Starting phenix.real_space_refine on Fri Aug 9 10:49:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bew_44484/08_2024/9bew_44484.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bew_44484/08_2024/9bew_44484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bew_44484/08_2024/9bew_44484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bew_44484/08_2024/9bew_44484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bew_44484/08_2024/9bew_44484.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bew_44484/08_2024/9bew_44484.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 16326 2.51 5 N 4389 2.21 5 O 5244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ASP 107": "OD1" <-> "OD2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 340": "OE1" <-> "OE2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 381": "OE1" <-> "OE2" Residue "G TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 474": "OD1" <-> "OD2" Residue "G TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 31": "OD1" <-> "OD2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 74": "OD1" <-> "OD2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1": "OD1" <-> "OD2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 27": "OD1" <-> "OD2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L ARG 94": "NH1" <-> "NH2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 584": "OE1" <-> "OE2" Residue "E TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 624": "OD1" <-> "OD2" Residue "E GLU 634": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 31": "OD1" <-> "OD2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 74": "OD1" <-> "OD2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1": "OD1" <-> "OD2" Residue "I ASP 50": "OD1" <-> "OD2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 53": "OD1" <-> "OD2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 92": "OD1" <-> "OD2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 83": "OE1" <-> "OE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 102": "OE1" <-> "OE2" Residue "M ASP 107": "OD1" <-> "OD2" Residue "M GLU 153": "OE1" <-> "OE2" Residue "M TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 190": "OE1" <-> "OE2" Residue "M PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 340": "OE1" <-> "OE2" Residue "M PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 381": "OE1" <-> "OE2" Residue "M TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 474": "OD1" <-> "OD2" Residue "M TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 584": "OE1" <-> "OE2" Residue "N TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 624": "OD1" <-> "OD2" Residue "N GLU 634": "OE1" <-> "OE2" Residue "O GLU 23": "OE1" <-> "OE2" Residue "O TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 31": "OD1" <-> "OD2" Residue "O PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 74": "OD1" <-> "OD2" Residue "O TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 98": "OD1" <-> "OD2" Residue "O TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 1": "OD1" <-> "OD2" Residue "P ASP 50": "OD1" <-> "OD2" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P GLU 81": "OE1" <-> "OE2" Residue "P TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 27": "OD1" <-> "OD2" Residue "Q TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 53": "OD1" <-> "OD2" Residue "Q GLU 55": "OE1" <-> "OE2" Residue "Q ASP 72": "OD1" <-> "OD2" Residue "Q ARG 96": "NH1" <-> "NH2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 9": "NH1" <-> "NH2" Residue "R GLU 17": "OE1" <-> "OE2" Residue "R ARG 20": "NH1" <-> "NH2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R GLU 79": "OE1" <-> "OE2" Residue "R ASP 82": "OD1" <-> "OD2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R ARG 94": "NH1" <-> "NH2" Residue "R PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 26100 Number of models: 1 Model: "" Number of chains: 51 Chain: "G" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3481 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 4 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: "B" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3481 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 4 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: "E" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "F" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "M" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3481 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 4 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: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "O" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "P" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "Q" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "R" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.88, per 1000 atoms: 0.57 Number of scatterers: 26100 At special positions: 0 Unit cell: (158.934, 150.166, 153.454, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 5244 8.00 N 4389 7.00 C 16326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 429A" distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 429A" distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 54 " - pdb=" SG CYS M 74 " distance=2.03 Simple disulfide: pdb=" SG CYS M 113 " - pdb=" SG CYS M 429A" distance=2.03 Simple disulfide: pdb=" SG CYS M 119 " - pdb=" SG CYS M 205 " distance=2.04 Simple disulfide: pdb=" SG CYS M 126 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS M 131 " - pdb=" SG CYS M 157 " distance=2.03 Simple disulfide: pdb=" SG CYS M 218 " - pdb=" SG CYS M 247 " distance=2.04 Simple disulfide: pdb=" SG CYS M 228 " - pdb=" SG CYS M 239 " distance=2.03 Simple disulfide: pdb=" SG CYS M 296 " - pdb=" SG CYS M 331 " distance=2.03 Simple disulfide: pdb=" SG CYS M 378 " - pdb=" SG CYS M 445 " distance=2.03 Simple disulfide: pdb=" SG CYS M 385 " - pdb=" SG CYS M 418 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN V 4 " - " MAN V 5 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 5 " - " MAN Z 6 " " MAN d 4 " - " MAN d 5 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " " MAN l 4 " - " MAN l 5 " " MAN p 4 " - " MAN p 5 " " MAN p 5 " - " MAN p 6 " ALPHA1-3 " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 7 " - " MAN Z 8 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " BMA h 3 " - " MAN h 4 " " MAN h 7 " - " MAN h 8 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 4 " " BMA p 3 " - " MAN p 4 " " MAN p 7 " - " MAN p 8 " ALPHA1-6 " BMA V 3 " - " MAN V 6 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 7 " " MAN Z 7 " - " MAN Z 9 " " BMA d 3 " - " MAN d 6 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 7 " " MAN h 7 " - " MAN h 9 " " BMA l 3 " - " MAN l 6 " " BMA m 3 " - " MAN m 5 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 7 " " MAN p 7 " - " MAN p 9 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 355 " " NAG A 609 " - " ASN A 392 " " NAG A 610 " - " ASN A 241 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG D 301 " - " ASN D 72 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 234 " " NAG G 604 " - " ASN G 276 " " NAG G 605 " - " ASN G 295 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 241 " " NAG I 301 " - " ASN I 72 " " NAG M 601 " - " ASN M 88 " " NAG M 602 " - " ASN M 133 " " NAG M 603 " - " ASN M 234 " " NAG M 604 " - " ASN M 276 " " NAG M 605 " - " ASN M 295 " " NAG M 606 " - " ASN M 301 " " NAG M 607 " - " ASN M 339 " " NAG M 608 " - " ASN M 355 " " NAG M 609 " - " ASN M 392 " " NAG M 610 " - " ASN M 241 " " NAG N 701 " - " ASN N 611 " " NAG N 702 " - " ASN N 637 " " NAG P 301 " - " ASN P 72 " " NAG S 1 " - " ASN G 156 " " NAG T 1 " - " ASN G 160 " " NAG U 1 " - " ASN G 197 " " NAG V 1 " - " ASN G 262 " " NAG W 1 " - " ASN G 363 " " NAG X 1 " - " ASN G 386 " " NAG Y 1 " - " ASN G 448 " " NAG Z 1 " - " ASN G 332 " " NAG a 1 " - " ASN A 156 " " NAG b 1 " - " ASN A 160 " " NAG c 1 " - " ASN A 197 " " NAG d 1 " - " ASN A 262 " " NAG e 1 " - " ASN A 363 " " NAG f 1 " - " ASN A 386 " " NAG g 1 " - " ASN A 448 " " NAG h 1 " - " ASN A 332 " " NAG i 1 " - " ASN M 156 " " NAG j 1 " - " ASN M 160 " " NAG k 1 " - " ASN M 197 " " NAG l 1 " - " ASN M 262 " " NAG m 1 " - " ASN M 363 " " NAG n 1 " - " ASN M 386 " " NAG o 1 " - " ASN M 448 " " NAG p 1 " - " ASN M 332 " Time building additional restraints: 11.94 Conformation dependent library (CDL) restraints added in 4.6 seconds 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5694 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 54 sheets defined 15.1% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'G' and resid 98 through 113 removed outlier: 4.049A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 4.178A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.569A pdb=" N LYS G 344 " --> pdb=" O GLU G 340 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.572A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 381 removed outlier: 3.549A pdb=" N GLY G 380 " --> pdb=" O ASN G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 429B removed outlier: 3.535A pdb=" N CYS G 429A" --> pdb=" O MET G 426 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY G 429B" --> pdb=" O TRP G 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 426 through 429B' Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.739A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.517A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 566 through 570 Processing helix chain 'B' and resid 573 through 597 removed outlier: 3.823A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.519A pdb=" N ASP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.577A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.755A pdb=" N ASP C 31 " --> pdb=" O ASN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.819A pdb=" N GLN C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.804A pdb=" N ASP C 86 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'A' and resid 98 through 113 removed outlier: 4.049A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.179A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.570A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.572A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.550A pdb=" N GLY A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429B removed outlier: 3.535A pdb=" N CYS A 429A" --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 429B" --> pdb=" O TRP A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 429B' Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.739A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 542 removed outlier: 3.518A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 566 through 570 Processing helix chain 'E' and resid 573 through 597 removed outlier: 3.823A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.519A pdb=" N ASP E 632 " --> pdb=" O TRP E 628 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 658 removed outlier: 3.577A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR E 643 " --> pdb=" O THR E 639 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN E 652 " --> pdb=" O GLU E 648 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 657 " --> pdb=" O GLN E 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.755A pdb=" N ASP F 31 " --> pdb=" O ASN F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.819A pdb=" N GLN F 64 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.805A pdb=" N ASP F 86 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 87' Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'M' and resid 98 through 113 removed outlier: 4.050A pdb=" N GLU M 102 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE M 109 " --> pdb=" O HIS M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 126 removed outlier: 4.178A pdb=" N CYS M 126 " --> pdb=" O THR M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 350 removed outlier: 