Starting phenix.real_space_refine on Wed Feb 21 19:35:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/02_2024/8fwj_29506_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/02_2024/8fwj_29506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/02_2024/8fwj_29506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/02_2024/8fwj_29506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/02_2024/8fwj_29506_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/02_2024/8fwj_29506_trim_updated.pdb" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 35292 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 60 5.49 5 Mg 24 5.21 5 S 216 5.16 5 C 37512 2.51 5 N 10872 2.21 5 O 11496 1.98 5 H 24 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 105": "OD1" <-> "OD2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 508": "NH1" <-> "NH2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "C ARG 508": "NH1" <-> "NH2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 441": "NH1" <-> "NH2" Residue "D ARG 508": "NH1" <-> "NH2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D GLU 519": "OE1" <-> "OE2" Residue "E ASP 105": "OD1" <-> "OD2" Residue "E PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 225": "OD1" <-> "OD2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 310": "NH1" <-> "NH2" Residue "E TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 441": "NH1" <-> "NH2" Residue "E ARG 508": "NH1" <-> "NH2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E GLU 519": "OE1" <-> "OE2" Residue "F ASP 105": "OD1" <-> "OD2" Residue "F PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 310": "NH1" <-> "NH2" Residue "F TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 441": "NH1" <-> "NH2" Residue "F ARG 508": "NH1" <-> "NH2" Residue "F ARG 510": "NH1" <-> "NH2" Residue "F GLU 519": "OE1" <-> "OE2" Residue "G ASP 105": "OD1" <-> "OD2" Residue "G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 225": "OD1" <-> "OD2" Residue "G PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 310": "NH1" <-> "NH2" Residue "G TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 441": "NH1" <-> "NH2" Residue "G ARG 508": "NH1" <-> "NH2" Residue "G ARG 510": "NH1" <-> "NH2" Residue "G GLU 519": "OE1" <-> "OE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 225": "OD1" <-> "OD2" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 310": "NH1" <-> "NH2" Residue "H TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 441": "NH1" <-> "NH2" Residue "H ARG 508": "NH1" <-> "NH2" Residue "H ARG 510": "NH1" <-> "NH2" Residue "H GLU 519": "OE1" <-> "OE2" Residue "I ASP 105": "OD1" <-> "OD2" Residue "I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 225": "OD1" <-> "OD2" Residue "I PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 310": "NH1" <-> "NH2" Residue "I TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 441": "NH1" <-> "NH2" Residue "I ARG 508": "NH1" <-> "NH2" Residue "I ARG 510": "NH1" <-> "NH2" Residue "I GLU 519": "OE1" <-> "OE2" Residue "J ASP 105": "OD1" <-> "OD2" Residue "J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 225": "OD1" <-> "OD2" Residue "J PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 310": "NH1" <-> "NH2" Residue "J TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 441": "NH1" <-> "NH2" Residue "J ARG 508": "NH1" <-> "NH2" Residue "J ARG 510": "NH1" <-> "NH2" Residue "J GLU 519": "OE1" <-> "OE2" Residue "K ASP 105": "OD1" <-> "OD2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 225": "OD1" <-> "OD2" Residue "K PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 310": "NH1" <-> "NH2" Residue "K TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 441": "NH1" <-> "NH2" Residue "K ARG 508": "NH1" <-> "NH2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K GLU 519": "OE1" <-> "OE2" Residue "L ASP 105": "OD1" <-> "OD2" Residue "L PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "L PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 225": "OD1" <-> "OD2" Residue "L PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 310": "NH1" <-> "NH2" Residue "L TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 441": "NH1" <-> "NH2" Residue "L ARG 508": "NH1" <-> "NH2" Residue "L ARG 510": "NH1" <-> "NH2" Residue "L GLU 519": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 60204 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "B" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "C" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "D" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "E" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "F" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "G" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "H" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "I" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "J" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "K" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "L" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "M" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 3, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 23.49, per 1000 atoms: 0.39 Number of scatterers: 60204 At special positions: 0 Unit cell: (113, 121, 367, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 216 16.00 P 60 15.00 Mg 24 11.99 O 11496 8.00 N 10872 7.00 C 37512 6.00 H 24 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 18.39 Conformation dependent library (CDL) restraints added in 8.4 seconds 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 228 helices and 48 sheets defined 41.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.15 Creating SS restraints... Processing helix chain 'A' and resid 11 through 17 Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 142 through 159 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 278 through 292 removed outlier: 3.552A pdb=" N ARG A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 340 through 354 Processing helix chain 'A' and resid 364 through 367 removed outlier: 3.849A pdb=" N PHE A 367 " --> pdb=" O ILE A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER A 533 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 17 Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'B' and resid 340 through 354 Processing helix chain 'B' and resid 364 through 367 removed outlier: 3.849A pdb=" N PHE B 367 " --> pdb=" O ILE B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 367' Processing helix chain 'B' and resid 373 through 390 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER B 533 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 17 Processing helix chain 'C' and resid 37 through 51 Processing helix chain 'C' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 142 through 159 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 278 through 292 removed outlier: 3.554A pdb=" N ARG C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 325 Processing helix chain 'C' and resid 340 through 354 Processing helix chain 'C' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE C 367 " --> pdb=" O ILE C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 367' Processing helix chain 'C' and resid 373 through 390 Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER C 533 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'D' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL D 72 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 109 through 122 Processing helix chain 'D' and resid 133 through 138 Processing helix chain 'D' and resid 142 through 159 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 315 removed outlier: 3.930A pdb=" N SER D 314 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU D 315 " --> pdb=" O ASN D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 325 Processing helix chain 'D' and resid 340 through 354 Processing helix chain 'D' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE D 367 " --> pdb=" O ILE D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 364 through 367' Processing helix chain 'D' and resid 373 through 390 Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER D 533 " --> pdb=" O LEU D 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 17 Processing helix chain 'E' and resid 37 through 51 Processing helix chain 'E' and resid 65 through 75 removed outlier: 3.846A pdb=" N VAL E 72 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 Processing helix chain 'E' and resid 109 through 122 Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 142 through 159 Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER E 314 " --> pdb=" O ARG E 310 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU E 315 " --> pdb=" O ASN E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 325 Processing helix chain 'E' and resid 340 through 354 Processing helix chain 'E' and resid 364 through 367 removed outlier: 3.849A pdb=" N PHE E 367 " --> pdb=" O ILE E 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 364 through 367' Processing helix chain 'E' and resid 373 through 390 Processing helix chain 'E' and resid 413 through 415 No H-bonds generated for 'chain 'E' and resid 413 through 415' Processing helix chain 'E' and resid 474 through 551 removed outlier: 3.686A pdb=" N SER E 533 " --> pdb=" O LEU E 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 Processing helix chain 'F' and resid 37 through 51 Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU F 75 " --> pdb=" O ASN F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 84 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 142 through 159 Processing helix chain 'F' and resid 251 through 256 Processing helix chain 'F' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER F 314 " --> pdb=" O ARG F 310 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU F 315 " --> pdb=" O ASN F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'F' and resid 340 through 354 Processing helix chain 'F' and resid 364 through 367 removed outlier: 3.849A pdb=" N PHE F 367 " --> pdb=" O ILE F 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 364 through 367' Processing helix chain 'F' and resid 373 through 390 Processing helix chain 'F' and resid 413 through 415 No H-bonds generated for 'chain 'F' and resid 413 through 415' Processing helix chain 'F' and resid 474 through 551 removed outlier: 3.684A pdb=" N SER F 533 " --> pdb=" O LEU F 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 17 Processing helix chain 'G' and resid 37 through 51 Processing helix chain 'G' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL G 72 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU G 75 " --> pdb=" O ASN G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 84 Processing helix chain 'G' and resid 109 through 122 Processing helix chain 'G' and resid 133 through 138 Processing helix chain 'G' and resid 142 through 159 Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 278 through 292 removed outlier: 3.554A pdb=" N ARG G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER G 314 " --> pdb=" O ARG G 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU G 315 " --> pdb=" O ASN G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 325 Processing helix chain 'G' and resid 340 through 354 Processing helix chain 'G' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE G 367 " --> pdb=" O ILE G 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 364 through 367' Processing helix chain 'G' and resid 373 through 390 Processing helix chain 'G' and resid 413 through 415 No H-bonds generated for 'chain 'G' and resid 413 through 415' Processing helix chain 'G' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER G 533 " --> pdb=" O LEU G 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 17 Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU H 75 " --> pdb=" O ASN H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 84 Processing helix chain 'H' and resid 109 through 122 Processing helix chain 'H' and resid 133 through 138 Processing helix chain 'H' and resid 142 through 159 Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'H' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 315 removed outlier: 3.928A pdb=" N SER H 314 " --> pdb=" O ARG H 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU H 315 " --> pdb=" O ASN H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 325 Processing helix chain 'H' and resid 340 through 354 Processing helix chain 'H' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE H 367 " --> pdb=" O ILE H 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 364 through 367' Processing helix chain 'H' and resid 373 through 390 Processing helix chain 'H' and resid 413 through 415 No H-bonds generated for 'chain 'H' and resid 413 through 415' Processing helix chain 'H' and resid 474 through 551 removed outlier: 3.686A pdb=" N SER H 533 " --> pdb=" O LEU H 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 17 Processing helix chain 'I' and resid 37 through 51 Processing helix chain 'I' and resid 65 through 75 removed outlier: 3.846A pdb=" N VAL I 72 " --> pdb=" O ILE I 68 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU I 75 " --> pdb=" O ASN I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 84 Processing helix chain 'I' and resid 109 through 122 Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 142 through 159 Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG I 292 " --> pdb=" O ALA I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER I 314 " --> pdb=" O ARG I 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU I 315 " --> pdb=" O ASN I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 325 Processing helix chain 'I' and resid 340 through 354 Processing helix chain 'I' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE I 367 " --> pdb=" O ILE I 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 364 through 367' Processing helix chain 'I' and resid 373 through 390 Processing helix chain 'I' and resid 413 through 415 No H-bonds generated for 'chain 'I' and resid 413 through 415' Processing helix chain 'I' and resid 474 through 551 removed outlier: 3.686A pdb=" N SER I 533 " --> pdb=" O LEU I 530 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 17 Processing helix chain 'J' and resid 37 through 51 Processing helix chain 'J' and resid 65 through 75 removed outlier: 3.846A pdb=" N VAL J 72 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU J 75 " --> pdb=" O ASN J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 84 Processing helix chain 'J' and resid 109 through 122 Processing helix chain 'J' and resid 133 through 138 Processing helix chain 'J' and resid 142 through 159 Processing helix chain 'J' and resid 251 through 256 Processing helix chain 'J' and resid 278 through 292 removed outlier: 3.554A pdb=" N ARG J 292 " --> pdb=" O ALA J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 305 through 315 removed outlier: 3.930A pdb=" N SER J 314 " --> pdb=" O ARG J 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU J 315 " --> pdb=" O ASN J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 325 Processing helix chain 'J' and resid 340 through 354 Processing helix chain 'J' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE J 367 " --> pdb=" O ILE J 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 364 through 367' Processing helix chain 'J' and resid 373 through 390 Processing helix chain 'J' and resid 413 through 415 No H-bonds generated for 'chain 'J' and resid 413 through 415' Processing helix chain 'J' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER J 533 " --> pdb=" O LEU J 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 17 Processing helix chain 'K' and resid 37 through 51 Processing helix chain 'K' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL K 72 " --> pdb=" O ILE K 68 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER K 74 " --> pdb=" O ASN K 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU K 75 " --> pdb=" O ASN K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 84 Processing helix chain 'K' and resid 109 through 122 Processing helix chain 'K' and resid 133 through 138 Processing helix chain 'K' and resid 142 through 159 Processing helix chain 'K' and resid 251 through 256 Processing helix chain 'K' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG K 292 " --> pdb=" O ALA K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER K 314 " --> pdb=" O ARG K 310 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU K 315 " --> pdb=" O ASN K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 325 Processing helix chain 'K' and resid 340 through 354 Processing helix chain 'K' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE K 367 " --> pdb=" O ILE K 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 364 through 367' Processing helix chain 'K' and resid 373 through 390 Processing helix chain 'K' and resid 413 through 415 No H-bonds generated for 'chain 'K' and resid 413 through 415' Processing helix chain 'K' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER K 533 " --> pdb=" O LEU K 530 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 17 Processing helix chain 'L' and resid 37 through 51 Processing helix chain 'L' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL L 72 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER L 74 " --> pdb=" O ASN L 70 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU L 75 " --> pdb=" O ASN L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 84 Processing helix chain 'L' and resid 109 through 122 Processing helix chain 'L' and resid 133 through 138 Processing helix chain 'L' and resid 142 through 159 Processing helix chain 'L' and resid 251 through 256 Processing helix chain 'L' and resid 278 through 292 removed outlier: 3.554A pdb=" N ARG L 292 " --> pdb=" O ALA L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER L 314 " --> pdb=" O ARG L 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU L 315 " --> pdb=" O ASN L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 325 Processing helix chain 'L' and resid 340 through 354 Processing helix chain 'L' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE L 367 " --> pdb=" O ILE L 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 364 through 367' Processing helix chain 'L' and resid 373 through 390 Processing helix chain 'L' and resid 413 through 415 No H-bonds generated for 'chain 'L' and resid 413 through 415' Processing helix chain 'L' and resid 474 through 551 removed outlier: 3.684A pdb=" N SER L 533 " --> pdb=" O LEU L 530 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 29 Processing helix chain 'M' and resid 46 through 52 Processing helix chain 'M' and resid 78 through 84 Processing helix chain 'N' and resid 14 through 29 Processing helix chain 'N' and resid 46 through 52 Processing helix chain 'N' and resid 78 through 84 Processing helix chain 'O' and resid 14 through 29 Processing helix chain 'O' and resid 46 through 52 Processing helix chain 'O' and resid 78 through 84 Processing helix chain 'P' and resid 14 through 29 Processing helix chain 'P' and resid 46 through 52 Processing helix chain 'P' and resid 78 through 84 Processing helix chain 'Q' and resid 14 through 29 Processing helix chain 'Q' and resid 46 through 52 Processing helix chain 'Q' and resid 78 through 84 Processing helix chain 'R' and resid 14 through 29 Processing helix chain 'R' and resid 46 through 52 Processing helix chain 'R' and resid 78 through 84 Processing helix chain 'S' and resid 14 through 29 Processing helix chain 'S' and resid 46 through 52 Processing helix chain 'S' and resid 78 through 84 Processing helix chain 'T' and resid 14 through 29 Processing helix chain 'T' and resid 46 through 52 Processing helix chain 'T' and resid 78 through 84 Processing helix chain 'U' and resid 14 through 29 Processing helix chain 'U' and resid 46 through 52 Processing helix