERT: U 522 PHE cc_start: 0.8835 (t80) cc_final: 0.8520 (t80) REVERT: U 577 GLN cc_start: 0.7750 (mt0) cc_final: 0.7401 (mt0) REVERT: U 647 GLU cc_start: 0.7269 (pt0) cc_final: 0.7000 (pt0) REVERT: V 579 ARG cc_start: 0.7783 (ptp-170) cc_final: 0.7254 (mtp180) REVERT: V 647 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6443 (mt-10) REVERT: V 650 GLN cc_start: 0.8528 (tp40) cc_final: 0.8273 (tp-100) REVERT: W 647 GLU cc_start: 0.7190 (tt0) cc_final: 0.6781 (tt0) REVERT: X 45 TRP cc_start: 0.8595 (p90) cc_final: 0.8213 (p90) REVERT: X 68 VAL cc_start: 0.8525 (m) cc_final: 0.8205 (p) REVERT: X 167 ASP cc_start: 0.7865 (t0) cc_final: 0.7651 (t0) REVERT: X 275 GLU cc_start: 0.7093 (tt0) cc_final: 0.6659 (tt0) REVERT: X 315 GLN cc_start: 0.8309 (mp10) cc_final: 0.7902 (mp10) REVERT: X 466 GLU cc_start: 0.7799 (tp30) cc_final: 0.7356 (mm-30) REVERT: X 482 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6728 (mm-30) REVERT: Y 97 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8334 (mtmm) REVERT: Y 190 GLU cc_start: 0.7167 (tt0) cc_final: 0.6888 (tt0) REVERT: Y 293 GLU cc_start: 0.7115 (tt0) cc_final: 0.6871 (tt0) REVERT: Y 335 ARG cc_start: 0.8575 (tpp80) cc_final: 0.8316 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7002 (tp30) cc_final: 0.6512 (tp30) REVERT: Z 39 TYR cc_start: 0.8577 (m-80) cc_final: 0.7814 (m-80) REVERT: Z 56 SER cc_start: 0.8311 (t) cc_final: 0.8056 (p) REVERT: Z 66 HIS cc_start: 0.7083 (t-90) cc_final: 0.6775 (t70) REVERT: Z 107 ASP cc_start: 0.7364 (m-30) cc_final: 0.7007 (t0) REVERT: Z 175 LEU cc_start: 0.8642 (mt) cc_final: 0.8257 (mt) REVERT: Z 208 VAL cc_start: 0.8643 (m) cc_final: 0.8386 (m) REVERT: Z 281 VAL cc_start: 0.8920 (p) cc_final: 0.8714 (m) REVERT: Z 282 LYS cc_start: 0.8394 (mmtt) cc_final: 0.8189 (mmtm) REVERT: Z 388 SER cc_start: 0.8360 (t) cc_final: 0.8146 (t) REVERT: Z 474 ASP cc_start: 0.5901 (t0) cc_final: 0.5449 (t0) outliers start: 73 outliers final: 59 residues processed: 630 average time/residue: 0.3403 time to fit residues: 318.2715 Evaluate side-chains 660 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 600 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 588 LYS Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 523 LEU Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 203 GLN Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 371 ILE Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 490 GLU Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 180 ASP Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 337 ASP Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 452 LEU Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Y residue 490 GLU Chi-restraints excluded: chain Y residue 492 LYS Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 347 LYS Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 630 GLN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN Y 302 ASN Z 33 ASN ** Z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20670 Z= 0.215 Angle : 0.615 13.435 28093 Z= 0.308 Chirality : 0.046 0.350 3546 Planarity : 0.004 0.046 3379 Dihedral : 8.020 69.869 5096 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.17 % Allowed : 21.12 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.34 (0.17), residues: 2340 helix: 2.08 (0.28), residues: 366 sheet: 0.14 (0.20), residues: 708 loop : -1.17 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 32 HIS 0.005 0.001 HIS Z 374 PHE 0.027 0.002 PHE Y 53 TYR 0.027 0.002 TYR Y 173 ARG 0.009 0.000 ARG X 469 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 601 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8344 (m100) cc_final: 0.7950 (m100) REVERT: A 55 LYS cc_start: 0.8334 (mmpt) cc_final: 0.7861 (mmpt) REVERT: C 73 LEU cc_start: 0.8365 (tp) cc_final: 0.8119 (tp) REVERT: D 22 LYS cc_start: 0.8403 (mtpp) cc_final: 0.7951 (mtpp) REVERT: D 50 GLN cc_start: 0.8078 (pt0) cc_final: 0.7824 (pt0) REVERT: E 4 