3.569A pdb=" N LYS M 344 " --> pdb=" O GLU M 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS M 347 " --> pdb=" O GLY M 343 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG M 350 " --> pdb=" O VAL M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 373 removed outlier: 3.573A pdb=" N THR M 373 " --> pdb=" O LEU M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 381 removed outlier: 3.549A pdb=" N GLY M 380 " --> pdb=" O ASN M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 429B removed outlier: 3.535A pdb=" N CYS M 429A" --> pdb=" O MET M 426 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY M 429B" --> pdb=" O TRP M 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 426 through 429B' Processing helix chain 'M' and resid 476 through 481 removed outlier: 3.739A pdb=" N SER M 481 " --> pdb=" O ASP M 477 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 534 Processing helix chain 'N' and resid 537 through 542 removed outlier: 3.517A pdb=" N ARG N 542 " --> pdb=" O THR N 538 " (cutoff:3.500A) Processing helix chain 'N' and resid 543 through 545 No H-bonds generated for 'chain 'N' and resid 543 through 545' Processing helix chain 'N' and resid 566 through 570 Processing helix chain 'N' and resid 573 through 597 removed outlier: 3.824A pdb=" N ASP N 589 " --> pdb=" O ARG N 585 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 636 removed outlier: 3.519A pdb=" N ASP N 632 " --> pdb=" O TRP N 628 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS N 633 " --> pdb=" O LEU N 629 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU N 634 " --> pdb=" O GLN N 630 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE N 635 " --> pdb=" O TRP N 631 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 658 removed outlier: 3.577A pdb=" N ILE N 642 " --> pdb=" O TYR N 638 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR N 643 " --> pdb=" O THR N 639 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU N 647 " --> pdb=" O TYR N 643 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN N 650 " --> pdb=" O LEU N 646 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN N 651 " --> pdb=" O GLU N 647 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN N 652 " --> pdb=" O GLU N 648 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN N 656 " --> pdb=" O GLN N 652 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU N 657 " --> pdb=" O GLN N 653 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.757A pdb=" N ASP O 31 " --> pdb=" O ASN O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 64 removed outlier: 3.819A pdb=" N GLN O 64 " --> pdb=" O ARG O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.805A pdb=" N ASP O 86 " --> pdb=" O ARG O 83 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR O 87 " --> pdb=" O SER O 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 83 through 87' Processing helix chain 'Q' and resid 61 through 64 Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.772A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.960A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G 86 " --> pdb=" O VAL G 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 7.157A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.538A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'G' and resid 181 through 183 removed outlier: 3.564A pdb=" N VAL G 182 " --> pdb=" O ARG G 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.850A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 287 current: chain 'G' and resid 315 through 322 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 315 through 322 current: chain 'G' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 382 through 385 current: chain 'G' and resid 465 through 470 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.143A pdb=" N ALA C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP C 37 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 19 removed outlier: 3.718A pdb=" N VAL C 18 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 82 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 81 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.611A pdb=" N ILE D 21 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.976A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.774A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP H 72 " --> pdb=" O GLN H 77 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 removed outlier: 3.747A pdb=" N THR H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100J through 100O Processing sheet with id=AB7, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.560A pdb=" N ARG L 9 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR L 105 " --> pdb=" O ARG L 9 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 19 through 21 Processing sheet with id=AB9, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.538A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.760A pdb=" N VAL A 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.959A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 86 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.156A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.539A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.563A pdb=" N VAL A 182 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.849A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 287 current: chain 'A' and resid 315 through 322 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 322 current: chain 'A' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 382 through 385 current: chain 'A' and resid 465 through 470 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 11 removed outlier: 7.143A pdb=" N ALA F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP F 37 " --> pdb=" O PHE F 91 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 18 through 19 removed outlier: 3.718A pdb=" N VAL F 18 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 82 