chain 'U' and resid 78 through 84 Processing helix chain 'V' and resid 14 through 29 Processing helix chain 'V' and resid 46 through 52 Processing helix chain 'V' and resid 78 through 84 Processing helix chain 'W' and resid 14 through 29 Processing helix chain 'W' and resid 46 through 52 Processing helix chain 'W' and resid 78 through 84 Processing helix chain 'X' and resid 14 through 29 Processing helix chain 'X' and resid 46 through 52 Processing helix chain 'X' and resid 78 through 84 Processing sheet with id= A, first strand: chain 'A' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG A 201 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 187 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE A 188 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 28 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 190 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS A 30 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS A 192 " --> pdb=" O CYS A 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR A 163 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL A 29 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 165 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL A 127 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 57 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU A 129 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 59 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 431 through 440 removed outlier: 6.505A pdb=" N TRP A 419 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY A 394 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL A 270 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 396 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLY A 272 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS A 398 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 452 through 455 removed outlier: 3.644A pdb=" N SER A 460 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 198 through 208 removed outlier: 6.711A pdb=" N VAL B 187 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ILE B 188 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 28 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU B 190 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS B 30 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS B 192 " --> pdb=" O CYS B 30 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 163 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL B 29 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 165 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B 127 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 57 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU B 129 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B 59 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 431 through 440 removed outlier: 6.504A pdb=" N TRP B 419 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY B 394 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 270 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE B 396 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY B 272 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS B 398 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 452 through 455 removed outlier: 3.642A pdb=" N SER B 460 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 198 through 208 removed outlier: 6.712A pdb=" N VAL C 187 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE C 188 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU C 28 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU C 190 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS C 30 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N HIS C 192 " --> pdb=" O CYS C 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C 163 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL C 29 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 165 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL C 127 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 57 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU C 129 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 59 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 431 through 440 removed outlier: 6.505A pdb=" N TRP C 419 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY C 394 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 270 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE C 396 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY C 272 " --> pdb=" O PHE C 396 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS C 398 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER C 460 " --> pdb=" O LEU C 453 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 218 through 220 removed outlier: 4.536A pdb=" N ARG D 201 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 187 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE D 188 " --> pdb=" O PRO D 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU D 28 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU D 190 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS D 30 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS D 192 " --> pdb=" O CYS D 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR D 163 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL D 29 " --> pdb=" O THR D 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE D 165 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL D 127 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 57 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU D 129 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL D 59 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 431 through 440 removed outlier: 6.505A pdb=" N TRP D 419 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY D 394 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL D 270 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE D 396 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY D 272 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS D 398 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER D 460 " --> pdb=" O LEU D 453 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 198 through 208 removed outlier: 6.712A pdb=" N VAL E 187 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE E 188 " --> pdb=" O PRO E 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU E 28 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU E 190 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS E 30 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS E 192 " --> pdb=" O CYS E 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR E 163 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL E 29 " --> pdb=" O THR E 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE E 165 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL E 127 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL E 57 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU E 129 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL E 59 " --> pdb=" O LEU E 129 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP E 419 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY E 394 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL E 270 " --> pdb=" O GLY E 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE E 396 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY E 272 " --> pdb=" O PHE E 396 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N HIS E 398 " --> pdb=" O GLY E 272 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER E 460 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG F 201 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL F 187 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE F 188 " --> pdb=" O PRO F 26 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU F 28 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU F 190 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS F 30 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N HIS F 192 " --> pdb=" O CYS F 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR F 163 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL F 29 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE F 165 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL F 127 " --> pdb=" O PRO F 55 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 57 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU F 129 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL F 59 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP F 419 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY F 394 " --> pdb=" O ILE F 268 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL F 270 " --> pdb=" O GLY F 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE F 396 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY F 272 " --> pdb=" O PHE F 396 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS F 398 " --> pdb=" O GLY F 272 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 452 through 455 removed outlier: 3.642A pdb=" N SER F 460 " --> pdb=" O LEU F 453 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG G 201 " --> pdb=" O PHE G 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL G 187 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ILE G 188 " --> pdb=" O PRO G 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU G 28 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU G 190 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS G 30 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS G 192 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR G 163 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL G 29 " --> pdb=" O THR G 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE G 165 " --> pdb=" O VAL G 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL G 127 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL G 57 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU G 129 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL G 59 " --> pdb=" O LEU G 129 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP G 419 " --> pdb=" O LEU G 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY G 394 " --> pdb=" O ILE G 268 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL G 270 " --> pdb=" O GLY G 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE G 396 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY G 272 " --> pdb=" O PHE G 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS G 398 " --> pdb=" O GLY G 272 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER G 460 " --> pdb=" O LEU G 453 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 198 through 208 removed outlier: 6.711A pdb=" N VAL H 187 " --> pdb=" O VAL H 206 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ILE H 188 " --> pdb=" O PRO H 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU H 28 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU H 190 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS H 30 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS H 192 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR H 163 " --> pdb=" O SER H 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL H 29 " --> pdb=" O THR H 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE H 165 " --> pdb=" O VAL H 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL H 127 " --> pdb=" O PRO H 55 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL H 57 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU H 129 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL H 59 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 431 through 440 removed outlier: 6.505A pdb=" N TRP H 419 " --> pdb=" O LEU H 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY H 394 " --> pdb=" O ILE H 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL H 270 " --> pdb=" O GLY H 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE H 396 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY H 272 " --> pdb=" O PHE H 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS H 398 " --> pdb=" O GLY H 272 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER H 460 " --> pdb=" O LEU H 453 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG I 201 " --> pdb=" O PHE I 220 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL I 187 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ILE I 188 " --> pdb=" O PRO I 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU I 28 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU I 190 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS I 30 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS I 192 " --> pdb=" O CYS I 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR I 163 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL I 29 " --> pdb=" O THR I 163 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE I 165 " --> pdb=" O VAL I 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL I 127 " --> pdb=" O PRO I 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL I 57 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU I 129 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL I 59 " --> pdb=" O LEU I 129 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP I 419 " --> pdb=" O LEU I 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY I 394 " --> pdb=" O ILE I 268 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL I 270 " --> pdb=" O GLY I 394 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE I 396 " --> pdb=" O VAL I 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY I 272 " --> pdb=" O PHE I 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS I 398 " --> pdb=" O GLY I 272 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER I 460 " --> pdb=" O LEU I 453 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG J 201 " --> pdb=" O PHE J 220 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL J 187 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE J 188 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU J 28 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU J 190 " --> pdb=" O LEU J 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS J 30 " --> pdb=" O LEU J 190 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N HIS J 192 " --> pdb=" O CYS J 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR J 163 " --> pdb=" O SER J 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL J 29 " --> pdb=" O THR J 163 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE J 165 " --> pdb=" O VAL J 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL J 127 " --> pdb=" O PRO J 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL J 57 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU J 129 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL J 59 " --> pdb=" O LEU J 129 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP J 419 " --> pdb=" O LEU J 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY J 394 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL J 270 " --> pdb=" O GLY J 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE J 396 " --> pdb=" O VAL J 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY J 272 " --> pdb=" O PHE J 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS J 398 " --> pdb=" O GLY J 272 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER J 460 " --> pdb=" O LEU J 453 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 198 through 208 removed outlier: 6.712A pdb=" N VAL K 187 " --> pdb=" O VAL K 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE K 188 " --> pdb=" O PRO K 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU K 28 " --> pdb=" O ILE K 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU K 190 " --> pdb=" O LEU K 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS K 30 " --> pdb=" O LEU K 190 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N HIS K 192 " --> pdb=" O CYS K 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR K 163 " --> pdb=" O SER K 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL K 29 " --> pdb=" O THR K 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE K 165 " --> pdb=" O VAL K 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL K 127 " --> pdb=" O PRO K 55 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL K 57 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU K 129 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL K 59 " --> pdb=" O LEU K 129 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP K 419 " --> pdb=" O LEU K 438 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY K 394 " --> pdb=" O ILE K 268 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL K 270 " --> pdb=" O GLY K 394 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE K 396 " --> pdb=" O VAL K 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY K 272 " --> pdb=" O PHE K 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS K 398 " --> pdb=" O GLY K 272 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 452 through 455 removed outlier: 3.644A pdb=" N SER K 460 " --> pdb=" O LEU K 453 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG L 201 " --> pdb=" O PHE L 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL L 187 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE L 188 " --> pdb=" O PRO L 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU L 28 " --> pdb=" O ILE L 188 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU L 190 " --> pdb=" O LEU L 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS L 30 " --> pdb=" O LEU L 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS L 192 " --> pdb=" O CYS L 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR L 163 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL L 29 " --> pdb=" O THR L 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE L 165 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL L 127 " --> pdb=" O PRO L 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL L 57 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU L 129 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL L 59 " --> pdb=" O LEU L 129 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 431 through 440 removed outlier: 6.504A pdb=" N TRP L 419 " --> pdb=" O LEU L 438 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY L 394 " --> pdb=" O ILE L 268 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL L 270 " --> pdb=" O GLY L 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE L 396 " --> pdb=" O VAL L 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY L 272 " --> pdb=" O PHE L 396 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS L 398 " --> pdb=" O GLY L 272 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER L 460 " --> pdb=" O LEU L 453 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 36 through 41 Processing sheet with id= AL, first strand: chain 'N' and resid 36 through 41 Processing sheet with id= AM, first strand: chain 'O' and resid 36 through 41 Processing sheet with id= AN, first strand: chain 'P' and resid 36 through 41 Processing sheet with id= AO, first strand: chain 'Q' and resid 36 through 41 Processing sheet with id= AP, first strand: chain 'R' and resid 36 through 41 Processing sheet with id= AQ, first strand: chain 'S' and resid 36 through 41 Processing sheet with id= AR, first strand: chain 'T' and resid 36 through 41 Processing sheet with id= AS, first strand: chain 'U' and resid 36 through 41 Processing sheet with id= AT, first strand: chain 'V' and resid 36 through 41 Processing sheet with id= AU, first strand: chain 'W' and resid 36 through 41 Processing sheet with id= AV, first strand: chain 'X' and resid 36 through 41 2901 hydrogen bonds defined for protein. 5838 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: 20.22 Time building geometry restraints manager: 20.