THR cc_start: 0.8145 (m) cc_final: 0.7588 (p) REVERT: H 92 ASP cc_start: 0.7994 (m-30) cc_final: 0.7584 (m-30) REVERT: H 110 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8830 (tt) REVERT: L 32 TRP cc_start: 0.8488 (m100) cc_final: 0.7703 (m100) REVERT: U 522 PHE cc_start: 0.8832 (t80) cc_final: 0.8523 (t80) REVERT: U 577 GLN cc_start: 0.7781 (mt0) cc_final: 0.7420 (mt0) REVERT: U 647 GLU cc_start: 0.7216 (pt0) cc_final: 0.6948 (pt0) REVERT: V 579 ARG cc_start: 0.7755 (ptp-170) cc_final: 0.7214 (mtp180) REVERT: V 647 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6454 (mt-10) REVERT: V 650 GLN cc_start: 0.8526 (tp40) cc_final: 0.8272 (tp-100) REVERT: W 647 GLU cc_start: 0.7200 (tt0) cc_final: 0.6826 (tt0) REVERT: X 45 TRP cc_start: 0.8591 (p90) cc_final: 0.8213 (p90) REVERT: X 68 VAL cc_start: 0.8527 (m) cc_final: 0.8221 (p) REVERT: X 167 ASP cc_start: 0.7875 (t0) cc_final: 0.7671 (t0) REVERT: X 275 GLU cc_start: 0.7090 (tt0) cc_final: 0.6659 (tt0) REVERT: X 315 GLN cc_start: 0.8318 (mp10) cc_final: 0.7910 (mp10) REVERT: X 466 GLU cc_start: 0.7825 (tp30) cc_final: 0.7379 (mm-30) REVERT: X 482 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6730 (mm-30) REVERT: Y 97 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8335 (mtmm) REVERT: Y 190 GLU cc_start: 0.7178 (tt0) cc_final: 0.6891 (tt0) REVERT: Y 293 GLU cc_start: 0.7125 (tt0) cc_final: 0.6882 (tt0) REVERT: Y 335 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8302 (ttm-80) REVERT: Y 381 GLU cc_start: 0.6856 (tp30) cc_final: 0.6534 (tp30) REVERT: Z 39 TYR cc_start: 0.8582 (m-80) cc_final: 0.7733 (m-80) REVERT: Z 56 SER cc_start: 0.8316 (t) cc_final: 0.8066 (p) REVERT: Z 66 HIS cc_start: 0.7112 (t-90) cc_final: 0.6717 (t-90) REVERT: Z 107 ASP cc_start: 0.7371 (m-30) cc_final: 0.7023 (t0) REVERT: Z 175 LEU cc_start: 0.8641 (mt) cc_final: 0.8258 (mt) REVERT: Z 208 VAL cc_start: 0.8639 (m) cc_final: 0.8391 (m) REVERT: Z 281 VAL cc_start: 0.8912 (p) cc_final: 0.8706 (m) REVERT: Z 282 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8218 (mmtm) REVERT: Z 388 SER cc_start: 0.8390 (t) cc_final: 0.8172 (t) REVERT: Z 474 ASP cc_start: 0.5934 (t0) cc_final: 0.5474 (t0) outliers start: 66 outliers final: 59 residues processed: 623 average time/residue: 0.3372 time to fit residues: 312.4868 Evaluate side-chains 657 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 597 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 588 LYS Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 523 LEU Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 203 GLN Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 371 ILE Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 180 ASP Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Y residue 490 GLU Chi-restraints excluded: chain Y residue 492 LYS Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 347 LYS Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 211 optimal weight: 0.0020 chunk 183 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 360 GLN X 425 ASN Y 302 ASN Z 33 ASN ** Z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20670 Z= 0.248 Angle : 0.640 12.354 28093 Z= 0.319 Chirality : 0.047 0.326 3546 Planarity : 0.004 0.048 3379 Dihedral : 7.951 68.038 5096 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.17 % Allowed : 21.55 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.38 (0.17), residues: 2340 helix: 2.04 (0.28), residues: 366 sheet: 0.11 (0.20), residues: 708 loop : -1.19 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 32 HIS 0.005 0.001 HIS X 374 PHE 0.038 0.002 PHE Y 53 TYR 0.027 0.002 TYR Y 173 ARG 0.010 0.001 ARG W 579 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 603 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8282 (mmpt) cc_final: 0.7800 (mmpt) REVERT: C 73 LEU cc_start: 0.8401 (tp) cc_final: 0.8125 (tp) REVERT: D 22 LYS cc_start: 0.8406 (mtpp) cc_final: 0.7962 (mtpp) REVERT: D 50 GLN cc_start: 0.8108 (pt0) cc_final: 0.7844 (pt0) REVERT: D 52 TRP cc_start: 0.8504 (t60) cc_final: 0.8151 (t60) REVERT: E 4 THR cc_start: 0.8140 (m) cc_final: 0.7646 (p) REVERT: H 110 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8836 (tt) REVERT: L 32 TRP cc_start: 0.8491 (m100) cc_final: 0.7695 (m100) REVERT: U 522 PHE cc_start: 0.8838 (t80) cc_final: 0.8610 (t80) REVERT: U 577 GLN cc_start: 0.7766 (mt0) cc_final: 0.7427 (mt0) REVERT: U 647 GLU cc_start: 0.7224 (pt0) cc_final: 0.6975 (pt0) REVERT: V 542 ARG cc_start: 0.8280 (ttm110) cc_final: 0.8060 (ttm110) REVERT: V 579 ARG cc_start: 0.7778 (ptp-170) cc_final: 0.7259 (mtp180) REVERT: V 650 GLN cc_start: 0.8554 (tp40) cc_final: 0.8285 (tp-100) REVERT: W 647 GLU cc_start: 0.7186 (tt0) cc_final: 0.6675 (tt0) REVERT: X 45 TRP cc_start: 0.8616 (p90) cc_final: 0.8245 (p90) REVERT: X 68 VAL cc_start: 0.8539 (m) cc_final: 0.8245 (p) REVERT: X 275 GLU cc_start: 0.7086 (tt0) cc_final: 0.6676 (tt0) REVERT: X 315 GLN cc_start: 0.8339 (mp10) cc_final: 0.7929 (mp10) REVERT: X 466 GLU cc_start: 0.7848 (tp30) cc_final: 0.7352 (mm-30) REVERT: X 482 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6767 (mm-30) REVERT: Y 97 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8311 (mtmm) REVERT: Y 190 GLU cc_start: 0.7195 (tt0) cc_final: 0.6911 (tt0) REVERT: Y 293 GLU cc_start: 0.7133 (tt0) cc_final: 0.6901 (tt0) REVERT: Y 335 ARG cc_start: 0.8553 (tpp80) cc_final: 0.8278 (ttm-80) REVERT: Y 381 GLU cc_start: 0.6896 (tp30) cc_final: 0.6552 (tp30) REVERT: Z 39 TYR cc_start: 0.8579 (m-80) cc_final: 0.7740 (m-80) REVERT: Z 56 SER cc_start: 0.8319 (t) cc_final: 0.8076 (p) REVERT: Z 66 HIS cc_start: 0.7143 (t-90) cc_final: 0.6752 (t-90) REVERT: Z 107 ASP cc_start: 0.7382 (m-30) cc_final: 0.7038 (t0) REVERT: Z 175 LEU cc_start: 0.8646 (mt) cc_final: 0.8263 (mt) REVERT: Z 208 VAL cc_start: 0.8629 (m) cc_final: 0.8392 (m) REVERT: Z 282 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8204 (mmtm) REVERT: Z 330 HIS cc_start: 0.8230 (p-80) cc_final: 0.7953 (p-80) REVERT: Z 388 SER cc_start: 0.8421 (t) cc_final: 0.8206 (t) REVERT: Z 474 ASP cc_start: 0.5937 (t0) cc_final: 0.5481 (t0) outliers start: 66 outliers final: 58 residues processed: 622 average time/residue: 0.3375 time to fit residues: 311.6487 Evaluate side-chains 662 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 603 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 588 LYS Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 360 GLN Chi-restraints excluded: chain X residue 371 ILE Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 180 ASP Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Y residue 490 GLU Chi-restraints excluded: chain Y residue 492 LYS Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 347 LYS Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 591 GLN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 360 GLN Y 302 ASN Z 33 ASN ** Z 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099207 restraints weight = 32867.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103091 restraints weight = 14300.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105588 restraints weight = 8051.306| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 20670 Z= 0.310 Angle : 0.816 59.200 28093 Z= 0.439 Chirality : 0.055 1.164 3546 Planarity : 0.004 0.045 3379 Dihedral : 8.210 76.429 5096 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.27 % Allowed : 21.74 % Favored : 74.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.38 (0.17), residues: 2340 helix: 2.05 (0.28), residues: 366 sheet: 0.10 (0.20), residues: 708 loop : -1.19 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 32 HIS 0.005 0.001 HIS X 374 PHE 0.035 0.002 PHE Y 53 TYR 0.026 0.002 TYR Y 173 ARG 0.008 0.000 ARG Y 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5362.37 seconds wall clock time: 97 minutes 4.59 seconds (5824.59 seconds total)