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 24 1.05 - 1.24: 6860 1.24 - 1.43: 18072 1.43 - 1.62: 35728 1.62 - 1.81: 372 Bond restraints: 61056 Sorted by residual: bond pdb=" CZ ARG B 310 " pdb=" NH2 ARG B 310 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.30e-02 5.92e+03 3.32e+00 bond pdb=" CZ ARG C 310 " pdb=" NH2 ARG C 310 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.30e-02 5.92e+03 3.30e+00 bond pdb=" CZ ARG D 310 " pdb=" NH2 ARG D 310 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.30e-02 5.92e+03 3.29e+00 bond pdb=" CZ ARG I 310 " pdb=" NH2 ARG I 310 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.30e-02 5.92e+03 3.26e+00 bond pdb=" CZ ARG L 310 " pdb=" NH2 ARG L 310 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.30e-02 5.92e+03 3.23e+00 ... (remaining 61051 not shown) Histogram of bond angle deviations from ideal: 100.18 - 108.12: 2465 108.12 - 116.06: 38060 116.06 - 124.00: 40608 124.00 - 131.94: 1331 131.94 - 139.88: 96 Bond angle restraints: 82560 Sorted by residual: angle pdb=" CB ARG H 310 " pdb=" CG ARG H 310 " pdb=" CD ARG H 310 " ideal model delta sigma weight residual 111.30 122.37 -11.07 2.30e+00 1.89e-01 2.31e+01 angle pdb=" CB ARG E 310 " pdb=" CG ARG E 310 " pdb=" CD ARG E 310 " ideal model delta sigma weight residual 111.30 122.35 -11.05 2.30e+00 1.89e-01 2.31e+01 angle pdb=" CB ARG A 310 " pdb=" CG ARG A 310 " pdb=" CD ARG A 310 " ideal model delta sigma weight residual 111.30 122.35 -11.05 2.30e+00 1.89e-01 2.31e+01 angle pdb=" CB ARG J 310 " pdb=" CG ARG J 310 " pdb=" CD ARG J 310 " ideal model delta sigma weight residual 111.30 122.34 -11.04 2.30e+00 1.89e-01 2.30e+01 angle pdb=" CB ARG L 310 " pdb=" CG ARG L 310 " pdb=" CD ARG L 310 " ideal model delta sigma weight residual 111.30 122.33 -11.03 2.30e+00 1.89e-01 2.30e+01 ... (remaining 82555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.89: 35599 27.89 - 55.79: 1445 55.79 - 83.68: 222 83.68 - 111.58: 18 111.58 - 139.47: 12 Dihedral angle restraints: 37296 sinusoidal: 15588 harmonic: 21708 Sorted by residual: dihedral pdb=" C5' ADP J 602 " pdb=" O5' ADP J 602 " pdb=" PA ADP J 602 " pdb=" O2A ADP J 602 " ideal model delta sinusoidal sigma weight residual -60.00 79.47 -139.47 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" C5' ADP K 602 " pdb=" O5' ADP K 602 " pdb=" PA ADP K 602 " pdb=" O2A ADP K 602 " ideal model delta sinusoidal sigma weight residual -60.00 79.44 -139.44 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" C5' ADP I 602 " pdb=" O5' ADP I 602 " pdb=" PA ADP I 602 " pdb=" O2A ADP I 602 " ideal model delta sinusoidal sigma weight residual -60.00 79.42 -139.42 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 37293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 8132 0.060 - 0.119: 1145 0.119 - 0.179: 59 0.179 - 0.239: 0 0.239 - 0.298: 36 Chirality restraints: 9372 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' ATP I 601 " pdb=" C1' ATP I 601 " pdb=" C3' ATP I 601 " pdb=" O2' ATP I 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2' ATP K 601 " pdb=" C1' ATP K 601 " pdb=" C3' ATP K 601 " pdb=" O2' ATP K 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 9369 not shown) Planarity restraints: 10752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 550 " -0.465 9.50e-02 1.11e+02 2.08e-01 2.70e+01 pdb=" NE ARG B 550 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG B 550 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 550 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 550 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 550 " -0.464 9.50e-02 1.11e+02 2.08e-01 2.69e+01 pdb=" NE ARG C 550 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 550 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 550 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 550 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 550 " 0.464 9.50e-02 1.11e+02 2.08e-01 2.69e+01 pdb=" NE ARG D 550 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG D 550 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 550 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 550 " 0.012 2.00e-02 2.50e+03 ... (remaining 10749 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.50: 510 2.50 - 3.03: 38458 3.03 - 3.55: 69697 3.55 - 4.08: 101394 4.08 - 4.60: 153223 Nonbonded interactions: 363282 Sorted by model distance: nonbonded pdb=" OG SER H 279 " pdb="MG MG H 603 " model vdw 1.976 2.050 nonbonded pdb=" OG SER F 279 " pdb="MG MG F 603 " model vdw 1.976 2.050 nonbonded pdb=" OG SER C 279 " pdb="MG MG C 603 " model vdw 1.976 2.050 nonbonded pdb=" OG SER E 279 " pdb="MG MG E 603 " model vdw 1.977 2.050 nonbonded pdb=" OG SER G 279 " pdb="MG MG G 603 " model vdw 1.977 2.050 ... (remaining 363277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'B' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'C' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'D' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'E' and (resid 2 through 558 or resid 601 through 603)) selection = chain 'F' selection = (chain 'G' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'H' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'I' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'J' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'K' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'L' and (resid 2 through 558 or resid 601 through 603)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.440 Construct map_model_manager: 1.160 Extract box with map and model: 28.970 Check model and map are aligned: 0.790 Set scattering table: 0.440 Process input model: 120.780 Find NCS groups from input model: 4.030 Set up NCS constraints: 0.660 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: 0.020 Load rotamer database and sin/cos tables:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 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 : 0.003 0.045 61032 Z= 0.199 Angle : 0.722 11.066 82500 Z= 0.397 Chirality : 0.044 0.298 9372 Planarity : 0.009 0.208 10740 Dihedral : 15.233 139.469 23292 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 31.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.45 % Allowed : 2.72 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.43 (0.10), residues: 7572 helix: 1.64 (0.09), residues: 3360 sheet: -0.69 (0.12), residues: 1728 loop : -0.76 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 155 HIS 0.003 0.001 HIS E 343 PHE 0.018 0.001 PHE I 263 TYR 0.031 0.003 TYR A 298 ARG 0.013 0.001 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2214 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1998 time to evaluate : 5.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 SER cc_start: 0.8216 (m) cc_final: 0.7953 (p) REVERT: A 352 MET cc_start: 0.6801 (mtp) cc_final: 0.6419 (mtp) REVERT: A 488 GLU cc_start: 0.5270 (OUTLIER) cc_final: 0.3478 (mm-30) REVERT: B 91 GLU cc_start: 0.7626 (tp30) cc_final: 0.6894 (tp30) REVERT: B 105 ASP cc_start: 0.7428 (m-30) cc_final: 0.6797 (p0) REVERT: B 375 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6635 (mm-30) REVERT: B 385 ASP cc_start: 0.7390 (t70) cc_final: 0.7159 (t70) REVERT: B 488 GLU cc_start: 0.5408 (OUTLIER) cc_final: 0.3764 (tp30) REVERT: B 534 GLU cc_start: 0.5378 (OUTLIER) cc_final: 0.5042 (tm-30) REVERT: C 137 SER cc_start: 0.8680 (t) cc_final: 0.8421 (p) REVERT: C 140 SER cc_start: 0.8342 (m) cc_final: 0.7903 (p) REVERT: C 211 THR cc_start: 0.6301 (t) cc_final: 0.6079 (t) REVERT: C 422 MET cc_start: 0.7901 (mtp) cc_final: 0.7611 (mtp) REVERT: C 488 GLU cc_start: 0.5256 (OUTLIER) cc_final: 0.3672 (tp30) REVERT: C 512 GLN cc_start: 0.5021 (OUTLIER) cc_final: 0.4739 (tt0) REVERT: D 120 ASP cc_start: 0.7523 (m-30) cc_final: 0.7228 (t70) REVERT: D 211 THR cc_start: 0.6453 (t) cc_final: 0.6198 (t) REVERT: D 233 SER cc_start: 0.8145 (m) cc_final: 0.7944 (p) REVERT: D 375 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6739 (mm-30) REVERT: D 438 LEU cc_start: 0.8423 (tt) cc_final: 0.8194 (mp) REVERT: D 451 GLU cc_start: 0.7246 (tt0) cc_final: 0.7014 (tt0) REVERT: D 488 GLU cc_start: 0.5079 (OUTLIER) cc_final: 0.3380 (mm-30) REVERT: E 91 GLU cc_start: 0.7650 (tp30) cc_final: 0.7011 (tp30) REVERT: E 195 GLU cc_start: 0.7392 (tt0) cc_final: 0.6932 (tp30) REVERT: E 375 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6627 (mm-30) REVERT: E 385 ASP cc_start: 0.7475 (t70) cc_final: 0.7265 (t70) REVERT: E 488 GLU cc_start: 0.5414 (OUTLIER) cc_final: 0.3725 (mm-30) REVERT: E 534 GLU cc_start: 0.5452 (OUTLIER) cc_final: 0.5123 (tm-30) REVERT: F 137 SER cc_start: 0.8758 (t) cc_final: 0.8534 (p) REVERT: F 352 MET cc_start: 0.7071 (mtp) cc_final: 0.6826 (mtm) REVERT: F 353 ARG cc_start: 0.7302 (ttm170) cc_final: 0.7064 (ttp80) REVERT: F 454 MET cc_start: 0.8163 (ptp) cc_final: 0.7928 (ptm) REVERT: F 488 GLU cc_start: 0.4966 (OUTLIER) cc_final: 0.3476 (tp30) REVERT: G 185 ASP cc_start: 0.7066 (m-30) cc_final: 0.6674 (m-30) REVERT: G 195 GLU cc_start: 0.7386 (tt0) cc_final: 0.6934 (tp30) REVERT: G 196 ASN cc_start: 0.8270 (m-40) cc_final: 0.8044 (m-40) REVERT: G 216 ASN cc_start: 0.8286 (m-40) cc_final: 0.7948 (m-40) REVERT: G 233 SER cc_start: 0.8480 (m) cc_final: 0.8191 (p) REVERT: G 352 MET cc_start: 0.6707 (mtp) cc_final: 0.6422 (mtm) REVERT: G 375 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6544 (mm-30) REVERT: G 451 GLU cc_start: 0.7295 (tt0) cc_final: 0.7034 (tt0) REVERT: H 191 ASP cc_start: 0.7080 (t0) cc_final: 0.6596 (t70) REVERT: H 352 MET cc_start: 0.7212 (mtp) cc_final: 0.6954 (mtm) REVERT: H 353 ARG cc_start: 0.7534 (ttm170) cc_final: 0.7283 (ttp80) REVERT: H 374 LEU cc_start: 0.8667 (mt) cc_final: 0.8384 (mt) REVERT: H 453 LEU cc_start: 0.8121 (tp) cc_final: 0.7844 (pt) REVERT: H 454 MET cc_start: 0.8166 (ptp) cc_final: 0.7860 (ptm) REVERT: H 488 GLU cc_start: 0.5015 (OUTLIER) cc_final: 0.4638 (tm-30) REVERT: H 512 GLN cc_start: 0.4994 (OUTLIER) cc_final: 0.4697 (tt0) REVERT: I 91 GLU cc_start: 0.7423 (tp30) cc_final: 0.6977 (tp30) REVERT: I 105 ASP cc_start: 0.7543 (m-30) cc_final: 0.6957 (p0) REVERT: I 211 THR cc_start: 0.6070 (t) cc_final: 0.5809 (t) REVERT: I 233 SER cc_start: 0.8237 (m) cc_final: 0.8014 (p) REVERT: I 385 ASP cc_start: 0.7925 (t70) cc_final: 0.7720 (t70) REVERT: I 454 MET cc_start: 0.7918 (ptp) cc_final: 0.7695 (ptm) REVERT: I 472 LEU cc_start: 0.7031 (mt) cc_final: 0.6802 (mt) REVERT: J 195 GLU cc_start: 0.7396 (tt0) cc_final: 0.6951 (tp30) REVERT: J 374 LEU cc_start: 0.8457 (mt) cc_final: 0.8255 (mm) REVERT: J 375 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6375 (mm-30) REVERT: J 512 GLN cc_start: 0.5197 (OUTLIER) cc_final: 0.4927 (mt0) REVERT: K 91 GLU cc_start: 0.7396 (tp30) cc_final: 0.7168 (tp30) REVERT: K 109 GLU cc_start: 0.8038 (tp30) cc_final: 0.7798 (tp30) REVERT: K 185 ASP cc_start: 0.7131 (m-30) cc_final: 0.6861 (m-30) REVERT: K 197 GLN cc_start: 0.8672 (mt0) cc_final: 0.8437 (mt0) REVERT: K 233 SER cc_start: 0.8402 (m) cc_final: 0.8195 (p) REVERT: K 352 MET cc_start: 0.6697 (mtp) cc_final: 0.6435 (mtm) REVERT: K 373 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7793 (ttt90) REVERT: K 454 MET cc_start: 0.7825 (ptp) cc_final: 0.7614 (ptm) REVERT: K 488 GLU cc_start: 0.5041 (OUTLIER) cc_final: 0.4775 (tm-30) REVERT: L 91 GLU cc_start: 0.7318 (tp30) cc_final: 0.6772 (tp30) REVERT: L 105 ASP cc_start: 0.7553 (m-30) cc_final: 0.6769 (p0) REVERT: L 375 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6618 (mm-30) REVERT: M 38 GLU cc_start: 0.6761 (tt0) cc_final: 0.6507 (tp30) REVERT: N 22 ASN cc_start: 0.7671 (m-40) cc_final: 0.7409 (m-40) REVERT: N 38 GLU cc_start: 0.6809 (tt0) cc_final: 0.6365 (tp30) REVERT: N 83 VAL cc_start: 0.7961 (p) cc_final: 0.7671 (m) REVERT: O 22 ASN cc_start: 0.7817 (m-40) cc_final: 0.7548 (m-40) REVERT: O 83 VAL cc_start: 0.7993 (p) cc_final: 0.7623 (m) REVERT: P 8 TYR cc_start: 0.6041 (m-80) cc_final: 0.5788 (m-80) REVERT: P 38 GLU cc_start: 0.6968 (tt0) cc_final: 0.6568 (tp30) REVERT: P 75 LEU cc_start: 0.8267 (mt) cc_final: 0.7991 (mp) REVERT: P 83 VAL cc_start: 0.7877 (p) cc_final: 0.7542 (m) REVERT: Q 38 GLU cc_start: 0.6905 (tt0) cc_final: 0.6540 (tp30) REVERT: Q 75 LEU cc_start: 0.8061 (mt) cc_final: 0.7742 (mp) REVERT: Q 83 VAL cc_start: 0.8089 (p) cc_final: 0.7679 (m) REVERT: R 22 ASN cc_start: 0.7414 (m-40) cc_final: 0.7072 (m-40) REVERT: R 38 GLU cc_start: 0.6839 (tt0) cc_final: 0.6452 (tp30) REVERT: R 71 ILE cc_start: 0.8377 (mt) cc_final: 0.8172 (mm) REVERT: R 83 VAL cc_start: 0.7963 (p) cc_final: 0.7538 (m) REVERT: S 38 GLU cc_start: 0.6781 (tt0) cc_final: 0.6283 (tp30) REVERT: S 75 LEU cc_start: 0.8078 (mt) cc_final: 0.7818 (mp) REVERT: S 83 VAL cc_start: 0.8055 (p) cc_final: 0.7634 (m) REVERT: T 22 ASN cc_start: 0.7181 (m-40) cc_final: 0.6870 (m-40) REVERT: T 38 GLU cc_start: 0.6904 (tt0) cc_final: 0.6430 (tp30) REVERT: T 83 VAL cc_start: 0.7777 (p) cc_final: 0.7384 (m) REVERT: U 7 LEU cc_start: 0.7626 (tp) cc_final: 0.7259 (tm) REVERT: U 38 GLU cc_start: 0.6922 (tt0) cc_final: 0.6554 (tp30) REVERT: U 83 VAL cc_start: 0.8144 (p) cc_final: 0.7671 (m) REVERT: V 28 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6124 (pt0) REVERT: V 32 PRO cc_start: 0.7753 (Cg_endo) cc_final: 0.7495 (Cg_exo) REVERT: V 38 GLU cc_start: 0.6693 (tt0) cc_final: 0.6162 (tp30) REVERT: W 83 VAL cc_start: 0.7830 (p) cc_final: 0.7428 (m) REVERT: X 7 LEU cc_start: 0.7592 (tp) cc_final: 0.7247 (tm) REVERT: X 22 ASN cc_start: 0.7424 (m-40) cc_final: 0.7154 (m-40) REVERT: X 38 GLU cc_start: 0.6806 (tt0) cc_final: 0.6429 (tp30) REVERT: X 83 VAL cc_start: 0.7917 (p) cc_final: 0.7534 (m) outliers start: 216 outliers final: 23 residues processed: 2110 average time/residue: 1.4409 time to fit residues: 3850.0490 Evaluate side-chains 1177 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1141 time to evaluate : 5.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 414 GLU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 512 GLN Chi-restraints excluded: chain H residue 534 GLU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain I residue 534 GLU Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain J residue 512 GLN Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 488 GLU Chi-restraints excluded: chain K residue 502 ILE Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 534 GLU Chi-restraints excluded: chain V residue 22 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 6.9990 chunk 573 optimal weight: 1.9990 chunk 317 optimal weight: 0.0980 chunk 195 optimal weight: 2.9990 chunk 386 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 592 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 chunk 360 optimal weight: 8.9990 chunk 441 optimal weight: 3.9990 chunk 686 optimal weight: 7.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 239 HIS ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 540 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 389 ASN ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN D 192 HIS D 239 HIS D 307 GLN ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 377 GLN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN F 389 ASN ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN G 192 HIS G 377 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN G 540 GLN ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 ASN H 540 GLN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 HIS I 307 GLN I 377 GLN I 432 ASN I 540 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 177 GLN J 239 HIS J 389 ASN ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 GLN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 GLN K 389 ASN ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 540 GLN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 177 GLN L 192 HIS L 196 ASN L 239 HIS L 377 GLN L 389 ASN L 432 ASN L 540 GLN M 22 ASN O 52 HIS U 22 ASN V 22 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 61032 Z= 0.348 Angle : 0.720 7.632 82500 Z= 0.368 Chirality : 0.044 0.233 9372 Planarity : 0.007 0.058 10740 Dihedral : 9.359 104.394 9039 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.29 % Allowed : 16.99 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.76 (0.10), residues: 7572 helix: -0.13 (0.09), residues: 3444 sheet: -0.48 (0.12), residues: 1764 loop : -0.77 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 322 HIS 0.012 0.003 HIS I 343 PHE 0.021 0.003 PHE H 136 TYR 0.038 0.003 TYR D 218 ARG 0.018 0.001 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1030 time to evaluate : 5.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 SER cc_start: 0.8810 (t) cc_final: 0.8512 (p) REVERT: A 233 SER cc_start: 0.8621 (m) cc_final: 0.8408 (p) REVERT: A 297 MET cc_start: 0.8991 (mtp) cc_final: 0.8725 (ttm) REVERT: A 352 MET cc_start: 0.7274 (mtp) cc_final: 0.7034 (mtp) REVERT: A 414 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6761 (mm-30) REVERT: B 137 SER cc_start: 0.8815 (t) cc_final: 0.8582 (p) REVERT: B 184 SER cc_start: 0.7947 (p) cc_final: 0.7710 (m) REVERT: B 375 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6783 (mm-30) REVERT: B 414 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6641 (mm-30) REVERT: B 488 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5647 (tp30) REVERT: C 50 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7591 (mtp180) REVERT: C 137 SER cc_start: 0.8736 (t) cc_final: 0.8451 (p) REVERT: C 140 SER cc_start: 0.8444 (m) cc_final: 0.7956 (p) REVERT: C 233 SER cc_start: 0.8637 (m) cc_final: 0.8399 (p) REVERT: C 256 MET cc_start: 0.8610 (mtp) cc_final: 0.8221 (mtp) REVERT: C 377 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: D 80 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7470 (p0) REVERT: D 109 GLU cc_start: 0.8270 (tp30) cc_final: 0.7948 (mm-30) REVERT: D 168 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7078 (mm-30) REVERT: D 321 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7615 (ttt90) REVERT: D 375 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7026 (mm-30) REVERT: D 453 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8444 (tt) REVERT: E 125 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8227 (mttp) REVERT: E 137 SER cc_start: 0.8813 (t) cc_final: 0.8568 (p) REVERT: E 184 SER cc_start: 0.7913 (p) cc_final: 0.7636 (m) REVERT: E 342 MET cc_start: 0.8317 (tpp) cc_final: 0.8100 (tpp) REVERT: E 375 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6755 (mm-30) REVERT: E 414 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6713 (mm-30) REVERT: E 488 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5739 (tp30) REVERT: F 50 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7705 (mtp85) REVERT: F 137 SER cc_start: 0.8806 (t) cc_final: 0.8490 (p) REVERT: F 140 SER cc_start: 0.8487 (m) cc_final: 0.8027 (p) REVERT: F 256 MET cc_start: 0.8645 (mtp) cc_final: 0.8281 (mtp) REVERT: F 257 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8665 (mtp) REVERT: F 321 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7900 (ttt180) REVERT: F 377 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: F 443 MET cc_start: 0.8752 (ptp) cc_final: 0.8508 (ptm) REVERT: G 75 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8078 (mm) REVERT: G 352 MET cc_start: 0.7372 (mtp) cc_final: 0.7078 (mtm) REVERT: G 375 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6639 (mm-30) REVERT: G 451 GLU cc_start: 0.7436 (tt0) cc_final: 0.7197 (tt0) REVERT: H 137 SER cc_start: 0.8675 (t) cc_final: 0.8357 (p) REVERT: H 182 TYR cc_start: 0.6519 (m-10) cc_final: 0.6207 (m-10) REVERT: H 451 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: H 454 MET cc_start: 0.8430 (ptp) cc_final: 0.8062 (ptm) REVERT: I 54 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6874 (mt-10) REVERT: I 109 GLU cc_start: 0.8227 (tp30) cc_final: 0.7888 (mm-30) REVERT: I 137 SER cc_start: 0.8731 (t) cc_final: 0.8442 (p) REVERT: I 233 SER cc_start: 0.8637 (m) cc_final: 0.8427 (p) REVERT: I 257 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8727 (ptm) REVERT: I 414 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6611 (mm-30) REVERT: I 451 GLU cc_start: 0.7388 (tt0) cc_final: 0.7188 (tt0) REVERT: J 50 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7620 (mtp180) REVERT: J 137 SER cc_start: 0.8798 (t) cc_final: 0.8486 (p) REVERT: J 157 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8264 (ttmp) REVERT: J 180 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: J 238 LEU cc_start: 0.8625 (mt) cc_final: 0.8402 (mt) REVERT: J 375 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6762 (mm-30) REVERT: J 388 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8561 (mmtm) REVERT: J 414 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6939 (mm-30) REVERT: K 50 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7547 (mtp180) REVERT: K 109 GLU cc_start: 0.8291 (tp30) cc_final: 0.8065 (mm-30) REVERT: K 140 SER cc_start: 0.8448 (m) cc_final: 0.8059 (p) REVERT: K 297 MET cc_start: 0.8965 (ttm) cc_final: 0.8398 (mtp) REVERT: K 414 GLU cc_start: 0.7360 (tp30) cc_final: 0.6746 (tp30) REVERT: K 454 MET cc_start: 0.8428 (ptp) cc_final: 0.8226 (ptm) REVERT: L 109 GLU cc_start: 0.8111 (tp30) cc_final: 0.7867 (mm-30) REVERT: L 137 SER cc_start: 0.8701 (t) cc_final: 0.8378 (p) REVERT: L 321 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7437 (ttt90) REVERT: L 353 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7305 (ttm170) REVERT: L 375 GLU cc_start: 0.7224 (mt-10) cc_final: 0.7005 (mm-30) REVERT: L 388 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8579 (mmtm) REVERT: M 35 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.4036 (p90) REVERT: N 4 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7459 (ptm160) REVERT: O 38 GLU cc_start: 0.7305 (tt0) cc_final: 0.6847 (tp30) REVERT: P 35 TYR cc_start: 0.6201 (OUTLIER) cc_final: 0.4367 (p90) REVERT: P 38 GLU cc_start: 0.7020 (tt0) cc_final: 0.6691 (tp30) REVERT: T 38 GLU cc_start: 0.6909 (tt0) cc_final: 0.6476 (tp30) REVERT: U 7 LEU cc_start: 0.7773 (tp) cc_final: 0.7419 (tm) REVERT: U 35 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.4457 (p90) REVERT: W 22 ASN cc_start: 0.8117 (m-40) cc_final: 0.7903 (m-40) REVERT: X 7 LEU cc_start: 0.7720 (tp) cc_final: 0.7352 (tm) REVERT: X 35 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.4289 (p90) outliers start: 331 outliers final: 102 residues processed: 1274 average time/residue: 1.4049 time to fit residues: 2279.9675 Evaluate side-chains 1018 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 894 time to evaluate : 5.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 377 GLN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 323 ARG Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 377 GLN Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 77 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 430 GLU Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 502 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 240 GLN Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 530 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 388 LYS Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain K residue 77 PHE Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 315 LEU Chi-restraints excluded: chain K residue 370 SER Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 240 GLN Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain L residue 321 ARG Chi-restraints excluded: chain L residue 388 LYS Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 488 GLU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain N residue 4 ARG Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain P residue 35 TYR Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 35 TYR Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 82 LEU Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain V residue 35 TYR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 35 TYR Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain X residue 35 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 571 optimal weight: 1.9990 chunk 467 optimal weight: 4.9990 chunk 189 optimal weight: 0.0770 chunk 687 optimal weight: 9.9990 chunk 742 optimal weight: 7.9990 chunk 612 optimal weight: 0.3980 chunk 682 optimal weight: 20.0000 chunk 234 optimal weight: 0.0570 chunk 551 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 192 HIS A 239 HIS ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 377 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS C 239 HIS ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 239 HIS D 307 GLN ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS F 11 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN H 192 HIS ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 GLN I 377 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 192 HIS J 239 HIS ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 HIS L 377 GLN M 52 HIS N 52 HIS O 52 HIS P 22 ASN P 52 HIS Q 22 ASN ** Q 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 ASN R 52 HIS S 22 ASN T 22 ASN T 52 HIS U 22 ASN U 52 HIS V 52 HIS W 52 HIS X 22 ASN X 52 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 61032 Z= 0.128 Angle : 0.469 6.299 82500 Z= 0.245 Chirality : 0.037 0.134 9372 Planarity : 0.004 0.036 10740 Dihedral : 8.481 98.450 8958 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.66 % Allowed : 20.01 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.46 (0.10), residues: 7572 helix: 0.02 (0.09), residues: 3444 sheet: -0.32 (0.13), residues: 1764 loop : -0.46 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 155 HIS 0.009 0.001 HIS Q 52 PHE 0.007 0.001 PHE D 77 TYR 0.012 0.001 TYR B 182 ARG 0.008 0.000 ARG J 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 965 time to evaluate : 5.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7649 (mtpp) REVERT: A 137 SER cc_start: 0.8791 (t) cc_final: 0.8481 (p) REVERT: A 264 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7612 (mtp180) REVERT: A 297 MET cc_start: 0.8975 (mtp) cc_final: 0.8731 (ttm) REVERT: B 137 SER cc_start: 0.8755 (t) cc_final: 0.8525 (p) REVERT: B 184 SER cc_start: 0.7822 (p) cc_final: 0.7617 (m) REVERT: B 302 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: B 350 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7759 (mm-30) REVERT: B 353 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7241 (ttp-110) REVERT: B 375 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6709 (mm-30) REVERT: B 414 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6649 (mm-30) REVERT: C 50 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7608 (mtp85) REVERT: C 137 SER cc_start: 0.8740 (t) cc_final: 0.8435 (p) REVERT: C 140 SER cc_start: 0.8357 (m) cc_final: 0.7896 (p) REVERT: C 302 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: C 422 MET cc_start: 0.8572 (mtp) cc_final: 0.7956 (mtp) REVERT: C 443 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8462 (ptm) REVERT: D 125 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7548 (mtpp) REVERT: D 146 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7285 (ttp-110) REVERT: D 168 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7046 (mm-30) REVERT: D 375 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7056 (mm-30) REVERT: E 137 SER cc_start: 0.8776 (t) cc_final: 0.8514 (p) REVERT: E 184 SER cc_start: 0.7784 (p) cc_final: 0.7559 (m) REVERT: E 342 MET cc_start: 0.8203 (tpp) cc_final: 0.7993 (tpp) REVERT: E 353 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7246 (ttp-110) REVERT: E 414 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6684 (mm-30) REVERT: E 428 ASN cc_start: 0.8428 (t0) cc_final: 0.8118 (t0) REVERT: F 50 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7648 (mtp85) REVERT: F 137 SER cc_start: 0.8782 (t) cc_final: 0.8486 (p) REVERT: F 257 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8649 (mtp) REVERT: F 302 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: G 50 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7601 (mtp180) REVERT: G 209 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7909 (mtm110) REVERT: G 217 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: G 352 MET cc_start: 0.7339 (mtp) cc_final: 0.7012 (mtm) REVERT: G 375 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6561 (mm-30) REVERT: G 451 GLU cc_start: 0.7402 (tt0) cc_final: 0.7134 (tt0) REVERT: H 137 SER cc_start: 0.8699 (t) cc_final: 0.8373 (p) REVERT: H 140 SER cc_start: 0.8484 (m) cc_final: 0.7943 (p) REVERT: H 191 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6967 (t0) REVERT: H 414 GLU cc_start: 0.7390 (tp30) cc_final: 0.6967 (tp30) REVERT: H 451 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: H 454 MET cc_start: 0.8347 (ptp) cc_final: 0.7989 (ptm) REVERT: I 54 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6879 (mt-10) REVERT: I 109 GLU cc_start: 0.8151 (tp30) cc_final: 0.7890 (mm-30) REVERT: I 137 SER cc_start: 0.8720 (t) cc_final: 0.8404 (p) REVERT: I 146 ARG cc_start: 0.7504 (ttm110) cc_final: 0.7245 (tpp80) REVERT: I 414 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6626 (mm-30) REVERT: I 488 GLU cc_start: 0.4847 (OUTLIER) cc_final: 0.4257 (tp30) REVERT: J 50 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7525 (mtp180) REVERT: J 125 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7377 (mtpp) REVERT: J 137 SER cc_start: 0.8785 (t) cc_final: 0.8468 (p) REVERT: J 140 SER cc_start: 0.8295 (m) cc_final: 0.7830 (p) REVERT: J 182 TYR cc_start: 0.5802 (m-10) cc_final: 0.5589 (m-10) REVERT: J 375 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6645 (mm-30) REVERT: J 414 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6944 (mm-30) REVERT: J 415 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7967 (pp) REVERT: J 434 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: K 50 ARG cc_start: 0.7980 (mtp85) cc_final: 0.7550 (mtp85) REVERT: K 105 ASP cc_start: 0.7639 (m-30) cc_final: 0.7199 (p0) REVERT: K 109 GLU cc_start: 0.8282 (tp30) cc_final: 0.8026 (mm-30) REVERT: K 140 SER cc_start: 0.8379 (m) cc_final: 0.8032 (p) REVERT: K 191 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6740 (t0) REVERT: K 297 MET cc_start: 0.8882 (ttm) cc_final: 0.8477 (mtp) REVERT: K 414 GLU cc_start: 0.7262 (tp30) cc_final: 0.6882 (tp30) REVERT: K 454 MET cc_start: 0.8318 (ptp) cc_final: 0.8056 (ptm) REVERT: L 125 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7516 (mtpp) REVERT: L 137 SER cc_start: 0.8703 (t) cc_final: 0.8368 (p) REVERT: L 146 ARG cc_start: 0.7354 (ttm110) cc_final: 0.7147 (tpp80) REVERT: L 333 THR cc_start: 0.8311 (m) cc_final: 0.7868 (t) REVERT: L 353 ARG cc_start: 0.7653 (ttp80) cc_final: 0.7236 (ttp-110) REVERT: L 375 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6981 (mm-30) REVERT: L 388 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8544 (mmtm) REVERT: L 451 GLU cc_start: 0.7279 (tt0) cc_final: 0.6976 (tt0) REVERT: L 488 GLU cc_start: 0.4841 (OUTLIER) cc_final: 0.4300 (tp30) REVERT: M 35 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4533 (p90) REVERT: N 35 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.4481 (p90) REVERT: N 70 LYS cc_start: 0.7861 (mttm) cc_final: 0.7563 (mttp) REVERT: O 38 GLU cc_start: 0.7356 (tt0) cc_final: 0.6832 (tp30) REVERT: O 50 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7748 (tttt) REVERT: P 35 TYR cc_start: 0.6104 (OUTLIER) cc_final: 0.4454 (p90) REVERT: P 38 GLU cc_start: 0.7032 (tt0) cc_final: 0.6669 (tp30) REVERT: Q 35 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5041 (p90) REVERT: Q 38 GLU cc_start: 0.6709 (tt0) cc_final: 0.6182 (tp30) REVERT: R 35 TYR cc_start: 0.5939 (OUTLIER) cc_final: 0.5229 (p90) REVERT: S 35 TYR cc_start: 0.6201 (OUTLIER) cc_final: 0.4850 (p90) REVERT: S 50 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7665 (tmmm) REVERT: T 35 TYR cc_start: 0.5876 (OUTLIER) cc_final: 0.4960 (p90) REVERT: T 38 GLU cc_start: 0.6885 (tt0) cc_final: 0.6480 (tp30) REVERT: U 7 LEU cc_start: 0.7735 (tp) cc_final: 0.7403 (tm) REVERT: U 35 TYR cc_start: 0.6135 (OUTLIER) cc_final: 0.4481 (p90) REVERT: V 35 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.4547 (p90) REVERT: W 28 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6280 (pt0) REVERT: W 35 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.5017 (p90) REVERT: W 55 VAL cc_start: 0.7557 (m) cc_final: 0.7356 (t) REVERT: W 87 MET cc_start: 0.6795 (tmm) cc_final: 0.5633 (tpt) REVERT: X 7 LEU cc_start: 0.7704 (tp) cc_final: 0.7387 (tm) REVERT: X 35 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.4319 (p90) outliers start: 229 outliers final: 73 residues processed: 1121 average time/residue: 1.5000 time to fit residues: 2185.6432 Evaluate side-chains 1016 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 911 time to evaluate : 5.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 323 ARG Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 502 ILE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 240 GLN Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 530 LEU Chi-restraints excluded: chain J residue 11 GLN Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 125 LYS Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain J residue 434 GLU Chi-restraints excluded: chain J residue 438 LEU Chi-restraints excluded: chain J residue 451 GLU Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain K residue 370 SER Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain L residue 240 GLN Chi-restraints excluded: chain L residue 388 LYS Chi-restraints excluded: chain L residue 488 GLU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain P residue 35 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain S residue 35 TYR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain V residue 35 TYR Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain W residue 35 TYR Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 35 TYR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 0.9980 chunk 517 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 328 optimal weight: 0.9980 chunk 461 optimal weight: 2.9990 chunk 690 optimal weight: 2.9990 chunk 730 optimal weight: 9.9990 chunk 360 optimal weight: 3.9990 chunk 654 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 377 GLN ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 GLN ** I 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS J 141 ASN J 240 GLN J 377 GLN ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 HIS L 377 GLN ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN M 52 HIS N 52 HIS ** O 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 HIS R 52 HIS S 52 HIS T 22 ASN T 52 HIS U 52 HIS V 52 HIS W 52 HIS X 52 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 61032 Z= 0.288 Angle : 0.581 7.408 82500 Z= 0.297 Chirality : 0.041 0.142 9372 Planarity : 0.005 0.038 10740 Dihedral : 8.759 109.307 8952 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.29 % Allowed : 18.78 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.61 (0.10), residues: 7572 helix: -0.29 (0.09), residues: 3444 sheet: -0.10 (0.13), residues: 1740 loop : -0.48 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP E 155 HIS 0.008 0.002 HIS D 343 PHE 0.014 0.002 PHE F 285 TYR 0.021 0.002 TYR D 218 ARG 0.009 0.001 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 919 time to evaluate : 5.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7756 (mtm-85) REVERT: A 105 ASP cc_start: 0.7892 (m-30) cc_final: 0.7122 (p0) REVERT: A 109 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8052 (mm-30) REVERT: A 137 SER cc_start: 0.8790 (t) cc_final: 0.8484 (p) REVERT: A 140 SER cc_start: 0.8362 (m) cc_final: 0.7912 (p) REVERT: A 144 ILE cc_start: 0.8946 (mt) cc_final: 0.8720 (mt) REVERT: A 297 MET cc_start: 0.8973 (mtp) cc_final: 0.8710 (ttm) REVERT: A 323 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7867 (mtm180) REVERT: A 399 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8393 (tp) REVERT: B 137 SER cc_start: 0.8635 (t) cc_final: 0.8372 (p) REVERT: B 350 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7672 (mm-30) REVERT: B 353 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7478 (ttp-110) REVERT: B 375 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6798 (mm-30) REVERT: B 414 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6978 (mp0) REVERT: C 50 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7790 (mmm160) REVERT: C 137 SER cc_start: 0.8775 (t) cc_final: 0.8491 (p) REVERT: C 140 SER cc_start: 0.8437 (m) cc_final: 0.8044 (p) REVERT: C 297 MET cc_start: 0.8686 (mtp) cc_final: 0.8475 (mtp) REVERT: C 302 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: C 377 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: C 414 GLU cc_start: 0.7566 (tp30) cc_final: 0.7139 (tp30) REVERT: C 443 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8691 (ptm) REVERT: D 50 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7553 (mtm-85) REVERT: D 54 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7520 (mt-10) REVERT: D 105 ASP cc_start: 0.7868 (m-30) cc_final: 0.7123 (p0) REVERT: D 140 SER cc_start: 0.8620 (m) cc_final: 0.8119 (p) REVERT: D 323 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7915 (mtm180) REVERT: D 375 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7201 (mm-30) REVERT: E 137 SER cc_start: 0.8606 (t) cc_final: 0.8323 (p) REVERT: E 302 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: E 342 MET cc_start: 0.8490 (tpp) cc_final: 0.8168 (tpp) REVERT: E 414 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6975 (mp0) REVERT: F 50 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7829 (mmm160) REVERT: F 109 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8012 (mm-30) REVERT: F 137 SER cc_start: 0.8793 (t) cc_final: 0.8506 (p) REVERT: F 140 SER cc_start: 0.8609 (m) cc_final: 0.8088 (p) REVERT: F 302 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: F 321 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8013 (ttt180) REVERT: F 377 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: G 50 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7725 (mtp180) REVERT: G 137 SER cc_start: 0.8718 (t) cc_final: 0.8423 (p) REVERT: G 373 ARG cc_start: 0.7776 (ttt90) cc_final: 0.7524 (ttt-90) REVERT: G 375 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6800 (mm-30) REVERT: G 451 GLU cc_start: 0.7376 (tt0) cc_final: 0.7151 (tt0) REVERT: H 50 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7845 (mtm110) REVERT: H 137 SER cc_start: 0.8638 (t) cc_final: 0.8354 (p) REVERT: H 140 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8084 (p) REVERT: H 191 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7142 (t0) REVERT: H 302 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: H 323 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7866 (mtm180) REVERT: H 451 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: H 454 MET cc_start: 0.8262 (ptp) cc_final: 0.7954 (ptm) REVERT: I 54 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7256 (mt-10) REVERT: I 137 SER cc_start: 0.8706 (t) cc_final: 0.8393 (p) REVERT: I 140 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.7986 (p) REVERT: I 303 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: I 330 PHE cc_start: 0.8386 (m-80) cc_final: 0.7852 (t80) REVERT: I 414 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6972 (mm-30) REVERT: I 488 GLU cc_start: 0.4922 (OUTLIER) cc_final: 0.4354 (tp30) REVERT: J 50 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7574 (mtp85) REVERT: J 137 SER cc_start: 0.8682 (t) cc_final: 0.8355 (p) REVERT: J 140 SER cc_start: 0.8430 (m) cc_final: 0.8003 (p) REVERT: J 302 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: J 331 MET cc_start: 0.7173 (mmm) cc_final: 0.6802 (mpm) REVERT: J 350 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7679 (mm-30) REVERT: J 353 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7490 (ttp-110) REVERT: J 375 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6832 (mm-30) REVERT: J 414 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7053 (mm-30) REVERT: K 140 SER cc_start: 0.8445 (m) cc_final: 0.8174 (p) REVERT: K 191 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.6961 (t0) REVERT: K 297 MET cc_start: 0.8881 (ttm) cc_final: 0.8341 (mtp) REVERT: K 302 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: K 323 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7768 (mtm180) REVERT: K 377 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: K 454 MET cc_start: 0.8218 (ptp) cc_final: 0.7998 (ptm) REVERT: L 109 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8120 (mm-30) REVERT: L 137 SER cc_start: 0.8694 (t) cc_final: 0.8375 (p) REVERT: L 353 ARG cc_start: 0.7679 (ttp80) cc_final: 0.7281 (ttp-110) REVERT: L 375 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7125 (mm-30) REVERT: L 388 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8562 (mmtm) REVERT: L 451 GLU cc_start: 0.7366 (tt0) cc_final: 0.7111 (tt0) REVERT: L 488 GLU cc_start: 0.4923 (OUTLIER) cc_final: 0.4478 (tp30) REVERT: M 35 TYR cc_start: 0.6123 (OUTLIER) cc_final: 0.4797 (p90) REVERT: N 35 TYR cc_start: 0.6045 (OUTLIER) cc_final: 0.4478 (p90) REVERT: N 53 SER cc_start: 0.7660 (m) cc_final: 0.7448 (p) REVERT: N 70 LYS cc_start: 0.7850 (mttm) cc_final: 0.7524 (mttp) REVERT: P 35 TYR cc_start: 0.6056 (OUTLIER) cc_final: 0.4811 (p90) REVERT: P 38 GLU cc_start: 0.7093 (tt0) cc_final: 0.6779 (tp30) REVERT: Q 35 TYR cc_start: 0.6164 (OUTLIER) cc_final: 0.4901 (p90) REVERT: R 35 TYR cc_start: 0.5908 (OUTLIER) cc_final: 0.4634 (p90) REVERT: R 53 SER cc_start: 0.7481 (m) cc_final: 0.6859 (p) REVERT: S 35 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.4794 (p90) REVERT: S 50 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7833 (tmmm) REVERT: T 35 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.4585 (p90) REVERT: T 55 VAL cc_start: 0.7899 (m) cc_final: 0.7698 (t) REVERT: U 7 LEU cc_start: 0.7752 (tp) cc_final: 0.7426 (tm) REVERT: U 35 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.4814 (p90) REVERT: V 35 TYR cc_start: 0.6019 (OUTLIER) cc_final: 0.4544 (p90) REVERT: W 28 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6268 (pt0) REVERT: W 35 TYR cc_start: 0.5890 (OUTLIER) cc_final: 0.4491 (p90) REVERT: W 55 VAL cc_start: 0.7865 (m) cc_final: 0.7658 (t) REVERT: X 7 LEU cc_start: 0.7743 (tp) cc_final: 0.7400 (tm) REVERT: X 35 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.4497 (p90) outliers start: 331 outliers final: 166 residues processed: 1150 average time/residue: 1.4411 time to fit residues: 2110.7907 Evaluate side-chains 1064 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 861 time to evaluate : 5.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 377 GLN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 323 ARG Chi-restraints excluded: chain E residue 330 PHE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 77 PHE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 377 GLN Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 77 PHE Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 323 ARG Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 430 GLU Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 502 ILE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 240 GLN Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 530 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 184 SER Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 302 GLU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 438 LEU Chi-restraints excluded: chain J residue 530 LEU Chi-restraints excluded: chain K residue 77 PHE Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 225 ASP Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 302 GLU Chi-restraints excluded: chain K residue 323 ARG Chi-restraints excluded: chain K residue 370 SER Chi-restraints excluded: chain K residue 373 ARG Chi-restraints excluded: chain K residue 377 GLN Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 240 GLN Chi-restraints excluded: chain L residue 388 LYS Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 488 GLU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain P residue 35 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain S residue 35 TYR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain V residue 35 TYR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain W residue 35 TYR Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain X residue 35 TYR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 75 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 544 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 623 optimal weight: 4.9990 chunk 505 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 373 optimal weight: 8.9990 chunk 655 optimal weight: 0.0670 chunk 184 optimal weight: 3.9990 overall best weight: 2.8524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 HIS G 141 ASN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 389 ASN ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 HIS I 377 GLN ** I 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 428 ASN ** J 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS L 377 GLN ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** N 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 ASN ** P 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 22 ASN ** Q 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 HIS S 22 ASN S 52 HIS T 22 ASN T 52 HIS U 52 HIS V 52 HIS W 22 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 61032 Z= 0.317 Angle : 0.556 6.923 82500 Z= 0.285 Chirality : 0.041 0.139 9372 Planarity : 0.005 0.053 10740 Dihedral : 8.831 112.626 8952 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.73 % Allowed : 19.45 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.69 (0.10), residues: 7572 helix: -0.35 (0.09), residues: 3420 sheet: -0.16 (0.13), residues: 1764 loop : -0.51 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP L 155 HIS 0.012 0.002 HIS C 192 PHE 0.013 0.002 PHE B 431 TYR 0.014 0.002 TYR D 218 ARG 0.013 0.001 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 915 time to evaluate : 5.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8282 (mtp85) cc_final: 0.7880 (mtm-85) REVERT: A 105 ASP cc_start: 0.7933 (m-30) cc_final: 0.7106 (p0) REVERT: A 109 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 137 SER cc_start: 0.8759 (t) cc_final: 0.8416 (p) REVERT: A 140 SER cc_start: 0.8439 (m) cc_final: 0.8049 (p) REVERT: A 175 THR cc_start: 0.8307 (m) cc_final: 0.7878 (p) REVERT: A 264 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7693 (mtp85) REVERT: A 297 MET cc_start: 0.8953 (mtp) cc_final: 0.8694 (ttm) REVERT: A 321 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8089 (ttt90) REVERT: B 81 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7994 (mtpt) REVERT: B 86 GLU cc_start: 0.7885 (mp0) cc_final: 0.7629 (mp0) REVERT: B 107 ASP cc_start: 0.8074 (p0) cc_final: 0.7818 (p0) REVERT: B 137 SER cc_start: 0.8525 (t) cc_final: 0.8236 (p) REVERT: B 140 SER cc_start: 0.8603 (m) cc_final: 0.8237 (p) REVERT: B 240 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8280 (pt0) REVERT: B 302 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: B 350 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7739 (mm-30) REVERT: B 353 ARG cc_start: 0.7633 (ttp80) cc_final: 0.7390 (ttp-110) REVERT: B 375 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6968 (mm-30) REVERT: B 414 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7053 (mp0) REVERT: B 443 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8640 (ptp) REVERT: C 50 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7825 (mmm160) REVERT: C 109 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7960 (mm-30) REVERT: C 137 SER cc_start: 0.8737 (t) cc_final: 0.8445 (p) REVERT: C 140 SER cc_start: 0.8420 (m) cc_final: 0.8049 (p) REVERT: C 233 SER cc_start: 0.8743 (m) cc_final: 0.8515 (p) REVERT: C 330 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: C 377 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: C 438 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8277 (mp) REVERT: C 443 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8715 (ptm) REVERT: D 50 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7742 (mtm-85) REVERT: D 63 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: D 140 SER cc_start: 0.8645 (m) cc_final: 0.8156 (p) REVERT: D 175 THR cc_start: 0.8222 (m) cc_final: 0.7804 (p) REVERT: D 264 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7642 (ttm-80) REVERT: D 321 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8046 (ttt90) REVERT: D 375 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7278 (mm-30) REVERT: E 81 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7793 (mmpt) REVERT: E 86 GLU cc_start: 0.7913 (mp0) cc_final: 0.7644 (mp0) REVERT: E 137 SER cc_start: 0.8541 (t) cc_final: 0.8215 (p) REVERT: E 140 SER cc_start: 0.8607 (m) cc_final: 0.8239 (p) REVERT: E 192 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.8070 (t70) REVERT: E 240 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8242 (pt0) REVERT: E 302 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: E 342 MET cc_start: 0.8485 (tpp) cc_final: 0.8200 (tpp) REVERT: E 414 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7058 (mp0) REVERT: F 50 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7876 (mmm160) REVERT: F 109 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7983 (mm-30) REVERT: F 137 SER cc_start: 0.8758 (t) cc_final: 0.8465 (p) REVERT: F 139 PHE cc_start: 0.8606 (m-80) cc_final: 0.8405 (m-80) REVERT: F 140 SER cc_start: 0.8618 (m) cc_final: 0.8165 (p) REVERT: F 321 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8141 (ttt180) REVERT: F 323 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7966 (ttp-170) REVERT: F 377 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: F 438 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8422 (mp) REVERT: G 50 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7656 (mtm-85) REVERT: G 137 SER cc_start: 0.8629 (t) cc_final: 0.8273 (p) REVERT: G 140 SER cc_start: 0.8492 (m) cc_final: 0.8104 (p) REVERT: G 175 THR cc_start: 0.8554 (m) cc_final: 0.8052 (p) REVERT: G 180 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: G 375 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6873 (mm-30) REVERT: G 414 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7235 (mp0) REVERT: G 415 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8121 (pp) REVERT: H 50 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7597 (mtm-85) REVERT: H 137 SER cc_start: 0.8622 (t) cc_final: 0.8329 (p) REVERT: H 140 SER cc_start: 0.8628 (m) cc_final: 0.8099 (p) REVERT: H 146 ARG cc_start: 0.7283 (ttm110) cc_final: 0.6979 (ttp-110) REVERT: H 168 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7454 (mm-30) REVERT: H 191 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7041 (t0) REVERT: H 323 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7844 (mtm180) REVERT: H 438 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8247 (mp) REVERT: H 451 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: H 454 MET cc_start: 0.8220 (ptp) cc_final: 0.7918 (ptm) REVERT: I 54 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7624 (mt-10) REVERT: I 107 ASP cc_start: 0.7665 (p0) cc_final: 0.7325 (p0) REVERT: I 137 SER cc_start: 0.8665 (t) cc_final: 0.8330 (p) REVERT: I 140 SER cc_start: 0.8593 (m) cc_final: 0.8072 (p) REVERT: I 257 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8011 (ptm) REVERT: I 303 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: I 321 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7938 (ttt90) REVERT: I 323 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7830 (ttp-170) REVERT: I 414 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6808 (mm-30) REVERT: I 488 GLU cc_start: 0.4613 (OUTLIER) cc_final: 0.4175 (tp30) REVERT: J 50 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7559 (mtp180) REVERT: J 107 ASP cc_start: 0.8047 (p0) cc_final: 0.7726 (p0) REVERT: J 109 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8134 (mm-30) REVERT: J 137 SER cc_start: 0.8590 (t) cc_final: 0.8233 (p) REVERT: J 140 SER cc_start: 0.8498 (m) cc_final: 0.8107 (p) REVERT: J 180 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: J 331 MET cc_start: 0.7231 (mmm) cc_final: 0.6853 (mpm) REVERT: J 350 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7706 (mm-30) REVERT: J 375 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6939 (mm-30) REVERT: J 414 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7048 (mp0) REVERT: J 415 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8110 (pp) REVERT: K 50 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7685 (mtm-85) REVERT: K 120 ASP cc_start: 0.8441 (m-30) cc_final: 0.8212 (m-30) REVERT: K 140 SER cc_start: 0.8485 (m) cc_final: 0.8121 (p) REVERT: K 191 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7085 (t0) REVERT: K 297 MET cc_start: 0.8888 (ttm) cc_final: 0.8346 (mtp) REVERT: K 302 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: K 323 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7929 (ttp-170) REVERT: K 330 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: K 377 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: K 454 MET cc_start: 0.8152 (ptp) cc_final: 0.7935 (ptm) REVERT: L 107 ASP cc_start: 0.7660 (p0) cc_final: 0.7382 (p0) REVERT: L 109 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8078 (mm-30) REVERT: L 137 SER cc_start: 0.8674 (t) cc_final: 0.8320 (p) REVERT: L 140 SER cc_start: 0.8600 (m) cc_final: 0.8079 (p) REVERT: L 175 THR cc_start: 0.8379 (m) cc_final: 0.7810 (p) REVERT: L 182 TYR cc_start: 0.7055 (m-80) cc_final: 0.6766 (m-80) REVERT: L 321 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7829 (ttt90) REVERT: L 323 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7821 (ttp-170) REVERT: L 369 GLU cc_start: 0.7407 (mp0) cc_final: 0.6931 (mt-10) REVERT: L 375 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7152 (mm-30) REVERT: L 451 GLU cc_start: 0.7360 (tt0) cc_final: 0.7107 (tt0) REVERT: L 488 GLU cc_start: 0.4683 (OUTLIER) cc_final: 0.4254 (tp30) REVERT: M 35 TYR cc_start: 0.6164 (OUTLIER) cc_final: 0.5056 (p90) REVERT: N 35 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.4480 (p90) REVERT: O 35 TYR cc_start: 0.5898 (OUTLIER) cc_final: 0.4798 (p90) REVERT: P 35 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.4867 (p90) REVERT: Q 4 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7647 (ptm160) REVERT: Q 35 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.4594 (p90) REVERT: R 35 TYR cc_start: 0.5954 (OUTLIER) cc_final: 0.4811 (p90) REVERT: S 35 TYR cc_start: 0.6184 (OUTLIER) cc_final: 0.4645 (p90) REVERT: T 35 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.4772 (p90) REVERT: T 50 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7677 (tptm) REVERT: U 35 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.4883 (p90) REVERT: U 53 SER cc_start: 0.7415 (m) cc_final: 0.7172 (p) REVERT: V 35 TYR cc_start: 0.6056 (OUTLIER) cc_final: 0.4332 (p90) REVERT: W 35 TYR cc_start: 0.5795 (OUTLIER) cc_final: 0.4763 (p90) REVERT: X 35 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.4624 (p90) REVERT: X 53 SER cc_start: 0.7402 (m) cc_final: 0.7184 (p) outliers start: 358 outliers final: 167 residues processed: 1167 average time/residue: 1.4168 time to fit residues: 2107.7356 Evaluate side-chains 1089 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 866 time to evaluate : 5.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 377 GLN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 264 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 323 ARG Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain F residue 77 PHE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 377 GLN Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 415 LEU Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 77 PHE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 240 GLN Chi-restraints excluded: chain H residue 323 ARG Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 430 GLU Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 502 ILE Chi-restraints excluded: chain H residue 530 LEU Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain I residue 323 ARG Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 530 LEU Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain J residue 438 LEU Chi-restraints excluded: chain J residue 530 LEU Chi-restraints excluded: chain K residue 77 PHE Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 302 GLU Chi-restraints excluded: chain K residue 323 ARG Chi-restraints excluded: chain K residue 330 PHE Chi-restraints excluded: chain K residue 370 SER Chi-restraints excluded: chain K residue 373 ARG Chi-restraints excluded: chain K residue 377 GLN Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain L residue 321 ARG Chi-restraints excluded: chain L residue 323 ARG Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 488 GLU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain P residue 35 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain Q residue 4 ARG Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain S residue 35 TYR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain V residue 35 TYR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain W residue 35 TYR Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain X residue 35 TYR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 75 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 8.9990 chunk 658 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 429 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 731 optimal weight: 7.9990 chunk 607 optimal weight: 7.9990 chunk 338 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 384 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 GLN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 HIS ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 ASN ** G 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 GLN ** I 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 GLN ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 HIS ** T 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 52 HIS X 22 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 61032 Z= 0.132 Angle : 0.448 7.297 82500 Z= 0.231 Chirality : 0.037 0.131 9372 Planarity : 0.004 0.036 10740 Dihedral : 8.296 101.186 8952 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.61 % Allowed : 21.63 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 (0.10), residues: 7572 helix: -0.02 (0.09), residues: 3432 sheet: -0.05 (0.13), residues: 1716 loop : -0.21 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 155 HIS 0.003 0.001 HIS C 192 PHE 0.009 0.001 PHE D 77 TYR 0.008 0.001 TYR D 182 ARG 0.012 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 943 time to evaluate : 5.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7846 (mtm-85) REVERT: A 105 ASP cc_start: 0.7872 (m-30) cc_final: 0.7106 (p0) REVERT: A 109 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 137 SER cc_start: 0.8760 (t) cc_final: 0.8423 (p) REVERT: A 140 SER cc_start: 0.8411 (m) cc_final: 0.8039 (p) REVERT: A 175 THR cc_start: 0.8135 (m) cc_final: 0.7905 (p) REVERT: A 297 MET cc_start: 0.8953 (mtp) cc_final: 0.8663 (ttm) REVERT: A 323 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7915 (ttp-170) REVERT: B 107 ASP cc_start: 0.8060 (p0) cc_final: 0.7838 (p0) REVERT: B 137 SER cc_start: 0.8502 (t) cc_final: 0.8247 (p) REVERT: B 175 THR cc_start: 0.8509 (m) cc_final: 0.8002 (p) REVERT: B 240 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: B 350 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7810 (mm-30) REVERT: B 353 ARG cc_start: 0.7586 (ttp80) cc_final: 0.7362 (ttp-110) REVERT: B 375 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6812 (mm-30) REVERT: B 443 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8559 (ptp) REVERT: C 50 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7848 (mtm110) REVERT: C 137 SER cc_start: 0.8744 (t) cc_final: 0.8457 (p) REVERT: C 140 SER cc_start: 0.8380 (m) cc_final: 0.8039 (p) REVERT: C 175 THR cc_start: 0.8512 (m) cc_final: 0.8068 (p) REVERT: C 177 GLN cc_start: 0.8518 (tp40) cc_final: 0.8152 (tp40) REVERT: C 233 SER cc_start: 0.8680 (m) cc_final: 0.8478 (p) REVERT: C 353 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7223 (ttm110) REVERT: C 438 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8235 (mp) REVERT: C 443 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8680 (ptm) REVERT: D 50 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7976 (mtp85) REVERT: D 140 SER cc_start: 0.8614 (m) cc_final: 0.8135 (p) REVERT: D 175 THR cc_start: 0.8107 (m) cc_final: 0.7884 (p) REVERT: D 264 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7662 (ttm-80) REVERT: D 321 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7858 (ttt90) REVERT: D 323 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7833 (ttp-170) REVERT: D 375 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7244 (mm-30) REVERT: E 125 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7977 (mttp) REVERT: E 137 SER cc_start: 0.8570 (t) cc_final: 0.8265 (p) REVERT: E 175 THR cc_start: 0.8521 (m) cc_final: 0.8027 (p) REVERT: E 342 MET cc_start: 0.8456 (tpp) cc_final: 0.8173 (tpp) REVERT: E 414 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6886 (mp0) REVERT: F 50 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7879 (mtm110) REVERT: F 86 GLU cc_start: 0.7683 (mp0) cc_final: 0.7345 (mp0) REVERT: F 109 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7990 (mm-30) REVERT: F 137 SER cc_start: 0.8792 (t) cc_final: 0.8501 (p) REVERT: F 139 PHE cc_start: 0.8565 (m-80) cc_final: 0.8352 (m-80) REVERT: F 140 SER cc_start: 0.8580 (m) cc_final: 0.8157 (p) REVERT: F 159 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7379 (mtt90) REVERT: F 175 THR cc_start: 0.8541 (m) cc_final: 0.8092 (p) REVERT: F 302 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7560 (mm-30) REVERT: F 323 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7934 (ttp-170) REVERT: F 377 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: G 50 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7676 (mtm-85) REVERT: G 120 ASP cc_start: 0.8521 (m-30) cc_final: 0.8064 (m-30) REVERT: G 137 SER cc_start: 0.8597 (t) cc_final: 0.8252 (p) REVERT: G 140 SER cc_start: 0.8436 (m) cc_final: 0.8166 (p) REVERT: G 175 THR cc_start: 0.8580 (m) cc_final: 0.8105 (p) REVERT: G 180 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: G 373 ARG cc_start: 0.7642 (ttt90) cc_final: 0.7418 (ttt90) REVERT: G 375 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6655 (mm-30) REVERT: H 137 SER cc_start: 0.8643 (t) cc_final: 0.8342 (p) REVERT: H 140 SER cc_start: 0.8575 (m) cc_final: 0.8081 (p) REVERT: H 146 ARG cc_start: 0.7389 (ttm110) cc_final: 0.6887 (ttp-110) REVERT: H 159 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7465 (mtt90) REVERT: H 175 THR cc_start: 0.8380 (m) cc_final: 0.7911 (p) REVERT: H 191 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6923 (t0) REVERT: H 323 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7827 (ttp-170) REVERT: H 342 MET cc_start: 0.8477 (tpp) cc_final: 0.8183 (tpt) REVERT: H 438 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8240 (mp) REVERT: H 451 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: H 454 MET cc_start: 0.8172 (ptp) cc_final: 0.7873 (ptm) REVERT: I 54 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7536 (mt-10) REVERT: I 137 SER cc_start: 0.8699 (t) cc_final: 0.8356 (p) REVERT: I 140 SER cc_start: 0.8567 (m) cc_final: 0.8064 (p) REVERT: I 144 ILE cc_start: 0.8826 (mm) cc_final: 0.8608 (mt) REVERT: I 175 THR cc_start: 0.8474 (m) cc_final: 0.7874 (p) REVERT: I 303 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8075 (mt-10) REVERT: I 321 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7735 (ttt90) REVERT: I 369 GLU cc_start: 0.7438 (mp0) cc_final: 0.7082 (mt-10) REVERT: J 50 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7611 (mtm-85) REVERT: J 137 SER cc_start: 0.8589 (t) cc_final: 0.8239 (p) REVERT: J 140 SER cc_start: 0.8362 (m) cc_final: 0.8083 (p) REVERT: J 146 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.7443 (ttm110) REVERT: J 175 THR cc_start: 0.8532 (m) cc_final: 0.7885 (p) REVERT: J 180 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: J 323 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7560 (mtm180) REVERT: J 331 MET cc_start: 0.7178 (mmm) cc_final: 0.6796 (mpm) REVERT: J 350 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7815 (mm-30) REVERT: J 375 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6704 (mm-30) REVERT: J 414 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6993 (mp0) REVERT: K 50 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7745 (mtm-85) REVERT: K 120 ASP cc_start: 0.8436 (m-30) cc_final: 0.8157 (m-30) REVERT: K 140 SER cc_start: 0.8343 (m) cc_final: 0.8015 (p) REVERT: K 159 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7189 (mtt90) REVERT: K 175 THR cc_start: 0.8499 (m) cc_final: 0.7996 (p) REVERT: K 177 GLN cc_start: 0.8141 (tp40) cc_final: 0.7798 (tp40) REVERT: K 191 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6846 (t0) REVERT: K 297 MET cc_start: 0.8806 (ttm) cc_final: 0.8385 (mtp) REVERT: K 330 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: K 373 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7782 (ttt90) REVERT: K 454 MET cc_start: 0.8080 (ptp) cc_final: 0.7861 (ptm) REVERT: L 54 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7555 (mt-10) REVERT: L 137 SER cc_start: 0.8679 (t) cc_final: 0.8322 (p) REVERT: L 140 SER cc_start: 0.8535 (m) cc_final: 0.8036 (p) REVERT: L 175 THR cc_start: 0.8206 (m) cc_final: 0.7877 (p) REVERT: L 303 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8059 (mt-10) REVERT: L 321 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7776 (ttt90) REVERT: L 323 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7822 (ttp-170) REVERT: L 369 GLU cc_start: 0.7386 (mp0) cc_final: 0.6898 (mt-10) REVERT: L 375 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7148 (mm-30) REVERT: L 451 GLU cc_start: 0.7349 (tt0) cc_final: 0.7074 (tt0) REVERT: M 35 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.4574 (p90) REVERT: N 35 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.4337 (p90) REVERT: O 35 TYR cc_start: 0.5827 (OUTLIER) cc_final: 0.4484 (p90) REVERT: P 35 TYR cc_start: 0.5993 (OUTLIER) cc_final: 0.4507 (p90) REVERT: P 38 GLU cc_start: 0.6998 (tt0) cc_final: 0.6771 (tp30) REVERT: P 70 LYS cc_start: 0.7924 (mttm) cc_final: 0.7613 (mttp) REVERT: Q 35 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.4235 (p90) REVERT: Q 70 LYS cc_start: 0.7825 (mttm) cc_final: 0.7494 (mttp) REVERT: R 35 TYR cc_start: 0.5942 (OUTLIER) cc_final: 0.4892 (p90) REVERT: R 53 SER cc_start: 0.7287 (m) cc_final: 0.6946 (p) REVERT: S 35 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.4409 (p90) REVERT: S 50 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7797 (tmmm) REVERT: T 35 TYR cc_start: 0.5868 (OUTLIER) cc_final: 0.4586 (p90) REVERT: T 50 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7645 (tptm) REVERT: T 84 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7253 (m110) REVERT: U 35 TYR cc_start: 0.6058 (OUTLIER) cc_final: 0.4459 (p90) REVERT: V 35 TYR cc_start: 0.6218 (OUTLIER) cc_final: 0.4189 (p90) REVERT: W 35 TYR cc_start: 0.5824 (OUTLIER) cc_final: 0.4648 (p90) REVERT: X 35 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4273 (p90) REVERT: X 53 SER cc_start: 0.7474 (m) cc_final: 0.7264 (p) outliers start: 226 outliers final: 91 residues processed: 1099 average time/residue: 1.4336 time to fit residues: 2006.9116 Evaluate side-chains 1020 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 889 time to evaluate : 5.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 264 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 323 ARG Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 377 GLN Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 264 ARG Chi-restraints excluded: chain H residue 323 ARG Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 430 GLU Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 502 ILE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 264 ARG Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 530 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 323 ARG Chi-restraints excluded: chain J residue 438 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 330 PHE Chi-restraints excluded: chain K residue 373 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 264 ARG Chi-restraints excluded: chain L residue 321 ARG Chi-restraints excluded: chain L residue 323 ARG Chi-restraints excluded: chain L residue 484 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain P residue 35 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain S residue 35 TYR Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 84 ASN Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain V residue 35 TYR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain W residue 35 TYR Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain X residue 35 TYR Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 75 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 416 optimal weight: 7.9990 chunk 534 optimal weight: 9.9990 chunk 413 optimal weight: 2.9990 chunk 615 optimal weight: 6.9990 chunk 408 optimal weight: 5.9990 chunk 728 optimal weight: 0.0270 chunk 456 optimal weight: 6.9990 chunk 444 optimal weight: 3.9990 chunk 336 optimal weight: 0.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 ASN ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 ASN ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 ASN ** I 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 554 ASN ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 554 ASN K 11 GLN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 HIS T 22 ASN ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 61032 Z= 0.238 Angle : 0.493 6.691 82500 Z= 0.252 Chirality : 0.038 0.134 9372 Planarity : 0.004 0.065 10740 Dihedral : 8.451 104.064 8952 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.21 % Allowed : 21.53 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 7572 helix: -0.11 (0.09), residues: 3432 sheet: -0.04 (0.13), residues: 1716 loop : -0.22 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 155 HIS 0.007 0.001 HIS A 343 PHE 0.010 0.001 PHE E 431 TYR 0.011 0.001 TYR D 218 ARG 0.010 0.000 ARG K 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 885 time to evaluate : 5.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7859 (mtm-85) REVERT: A 105 ASP cc_start: 0.7884 (m-30) cc_final: 0.7108 (p0) REVERT: A 109 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 137 SER cc_start: 0.8793 (t) cc_final: 0.8459 (p) REVERT: A 140 SER cc_start: 0.8365 (m) cc_final: 0.8152 (p) REVERT: A 175 THR cc_start: 0.8145 (m) cc_final: 0.7808 (p) REVERT: A 264 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7684 (mtp85) REVERT: A 297 MET cc_start: 0.8961 (mtp) cc_final: 0.8678 (ttm) REVERT: A 323 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7809 (ttp-170) REVERT: B 107 ASP cc_start: 0.8089 (p0) cc_final: 0.7833 (p0) REVERT: B 137 SER cc_start: 0.8491 (t) cc_final: 0.8241 (p) REVERT: B 140 SER cc_start: 0.8554 (m) cc_final: 0.8325 (p) REVERT: B 175 THR cc_start: 0.8524 (m) cc_final: 0.8010 (p) REVERT: B 240 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: B 350 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7776 (mm-30) REVERT: B 375 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6861 (mm-30) REVERT: B 443 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8594 (ptp) REVERT: C 50 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7856 (mmm160) REVERT: C 109 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7955 (mm-30) REVERT: C 137 SER cc_start: 0.8756 (t) cc_final: 0.8473 (p) REVERT: C 140 SER cc_start: 0.8445 (m) cc_final: 0.8099 (p) REVERT: C 146 ARG cc_start: 0.7465 (ttm110) cc_final: 0.7005 (ttp-110) REVERT: C 168 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7262 (mm-30) REVERT: C 175 THR cc_start: 0.8550 (m) cc_final: 0.8086 (p) REVERT: C 377 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: C 438 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8292 (mp) REVERT: C 443 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8672 (ptm) REVERT: D 50 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7961 (mtp85) REVERT: D 140 SER cc_start: 0.8598 (m) cc_final: 0.8127 (p) REVERT: D 175 THR cc_start: 0.8094 (m) cc_final: 0.7801 (p) REVERT: D 264 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7638 (ttm-80) REVERT: D 321 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7929 (ttt90) REVERT: D 323 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7896 (ttp-170) REVERT: D 330 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: D 375 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7309 (mm-30) REVERT: E 137 SER cc_start: 0.8535 (t) cc_final: 0.8229 (p) REVERT: E 175 THR cc_start: 0.8533 (m) cc_final: 0.8033 (p) REVERT: E 302 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: E 342 MET cc_start: 0.8484 (tpp) cc_final: 0.8196 (tpp) REVERT: E 414 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6929 (mp0) REVERT: F 50 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7886 (mtm110) REVERT: F 86 GLU cc_start: 0.7631 (mp0) cc_final: 0.7392 (mp0) REVERT: F 109 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8019 (mm-30) REVERT: F 137 SER cc_start: 0.8782 (t) cc_final: 0.8500 (p) REVERT: F 139 PHE cc_start: 0.8591 (m-80) cc_final: 0.8387 (m-80) REVERT: F 140 SER cc_start: 0.8636 (m) cc_final: 0.8188 (p) REVERT: F 159 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7376 (mtt90) REVERT: F 175 THR cc_start: 0.8516 (m) cc_final: 0.8049 (p) REVERT: F 312 MET cc_start: 0.8875 (mmt) cc_final: 0.8465 (mmp) REVERT: F 323 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7951 (ttp-170) REVERT: F 377 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: F 438 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8366 (mp) REVERT: G 50 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7686 (mtm-85) REVERT: G 137 SER cc_start: 0.8627 (t) cc_final: 0.8271 (p) REVERT: G 140 SER cc_start: 0.8474 (m) cc_final: 0.8225 (p) REVERT: G 175 THR cc_start: 0.8569 (m) cc_final: 0.8074 (p) REVERT: G 180 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: G 375 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6884 (mm-30) REVERT: H 137 SER cc_start: 0.8651 (t) cc_final: 0.8351 (p) REVERT: H 140 SER cc_start: 0.8595 (m) cc_final: 0.8106 (p) REVERT: H 146 ARG cc_start: 0.7429 (ttm110) cc_final: 0.6938 (ttp-110) REVERT: H 159 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7200 (mtt90) REVERT: H 175 THR cc_start: 0.8465 (m) cc_final: 0.7992 (p) REVERT: H 191 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7026 (t0) REVERT: H 323 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7854 (mtm180) REVERT: H 342 MET cc_start: 0.8547 (tpp) cc_final: 0.8306 (tpt) REVERT: H 438 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8323 (mp) REVERT: H 451 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: H 454 MET cc_start: 0.8208 (ptp) cc_final: 0.7917 (ptm) REVERT: I 54 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7580 (mt-10) REVERT: I 107 ASP cc_start: 0.7685 (p0) cc_final: 0.7331 (p0) REVERT: I 137 SER cc_start: 0.8672 (t) cc_final: 0.8389 (p) REVERT: I 140 SER cc_start: 0.8586 (m) cc_final: 0.8178 (p) REVERT: I 159 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7197 (mtt90) REVERT: I 181 GLU cc_start: 0.7728 (mp0) cc_final: 0.7266 (mp0) REVERT: I 257 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8009 (ptm) REVERT: I 264 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7654 (ttm-80) REVERT: I 303 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: I 321 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7810 (ttt90) REVERT: I 323 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7842 (ttp-170) REVERT: I 369 GLU cc_start: 0.7462 (mp0) cc_final: 0.7108 (mt-10) REVERT: J 50 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7644 (mtm-85) REVERT: J 137 SER cc_start: 0.8586 (t) cc_final: 0.8237 (p) REVERT: J 140 SER cc_start: 0.8391 (m) cc_final: 0.8121 (p) REVERT: J 175 THR cc_start: 0.8543 (m) cc_final: 0.7904 (p) REVERT: J 180 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: J 323 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7588 (mtm180) REVERT: J 331 MET cc_start: 0.7207 (mmm) cc_final: 0.6857 (mpm) REVERT: J 350 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7865 (mm-30) REVERT: J 375 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6890 (mm-30) REVERT: J 414 GLU cc_start: 0.7225 (mt-10) cc_final: 0.7007 (mp0) REVERT: K 50 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7708 (mtm-85) REVERT: K 120 ASP cc_start: 0.8464 (m-30) cc_final: 0.8196 (m-30) REVERT: K 140 SER cc_start: 0.8336 (m) cc_final: 0.8105 (p) REVERT: K 146 ARG cc_start: 0.7432 (ttm110) cc_final: 0.6918 (ttp-110) REVERT: K 159 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7393 (mtt90) REVERT: K 175 THR cc_start: 0.8479 (m) cc_final: 0.7963 (p) REVERT: K 177 GLN cc_start: 0.8151 (tp40) cc_final: 0.7775 (tp40) REVERT: K 191 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6834 (t0) REVERT: K 297 MET cc_start: 0.8845 (ttm) cc_final: 0.8378 (mtp) REVERT: K 302 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7499 (mm-30) REVERT: K 323 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7957 (ttp-170) REVERT: K 330 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: K 454 MET cc_start: 0.8111 (ptp) cc_final: 0.7896 (ptm) REVERT: L 54 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7588 (mt-10) REVERT: L 137 SER cc_start: 0.8682 (t) cc_final: 0.8337 (p) REVERT: L 140 SER cc_start: 0.8583 (m) cc_final: 0.8075 (p) REVERT: L 146 ARG cc_start: 0.7659 (ttm110) cc_final: 0.7383 (ttp-110) REVERT: L 175 THR cc_start: 0.8241 (m) cc_final: 0.7887 (p) REVERT: L 264 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7645 (ttm-80) REVERT: L 303 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8060 (mt-10) REVERT: L 321 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7739 (ttt90) REVERT: L 323 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7810 (ttp-170) REVERT: L 369 GLU cc_start: 0.7444 (mp0) cc_final: 0.7079 (mt-10) REVERT: L 375 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7131 (mm-30) REVERT: L 451 GLU cc_start: 0.7339 (tt0) cc_final: 0.7065 (tt0) REVERT: M 35 TYR cc_start: 0.6104 (OUTLIER) cc_final: 0.4993 (p90) REVERT: N 35 TYR cc_start: 0.6291 (OUTLIER) cc_final: 0.4417 (p90) REVERT: O 35 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.4688 (p90) REVERT: P 35 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.4777 (p90) REVERT: P 70 LYS cc_start: 0.7860 (mttm) cc_final: 0.7589 (mttt) REVERT: Q 35 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.4400 (p90) REVERT: Q 65 PRO cc_start: 0.5891 (Cg_exo) cc_final: 0.5583 (Cg_endo) REVERT: Q 70 LYS cc_start: 0.7866 (mttm) cc_final: 0.7548 (mttp) REVERT: R 35 TYR cc_start: 0.5931 (OUTLIER) cc_final: 0.4781 (p90) REVERT: R 53 SER cc_start: 0.7345 (m) cc_final: 0.7034 (p) REVERT: S 35 TYR cc_start: 0.6259 (OUTLIER) cc_final: 0.4511 (p90) REVERT: S 50 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7820 (tmmm) REVERT: T 35 TYR cc_start: 0.5865 (OUTLIER) cc_final: 0.4662 (p90) REVERT: T 50 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7624 (tptm) REVERT: T 84 ASN cc_start: 0.7737 (m110) cc_final: 0.7210 (m110) REVERT: U 35 TYR cc_start: 0.6087 (OUTLIER) cc_final: 0.4622 (p90) REVERT: V 35 TYR cc_start: 0.6053 (OUTLIER) cc_final: 0.4142 (p90) REVERT: W 35 TYR cc_start: 0.5767 (OUTLIER) cc_final: 0.4714 (p90) REVERT: X 35 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.4399 (p90) REVERT: X 53 SER cc_start: 0.7502 (m) cc_final: 0.7280 (p) outliers start: 263 outliers final: 138 residues processed: 1070 average time/residue: 1.4116 time to fit residues: 1932.7160 Evaluate side-chains 1054 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 868 time to evaluate : 5.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 377 GLN Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 264 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 377 GLN Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 525 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 264 ARG Chi-restraints excluded: chain H residue 323 ARG Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 430 GLU Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 502 ILE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 264 ARG Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain I residue 323 ARG Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 525 ILE Chi-restraints excluded: chain I residue 530 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 184 SER Chi-restraints excluded: chain J residue 323 ARG Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 438 LEU Chi-restraints excluded: chain J residue 451 GLU Chi-restraints excluded: chain J residue 530 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 323 ARG Chi-restraints excluded: chain K residue 330 PHE Chi-restraints excluded: chain K residue 373 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 264 ARG Chi-restraints excluded: chain L residue 321 ARG Chi-restraints excluded: chain L residue 323 ARG Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 484 LEU Chi-restraints excluded: chain L residue 525 ILE Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain P residue 35 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain S residue 35 TYR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain V residue 35 TYR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 57 ILE Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain W residue 35 TYR Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain X residue 35 TYR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 75 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 435 optimal weight: 5.9990 chunk 219 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 463 optimal weight: 4.9990 chunk 496 optimal weight: 4.9990 chunk 360 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 572 optimal weight: 0.0470 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 ASN ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 HIS ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 61032 Z= 0.174 Angle : 0.463 6.328 82500 Z= 0.238 Chirality : 0.037 0.131 9372 Planarity : 0.004 0.053 10740 Dihedral : 8.290 102.035 8952 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.84 % Allowed : 22.14 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.24 (0.10), residues: 7572 helix: -0.02 (0.09), residues: 3432 sheet: -0.03 (0.13), residues: 1740 loop : -0.12 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 155 HIS 0.005 0.001 HIS A 343 PHE 0.008 0.001 PHE E 431 TYR 0.008 0.001 TYR D 218 ARG 0.009 0.000 ARG L 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 892 time to evaluate : 5.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8232 (mtp85) cc_final: 0.7861 (mtm-85) REVERT: A 86 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7771 (mt-10) REVERT: A 105 ASP cc_start: 0.7866 (m-30) cc_final: 0.7115 (p0) REVERT: A 109 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7927 (mm-30) REVERT: A 137 SER cc_start: 0.8794 (t) cc_final: 0.8464 (p) REVERT: A 140 SER cc_start: 0.8419 (m) cc_final: 0.8189 (p) REVERT: A 175 THR cc_start: 0.8109 (m) cc_final: 0.7835 (p) REVERT: A 264 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7680 (mtp85) REVERT: A 297 MET cc_start: 0.8953 (mtp) cc_final: 0.8671 (ttm) REVERT: A 323 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7792 (ttp-170) REVERT: B 107 ASP cc_start: 0.8096 (p0) cc_final: 0.7848 (p0) REVERT: B 125 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7991 (mttp) REVERT: B 137 SER cc_start: 0.8393 (t) cc_final: 0.8169 (p) REVERT: B 175 THR cc_start: 0.8521 (m) cc_final: 0.8032 (p) REVERT: B 375 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6828 (mm-30) REVERT: B 443 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8530 (ptp) REVERT: C 50 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7875 (mtm110) REVERT: C 86 GLU cc_start: 0.7742 (mp0) cc_final: 0.7458 (mp0) REVERT: C 109 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7946 (mm-30) REVERT: C 137 SER cc_start: 0.8784 (t) cc_final: 0.8497 (p) REVERT: C 140 SER cc_start: 0.8428 (m) cc_final: 0.8114 (p) REVERT: C 146 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7004 (ttp-110) REVERT: C 175 THR cc_start: 0.8493 (m) cc_final: 0.8033 (p) REVERT: C 377 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: C 438 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8288 (mp) REVERT: C 443 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8741 (ptm) REVERT: D 50 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7969 (mtp85) REVERT: D 63 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: D 86 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7777 (mt-10) REVERT: D 140 SER cc_start: 0.8559 (m) cc_final: 0.8154 (p) REVERT: D 175 THR cc_start: 0.8110 (m) cc_final: 0.7838 (p) REVERT: D 264 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7642 (ttm-80) REVERT: D 321 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7907 (ttt90) REVERT: D 323 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7919 (ttp-170) REVERT: D 330 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: D 375 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7305 (mm-30) REVERT: E 137 SER cc_start: 0.8544 (t) cc_final: 0.8242 (p) REVERT: E 175 THR cc_start: 0.8526 (m) cc_final: 0.8051 (p) REVERT: E 302 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: E 414 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6898 (mp0) REVERT: F 50 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7897 (mtm110) REVERT: F 86 GLU cc_start: 0.7571 (mp0) cc_final: 0.7324 (mp0) REVERT: F 109 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8073 (mm-30) REVERT: F 137 SER cc_start: 0.8797 (t) cc_final: 0.8515 (p) REVERT: F 140 SER cc_start: 0.8606 (m) cc_final: 0.8188 (p) REVERT: F 159 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7461 (mtt90) REVERT: F 175 THR cc_start: 0.8546 (m) cc_final: 0.8088 (p) REVERT: F 323 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7960 (ttp-170) REVERT: F 377 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: G 50 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7675 (mtm-85) REVERT: G 120 ASP cc_start: 0.8514 (m-30) cc_final: 0.8066 (m-30) REVERT: G 137 SER cc_start: 0.8599 (t) cc_final: 0.8241 (p) REVERT: G 140 SER cc_start: 0.8466 (m) cc_final: 0.8230 (p) REVERT: G 175 THR cc_start: 0.8566 (m) cc_final: 0.8116 (p) REVERT: G 180 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: G 375 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6875 (mm-30) REVERT: H 137 SER cc_start: 0.8674 (t) cc_final: 0.8383 (p) REVERT: H 140 SER cc_start: 0.8597 (m) cc_final: 0.8111 (p) REVERT: H 146 ARG cc_start: 0.7444 (ttm110) cc_final: 0.6995 (ttp-110) REVERT: H 159 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7294 (mtt90) REVERT: H 175 THR cc_start: 0.8451 (m) cc_final: 0.7969 (p) REVERT: H 191 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6897 (t0) REVERT: H 323 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7886 (mtm180) REVERT: H 342 MET cc_start: 0.8559 (tpp) cc_final: 0.8221 (tpt) REVERT: H 414 GLU cc_start: 0.7670 (tp30) cc_final: 0.7003 (tp30) REVERT: H 438 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8281 (mp) REVERT: H 451 GLU cc_start: 0.7305 (tt0) cc_final: 0.7007 (tt0) REVERT: H 454 MET cc_start: 0.8171 (ptp) cc_final: 0.7880 (ptm) REVERT: I 54 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7588 (mt-10) REVERT: I 107 ASP cc_start: 0.7665 (p0) cc_final: 0.7309 (p0) REVERT: I 137 SER cc_start: 0.8724 (t) cc_final: 0.8425 (p) REVERT: I 140 SER cc_start: 0.8545 (m) cc_final: 0.8099 (p) REVERT: I 175 THR cc_start: 0.8476 (m) cc_final: 0.7933 (p) REVERT: I 181 GLU cc_start: 0.7681 (mp0) cc_final: 0.7287 (mp0) REVERT: I 257 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7989 (ptm) REVERT: I 264 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7652 (ttm-80) REVERT: I 321 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7797 (ttt90) REVERT: I 323 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7851 (ttp-170) REVERT: I 369 GLU cc_start: 0.7464 (mp0) cc_final: 0.7253 (mt-10) REVERT: J 50 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7626 (mtm-85) REVERT: J 137 SER cc_start: 0.8587 (t) cc_final: 0.8243 (p) REVERT: J 140 SER cc_start: 0.8431 (m) cc_final: 0.8182 (p) REVERT: J 175 THR cc_start: 0.8585 (m) cc_final: 0.7893 (p) REVERT: J 180 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: J 323 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7423 (mtm180) REVERT: J 331 MET cc_start: 0.7192 (mmm) cc_final: 0.6850 (mpm) REVERT: J 375 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6892 (mm-30) REVERT: J 414 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6944 (mp0) REVERT: K 50 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7740 (mtm-85) REVERT: K 120 ASP cc_start: 0.8452 (m-30) cc_final: 0.8152 (m-30) REVERT: K 140 SER cc_start: 0.8331 (m) cc_final: 0.8110 (p) REVERT: K 146 ARG cc_start: 0.7433 (ttm110) cc_final: 0.6960 (ttp-110) REVERT: K 159 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7147 (mtt90) REVERT: K 175 THR cc_start: 0.8421 (m) cc_final: 0.7940 (p) REVERT: K 177 GLN cc_start: 0.8244 (tp40) cc_final: 0.7830 (tp40) REVERT: K 191 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6873 (t0) REVERT: K 297 MET cc_start: 0.8815 (ttm) cc_final: 0.8405 (mtp) REVERT: K 330 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: K 454 MET cc_start: 0.8090 (ptp) cc_final: 0.7875 (ptm) REVERT: L 54 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7601 (mt-10) REVERT: L 137 SER cc_start: 0.8681 (t) cc_final: 0.8331 (p) REVERT: L 140 SER cc_start: 0.8527 (m) cc_final: 0.8076 (p) REVERT: L 175 THR cc_start: 0.8187 (m) cc_final: 0.7870 (p) REVERT: L 264 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7643 (ttm-80) REVERT: L 303 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8051 (mt-10) REVERT: L 321 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7791 (ttt90) REVERT: L 323 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7814 (ttp-170) REVERT: L 369 GLU cc_start: 0.7431 (mp0) cc_final: 0.7061 (mt-10) REVERT: L 375 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7125 (mm-30) REVERT: L 451 GLU cc_start: 0.7349 (tt0) cc_final: 0.7077 (tt0) REVERT: M 35 TYR cc_start: 0.6019 (OUTLIER) cc_final: 0.4714 (p90) REVERT: N 35 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.4240 (p90) REVERT: O 35 TYR cc_start: 0.5914 (OUTLIER) cc_final: 0.4475 (p90) REVERT: O 50 LYS cc_start: 0.8144 (tttp) cc_final: 0.7839 (tttt) REVERT: P 35 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.4720 (p90) REVERT: P 70 LYS cc_start: 0.7779 (mttm) cc_final: 0.7530 (mttt) REVERT: Q 35 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.4288 (p90) REVERT: Q 65 PRO cc_start: 0.6047 (Cg_exo) cc_final: 0.5739 (Cg_endo) REVERT: Q 70 LYS cc_start: 0.7924 (mttm) cc_final: 0.7596 (mttp) REVERT: R 35 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.4795 (p90) REVERT: R 53 SER cc_start: 0.7337 (m) cc_final: 0.7054 (p) REVERT: S 35 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.4402 (p90) REVERT: S 50 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7793 (tmmm) REVERT: T 35 TYR cc_start: 0.5753 (OUTLIER) cc_final: 0.4632 (p90) REVERT: T 84 ASN cc_start: 0.7737 (m110) cc_final: 0.7171 (m110) REVERT: U 35 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.4629 (p90) REVERT: V 35 TYR cc_start: 0.6041 (OUTLIER) cc_final: 0.4065 (p90) REVERT: W 35 TYR cc_start: 0.5733 (OUTLIER) cc_final: 0.4595 (p90) REVERT: X 35 TYR cc_start: 0.6005 (OUTLIER) cc_final: 0.4312 (p90) REVERT: X 53 SER cc_start: 0.7510 (m) cc_final: 0.7291 (p) outliers start: 240 outliers final: 138 residues processed: 1051 average time/residue: 1.4263 time to fit residues: 1915.9504 Evaluate side-chains 1044 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 861 time to evaluate : 5.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 377 GLN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 264 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 159 ARG Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 377 GLN Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 530 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 264 ARG Chi-restraints excluded: chain H residue 323 ARG Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 430 GLU Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 502 ILE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 264 ARG Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain I residue 323 ARG Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 525 ILE Chi-restraints excluded: chain I residue 530 LEU Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 323 ARG Chi-restraints excluded: chain J residue 438 LEU Chi-restraints excluded: chain J residue 525 ILE Chi-restraints excluded: chain J residue 530 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 330 PHE Chi-restraints excluded: chain K residue 373 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 264 ARG Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain L residue 321 ARG Chi-restraints excluded: chain L residue 323 ARG Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 50 LYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 52 HIS Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain P residue 35 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain S residue 35 TYR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain V residue 35 TYR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain W residue 35 TYR Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain X residue 35 TYR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 75 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 2.9990 chunk 698 optimal weight: 6.9990 chunk 636 optimal weight: 5.9990 chunk 679 optimal weight: 8.9990 chunk 697 optimal weight: 6.9990 chunk 408 optimal weight: 0.1980 chunk 295 optimal weight: 5.9990 chunk 533 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 613 optimal weight: 5.9990 chunk 642 optimal weight: 3.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 ASN ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 HIS ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 428 ASN ** H 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 ASN ** I 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 ASN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 22 ASN ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 ASN ** W 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 61032 Z= 0.383 Angle : 0.592 8.911 82500 Z= 0.300 Chirality : 0.042 0.140 9372 Planarity : 0.005 0.050 10740 Dihedral : 8.802 116.225 8952 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.17 % Allowed : 21.94 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.63 (0.10), residues: 7572 helix: -0.33 (0.09), residues: 3420 sheet: -0.07 (0.13), residues: 1704 loop : -0.47 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 155 HIS 0.010 0.002 HIS D 343 PHE 0.014 0.002 PHE E 431 TYR 0.015 0.002 TYR D 218 ARG 0.019 0.001 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 856 time to evaluate : 5.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7909 (mtm-85) REVERT: A 63 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: A 80 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8153 (p0) REVERT: A 86 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 105 ASP cc_start: 0.7939 (m-30) cc_final: 0.7136 (p0) REVERT: A 109 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 137 SER cc_start: 0.8789 (t) cc_final: 0.8464 (p) REVERT: A 140 SER cc_start: 0.8487 (m) cc_final: 0.8262 (p) REVERT: A 175 THR cc_start: 0.8144 (m) cc_final: 0.7734 (p) REVERT: A 264 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7702 (mtp85) REVERT: A 297 MET cc_start: 0.8992 (mtp) cc_final: 0.8718 (ttm) REVERT: A 323 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7894 (ttp-170) REVERT: A 414 GLU cc_start: 0.7564 (tp30) cc_final: 0.7104 (tp30) REVERT: B 107 ASP cc_start: 0.8152 (p0) cc_final: 0.7921 (p0) REVERT: B 137 SER cc_start: 0.8356 (t) cc_final: 0.8126 (p) REVERT: B 375 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7019 (mm-30) REVERT: B 443 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8536 (ptp) REVERT: C 50 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7929 (mmm160) REVERT: C 86 GLU cc_start: 0.7758 (mp0) cc_final: 0.7538 (mp0) REVERT: C 109 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7976 (mm-30) REVERT: C 137 SER cc_start: 0.8781 (t) cc_final: 0.8494 (p) REVERT: C 140 SER cc_start: 0.8470 (m) cc_final: 0.8135 (p) REVERT: C 146 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7062 (ttp-110) REVERT: C 323 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7881 (mtm180) REVERT: C 377 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: C 438 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8287 (mp) REVERT: C 443 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8639 (ptm) REVERT: D 50 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7782 (mtm-85) REVERT: D 63 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: D 86 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7698 (mt-10) REVERT: D 140 SER cc_start: 0.8634 (m) cc_final: 0.8322 (p) REVERT: D 175 THR cc_start: 0.8124 (m) cc_final: 0.7695 (p) REVERT: D 264 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7641 (ttm-80) REVERT: D 321 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8077 (ttt90) REVERT: D 323 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7894 (ttp-170) REVERT: D 330 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: D 375 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7276 (mm-30) REVERT: E 137 SER cc_start: 0.8501 (t) cc_final: 0.8203 (p) REVERT: E 302 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: F 50 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7946 (mmm160) REVERT: F 109 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8042 (mm-30) REVERT: F 137 SER cc_start: 0.8789 (t) cc_final: 0.8507 (p) REVERT: F 140 SER cc_start: 0.8677 (m) cc_final: 0.8247 (p) REVERT: F 159 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7493 (mtt90) REVERT: F 323 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7846 (mtm180) REVERT: F 369 GLU cc_start: 0.7350 (mp0) cc_final: 0.7148 (mt-10) REVERT: F 377 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: F 438 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8365 (mp) REVERT: G 50 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7664 (mtp180) REVERT: G 137 SER cc_start: 0.8584 (t) cc_final: 0.8214 (p) REVERT: G 140 SER cc_start: 0.8563 (m) cc_final: 0.8338 (p) REVERT: G 175 THR cc_start: 0.8617 (m) cc_final: 0.8082 (p) REVERT: G 180 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: G 375 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6872 (mm-30) REVERT: H 137 SER cc_start: 0.8650 (t) cc_final: 0.8358 (p) REVERT: H 140 SER cc_start: 0.8643 (m) cc_final: 0.8167 (p) REVERT: H 146 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7047 (ttp-110) REVERT: H 159 ARG cc_start: 0.7808 (ttm110) cc_final: 0.7303 (mtt90) REVERT: H 191 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7094 (t0) REVERT: H 323 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7848 (mtm180) REVERT: H 414 GLU cc_start: 0.7739 (tp30) cc_final: 0.7068 (tp30) REVERT: H 451 GLU cc_start: 0.7266 (tt0) cc_final: 0.6983 (tt0) REVERT: H 454 MET cc_start: 0.8216 (ptp) cc_final: 0.7972 (ptm) REVERT: I 54 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7662 (mt-10) REVERT: I 107 ASP cc_start: 0.7754 (p0) cc_final: 0.7373 (p0) REVERT: I 137 SER cc_start: 0.8706 (t) cc_final: 0.8425 (p) REVERT: I 140 SER cc_start: 0.8625 (m) cc_final: 0.8119 (p) REVERT: I 181 GLU cc_start: 0.7722 (mp0) cc_final: 0.7342 (mp0) REVERT: I 264 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7650 (ttm-80) REVERT: I 321 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7869 (ttt90) REVERT: I 323 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7852 (ttp-170) REVERT: J 50 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7557 (mtp180) REVERT: J 137 SER cc_start: 0.8565 (t) cc_final: 0.8200 (p) REVERT: J 180 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: J 323 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7415 (mtm180) REVERT: J 331 MET cc_start: 0.7263 (mmm) cc_final: 0.6901 (mpm) REVERT: J 375 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6879 (mm-30) REVERT: J 414 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6957 (mp0) REVERT: K 50 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7756 (mtm-85) REVERT: K 120 ASP cc_start: 0.8470 (m-30) cc_final: 0.8242 (m-30) REVERT: K 140 SER cc_start: 0.8409 (m) cc_final: 0.8154 (p) REVERT: K 146 ARG cc_start: 0.7381 (ttm110) cc_final: 0.6904 (ttp-110) REVERT: K 159 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7455 (mtt90) REVERT: K 175 THR cc_start: 0.8476 (m) cc_final: 0.7981 (p) REVERT: K 177 GLN cc_start: 0.8334 (tp40) cc_final: 0.7916 (tp40) REVERT: K 191 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7007 (t0) REVERT: K 297 MET cc_start: 0.8904 (ttm) cc_final: 0.8324 (mtp) REVERT: L 50 ARG cc_start: 0.8294 (mtp85) cc_final: 0.7785 (mtt-85) REVERT: L 54 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7679 (mt-10) REVERT: L 137 SER cc_start: 0.8677 (t) cc_final: 0.8386 (p) REVERT: L 140 SER cc_start: 0.8617 (m) cc_final: 0.8108 (p) REVERT: L 175 THR cc_start: 0.8242 (m) cc_final: 0.7833 (p) REVERT: L 264 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7650 (ttm-80) REVERT: L 303 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8018 (mt-10) REVERT: L 321 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7867 (ttt90) REVERT: L 323 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7729 (ttp-170) REVERT: L 375 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7158 (mm-30) REVERT: L 451 GLU cc_start: 0.7381 (tt0) cc_final: 0.7072 (tt0) REVERT: M 35 TYR cc_start: 0.6221 (OUTLIER) cc_final: 0.4832 (p90) REVERT: M 79 GLU cc_start: 0.7932 (pt0) cc_final: 0.7688 (pm20) REVERT: N 35 TYR cc_start: 0.6073 (OUTLIER) cc_final: 0.4044 (p90) REVERT: O 35 TYR cc_start: 0.5945 (OUTLIER) cc_final: 0.4425 (p90) REVERT: P 35 TYR cc_start: 0.5931 (OUTLIER) cc_final: 0.4550 (p90) REVERT: P 70 LYS cc_start: 0.7862 (mttm) cc_final: 0.7551 (mttp) REVERT: Q 35 TYR cc_start: 0.5922 (OUTLIER) cc_final: 0.3978 (p90) REVERT: Q 65 PRO cc_start: 0.6191 (Cg_exo) cc_final: 0.5885 (Cg_endo) REVERT: R 35 TYR cc_start: 0.5818 (OUTLIER) cc_final: 0.4337 (p90) REVERT: R 53 SER cc_start: 0.7383 (m) cc_final: 0.7024 (p) REVERT: S 35 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.4247 (p90) REVERT: S 50 LYS cc_start: 0.8062 (tttp) cc_final: 0.7837 (tmmm) REVERT: T 35 TYR cc_start: 0.5921 (OUTLIER) cc_final: 0.4612 (p90) REVERT: U 35 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.4846 (p90) REVERT: V 35 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.4210 (p90) REVERT: W 35 TYR cc_start: 0.5825 (OUTLIER) cc_final: 0.4615 (p90) REVERT: X 35 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.4690 (p90) REVERT: X 53 SER cc_start: 0.7471 (m) cc_final: 0.7263 (p) outliers start: 261 outliers final: 164 residues processed: 1041 average time/residue: 1.3992 time to fit residues: 1863.3284 Evaluate side-chains 1048 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 840 time to evaluate : 5.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 377 GLN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 264 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 77 PHE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 159 ARG Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 377 GLN Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 530 LEU Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 77 PHE Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 264 ARG Chi-restraints excluded: chain H residue 323 ARG Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 430 GLU Chi-restraints excluded: chain H residue 502 ILE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 264 ARG Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain I residue 323 ARG Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 530 LEU Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 184 SER Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 323 ARG Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 438 LEU Chi-restraints excluded: chain J residue 451 GLU Chi-restraints excluded: chain J residue 530 LEU Chi-restraints excluded: chain K residue 77 PHE Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 373 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain K residue 530 LEU Chi-restraints excluded: chain K residue 531 VAL Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 264 ARG Chi-restraints excluded: chain L residue 321 ARG Chi-restraints excluded: chain L residue 323 ARG Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain P residue 35 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain S residue 35 TYR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain V residue 35 TYR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain W residue 35 TYR Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain X residue 35 TYR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 10.0000 chunk 445 optimal weight: 0.8980 chunk 718 optimal weight: 10.0000 chunk 438 optimal weight: 3.9990 chunk 340 optimal weight: 10.0000 chunk 499 optimal weight: 1.9990 chunk 753 optimal weight: 2.9990 chunk 693 optimal weight: 9.9990 chunk 599 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 463 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 HIS ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 ASN ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 61032 Z= 0.219 Angle : 0.495 7.404 82500 Z= 0.255 Chirality : 0.038 0.134 9372 Planarity : 0.004 0.054 10740 Dihedral : 8.563 109.696 8952 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.29 % Allowed : 23.00 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.48 (0.10), residues: 7572 helix: -0.19 (0.09), residues: 3420 sheet: -0.08 (0.13), residues: 1704 loop : -0.36 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 155 HIS 0.006 0.001 HIS D 343 PHE 0.009 0.001 PHE K 431 TYR 0.013 0.001 TYR I 182 ARG 0.012 0.000 ARG A 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 879 time to evaluate : 5.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7800 (mtm-85) REVERT: A 63 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: A 80 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8170 (p0) REVERT: A 86 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7834 (mt-10) REVERT: A 105 ASP cc_start: 0.7913 (m-30) cc_final: 0.7136 (p0) REVERT: A 109 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7920 (mm-30) REVERT: A 137 SER cc_start: 0.8785 (t) cc_final: 0.8455 (p) REVERT: A 140 SER cc_start: 0.8450 (m) cc_final: 0.8239 (p) REVERT: A 175 THR cc_start: 0.8137 (m) cc_final: 0.7845 (p) REVERT: A 264 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7681 (mtp85) REVERT: A 297 MET cc_start: 0.8955 (mtp) cc_final: 0.8692 (ttm) REVERT: A 323 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7924 (ttp-170) REVERT: A 414 GLU cc_start: 0.7461 (tp30) cc_final: 0.7116 (tp30) REVERT: B 107 ASP cc_start: 0.8105 (p0) cc_final: 0.7868 (p0) REVERT: B 137 SER cc_start: 0.8325 (t) cc_final: 0.8103 (p) REVERT: B 175 THR cc_start: 0.8526 (m) cc_final: 0.8021 (p) REVERT: B 375 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6971 (mm-30) REVERT: B 443 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8502 (ptp) REVERT: C 50 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7912 (mmm160) REVERT: C 86 GLU cc_start: 0.7707 (mp0) cc_final: 0.7466 (mp0) REVERT: C 109 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7969 (mm-30) REVERT: C 137 SER cc_start: 0.8766 (t) cc_final: 0.8475 (p) REVERT: C 140 SER cc_start: 0.8432 (m) cc_final: 0.8125 (p) REVERT: C 146 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7028 (ttp-110) REVERT: C 175 THR cc_start: 0.8472 (m) cc_final: 0.8014 (p) REVERT: C 312 MET cc_start: 0.8885 (mmt) cc_final: 0.8445 (mmp) REVERT: C 377 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: C 438 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8348 (mp) REVERT: C 443 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8667 (ptm) REVERT: D 63 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: D 86 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7714 (mt-10) REVERT: D 140 SER cc_start: 0.8632 (m) cc_final: 0.8211 (p) REVERT: D 175 THR cc_start: 0.8162 (m) cc_final: 0.7853 (p) REVERT: D 264 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7635 (ttm-80) REVERT: D 321 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7993 (ttt90) REVERT: D 323 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7878 (ttp-170) REVERT: D 330 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: E 137 SER cc_start: 0.8488 (t) cc_final: 0.8191 (p) REVERT: E 175 THR cc_start: 0.8536 (m) cc_final: 0.8039 (p) REVERT: E 302 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: F 50 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7921 (mmm160) REVERT: F 109 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8034 (mm-30) REVERT: F 137 SER cc_start: 0.8776 (t) cc_final: 0.8484 (p) REVERT: F 140 SER cc_start: 0.8640 (m) cc_final: 0.8230 (p) REVERT: F 159 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7503 (mtt90) REVERT: F 175 THR cc_start: 0.8524 (m) cc_final: 0.8047 (p) REVERT: F 312 MET cc_start: 0.8863 (mmt) cc_final: 0.8473 (mmp) REVERT: F 323 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7902 (mtm180) REVERT: F 377 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: F 438 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8368 (mp) REVERT: G 50 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7556 (mtp180) REVERT: G 120 ASP cc_start: 0.8540 (m-30) cc_final: 0.8042 (m-30) REVERT: G 137 SER cc_start: 0.8577 (t) cc_final: 0.8226 (p) REVERT: G 140 SER cc_start: 0.8556 (m) cc_final: 0.8338 (p) REVERT: G 175 THR cc_start: 0.8581 (m) cc_final: 0.8084 (p) REVERT: G 180 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: G 375 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6887 (mm-30) REVERT: H 137 SER cc_start: 0.8662 (t) cc_final: 0.8367 (p) REVERT: H 140 SER cc_start: 0.8619 (m) cc_final: 0.8132 (p) REVERT: H 146 ARG cc_start: 0.7460 (ttm110) cc_final: 0.7000 (ttp-110) REVERT: H 159 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7301 (mtt90) REVERT: H 175 THR cc_start: 0.8406 (m) cc_final: 0.7917 (p) REVERT: H 191 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7040 (t0) REVERT: H 323 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7816 (mtm180) REVERT: H 369 GLU cc_start: 0.7513 (mp0) cc_final: 0.7302 (mt-10) REVERT: H 414 GLU cc_start: 0.7639 (tp30) cc_final: 0.6997 (tp30) REVERT: H 451 GLU cc_start: 0.7291 (tt0) cc_final: 0.6999 (tt0) REVERT: H 454 MET cc_start: 0.8168 (ptp) cc_final: 0.7930 (ptm) REVERT: I 54 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7619 (mt-10) REVERT: I 107 ASP cc_start: 0.7727 (p0) cc_final: 0.7344 (p0) REVERT: I 137 SER cc_start: 0.8686 (t) cc_final: 0.8423 (p) REVERT: I 140 SER cc_start: 0.8599 (m) cc_final: 0.8098 (p) REVERT: I 175 THR cc_start: 0.8367 (m) cc_final: 0.7943 (p) REVERT: I 181 GLU cc_start: 0.7695 (mp0) cc_final: 0.7321 (mp0) REVERT: I 264 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7660 (ttm-80) REVERT: I 321 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7831 (ttt90) REVERT: I 323 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7853 (ttp-170) REVERT: I 369 GLU cc_start: 0.7433 (mp0) cc_final: 0.7169 (mt-10) REVERT: I 377 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: J 50 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7520 (mtm-85) REVERT: J 137 SER cc_start: 0.8546 (t) cc_final: 0.8199 (p) REVERT: J 175 THR cc_start: 0.8588 (m) cc_final: 0.7942 (p) REVERT: J 180 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: J 181 GLU cc_start: 0.7919 (mp0) cc_final: 0.7714 (mp0) REVERT: J 323 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7439 (mtm180) REVERT: J 331 MET cc_start: 0.7265 (mmm) cc_final: 0.6910 (mpm) REVERT: J 375 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6892 (mm-30) REVERT: J 414 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6961 (mp0) REVERT: K 50 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7782 (mtm-85) REVERT: K 120 ASP cc_start: 0.8460 (m-30) cc_final: 0.8192 (m-30) REVERT: K 140 SER cc_start: 0.8406 (m) cc_final: 0.8081 (p) REVERT: K 146 ARG cc_start: 0.7414 (ttm110) cc_final: 0.6931 (ttp-110) REVERT: K 159 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7615 (mtt90) REVERT: K 175 THR cc_start: 0.8420 (m) cc_final: 0.7936 (p) REVERT: K 177 GLN cc_start: 0.8232 (tp40) cc_final: 0.7836 (tp40) REVERT: K 191 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.6854 (t0) REVERT: K 297 MET cc_start: 0.8861 (ttm) cc_final: 0.8351 (mtp) REVERT: K 330 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: K 373 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7768 (ttt90) REVERT: L 54 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7679 (mt-10) REVERT: L 107 ASP cc_start: 0.7857 (p0) cc_final: 0.7555 (p0) REVERT: L 137 SER cc_start: 0.8694 (t) cc_final: 0.8341 (p) REVERT: L 140 SER cc_start: 0.8592 (m) cc_final: 0.8089 (p) REVERT: L 159 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7540 (mtt90) REVERT: L 175 THR cc_start: 0.8211 (m) cc_final: 0.7885 (p) REVERT: L 264 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7653 (ttm-80) REVERT: L 303 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8040 (mt-10) REVERT: L 321 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7723 (ttt90) REVERT: L 323 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7707 (ttp-170) REVERT: L 369 GLU cc_start: 0.7370 (mp0) cc_final: 0.7140 (mt-10) REVERT: L 375 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7157 (mm-30) REVERT: L 451 GLU cc_start: 0.7361 (tt0) cc_final: 0.7091 (tt0) REVERT: M 35 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5134 (p90) REVERT: M 79 GLU cc_start: 0.7931 (pt0) cc_final: 0.7677 (pm20) REVERT: N 35 TYR cc_start: 0.6114 (OUTLIER) cc_final: 0.3961 (p90) REVERT: O 35 TYR cc_start: 0.5920 (OUTLIER) cc_final: 0.4442 (p90) REVERT: O 50 LYS cc_start: 0.8183 (tttp) cc_final: 0.7920 (tttt) REVERT: P 35 TYR cc_start: 0.5877 (OUTLIER) cc_final: 0.4861 (p90) REVERT: P 70 LYS cc_start: 0.7760 (mttm) cc_final: 0.7500 (mttt) REVERT: Q 35 TYR cc_start: 0.5871 (OUTLIER) cc_final: 0.3834 (p90) REVERT: Q 65 PRO cc_start: 0.6263 (Cg_exo) cc_final: 0.5945 (Cg_endo) REVERT: Q 70 LYS cc_start: 0.7871 (mttm) cc_final: 0.7483 (mttp) REVERT: R 35 TYR cc_start: 0.5771 (OUTLIER) cc_final: 0.4706 (p90) REVERT: S 35 TYR cc_start: 0.6107 (OUTLIER) cc_final: 0.4119 (p90) REVERT: S 50 LYS cc_start: 0.8091 (tttp) cc_final: 0.7875 (tmmm) REVERT: T 35 TYR cc_start: 0.5861 (OUTLIER) cc_final: 0.4650 (p90) REVERT: U 35 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.4661 (p90) REVERT: V 35 TYR cc_start: 0.5934 (OUTLIER) cc_final: 0.3952 (p90) REVERT: W 35 TYR cc_start: 0.5812 (OUTLIER) cc_final: 0.4630 (p90) REVERT: X 35 TYR cc_start: 0.5939 (OUTLIER) cc_final: 0.4395 (p90) outliers start: 206 outliers final: 141 residues processed: 1018 average time/residue: 1.4236 time to fit residues: 1846.5152 Evaluate side-chains 1040 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 853 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 377 GLN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 264 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 159 ARG Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 377 GLN Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 530 LEU Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 264 ARG Chi-restraints excluded: chain H residue 323 ARG Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 430 GLU Chi-restraints excluded: chain H residue 502 ILE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 264 ARG Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain I residue 323 ARG Chi-restraints excluded: chain I residue 377 GLN Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 530 LEU Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 184 SER Chi-restraints excluded: chain J residue 323 ARG Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 438 LEU Chi-restraints excluded: chain J residue 451 GLU Chi-restraints excluded: chain J residue 530 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 330 PHE Chi-restraints excluded: chain K residue 373 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain K residue 531 VAL Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 264 ARG Chi-restraints excluded: chain L residue 321 ARG Chi-restraints excluded: chain L residue 323 ARG Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain P residue 35 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain S residue 35 TYR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain V residue 35 TYR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain W residue 35 TYR Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain X residue 35 TYR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 2.9990 chunk 476 optimal weight: 5.9990 chunk 638 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 553 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 600 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 616 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 ASN ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 ASN ** G 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 ASN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.161587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120944 restraints weight = 76451.587| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.82 r_work: 0.3470 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 61032 Z= 0.289 Angle : 0.537 8.627 82500 Z= 0.274 Chirality : 0.040 0.136 9372 Planarity : 0.005 0.054 10740 Dihedral : 8.593 113.686 8952 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.74 % Allowed : 22.79 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.57 (0.10), residues: 7572 helix: -0.26 (0.09), residues: 3420 sheet: -0.07 (0.13), residues: 1704 loop : -0.44 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 155 HIS 0.008 0.001 HIS A 343 PHE 0.012 0.002 PHE E 431 TYR 0.014 0.001 TYR I 182 ARG 0.011 0.000 ARG G 146 =============================================================================== Job complete usr+sys time: 28417.99 seconds wall clock time: 491 minutes 44.85 seconds (29504.85 seconds total)