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 70 " --> pdb=" O TYR F 79 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP F 81 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 18 through 23 removed outlier: 3.610A pdb=" N ILE I 21 " --> pdb=" O LEU I 73 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.976A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.774A pdb=" N THR J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP J 72 " --> pdb=" O GLN J 77 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER J 70 " --> pdb=" O SER J 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 12 current: chain 'J' and resid 45 through 51 removed outlier: 3.747A pdb=" N THR J 58 " --> pdb=" O TYR J 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100J through 100O Processing sheet with id=AD7, first strand: chain 'K' and resid 8 through 13 removed outlier: 6.560A pdb=" N ARG K 9 " --> pdb=" O ARG K 103 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR K 105 " --> pdb=" O ARG K 9 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 19 through 21 Processing sheet with id=AD9, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.538A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 494 through 499 removed outlier: 5.754A pdb=" N VAL M 36 " --> pdb=" O THR N 606 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR N 606 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 45 through 47 removed outlier: 3.960A pdb=" N ILE M 225 " --> pdb=" O VAL M 245 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL M 242 " --> pdb=" O LEU M 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU M 86 " --> pdb=" O VAL M 242 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 75 through 76 removed outlier: 7.156A pdb=" N CYS M 54 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 91 through 94 removed outlier: 3.538A pdb=" N GLY M 237 " --> pdb=" O PHE M 93 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 130 through 133 Processing sheet with id=AE6, first strand: chain 'M' and resid 181 through 183 removed outlier: 3.565A pdb=" N VAL M 182 " --> pdb=" O ARG M 192 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 201 through 203 removed outlier: 6.849A pdb=" N THR M 202 " --> pdb=" O TYR M 435 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 259 through 261 current: chain 'M' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 284 through 287 current: chain 'M' and resid 315 through 322 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 315 through 322 current: chain 'M' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 382 through 385 current: chain 'M' and resid 465 through 470 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AF1, first strand: chain 'O' and resid 10 through 11 removed outlier: 7.143A pdb=" N ALA O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP O 37 " --> pdb=" O PHE O 91 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 18 through 19 removed outlier: 3.719A pdb=" N VAL O 18 " --> pdb=" O LEU O 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU O 82 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR O 70 " --> pdb=" O TYR O 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP O 81 " --> pdb=" O SER O 68 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 18 through 23 removed outlier: 3.610A pdb=" N ILE P 21 " --> pdb=" O LEU P 73 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR P 71 " --> pdb=" O CYS P 23 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER P 63 " --> pdb=" O THR P 74 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 53 through 54 removed outlier: 6.976A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.775A pdb=" N THR Q 21 " --> pdb=" O SER Q 7 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU Q 78 " --> pdb=" O CYS Q 22 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP Q 72 " --> pdb=" O GLN Q 77 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER Q 70 " --> pdb=" O SER Q 79 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 11 through 12 current: chain 'Q' and resid 45 through 51 removed outlier: 3.748A pdb=" N THR Q 58 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 57 through 59 current: chain 'Q' and resid 100J through 100O Processing sheet with id=AF7, first strand: chain 'R' and resid 8 through 13 removed outlier: 6.560A pdb=" N ARG R 9 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR R 105 " --> pdb=" O ARG R 9 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR R 102 " --> pdb=" O TYR R 86 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 19 through 21 Processing sheet with id=AF9, first strand: chain 'R' and resid 45 through 48 removed outlier: 6.538A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1224 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: 8.94 Time building geometry restraints manager: 12.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8176 1.35 - 1.48: 7230 1.48 - 1.61: 11057 1.61 - 1.74: 0 1.74 - 1.86: 192 Bond restraints: 26655 Sorted by residual: bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C1 NAG e 1 " pdb=" O5 NAG e 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.25e+00 ... (remaining 26650 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.27: 1043 107.27 - 113.97: 15526 113.97 - 120.66: 9358 120.66 - 127.35: 9941 127.35 - 134.05: 336 Bond angle restraints: 36204 Sorted by residual: angle pdb=" CA THR A 123 " pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 118.44 123.74 -5.30 1.59e+00 3.96e-01 1.11e+01 angle pdb=" CA THR M 123 " pdb=" C THR M 123 " pdb=" N PRO M 124 " ideal model delta sigma weight residual 118.44 123.68 -5.24 1.59e+00 3.96e-01 1.09e+01 angle pdb=" CA THR G 123 " pdb=" C THR G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 118.44 123.68 -5.24 1.59e+00 3.96e-01 1.09e+01 angle pdb=" C ASN R 50 " pdb=" N ASN R 51 " pdb=" CA ASN R 51 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C ASN K 50 " pdb=" N ASN K 51 " pdb=" CA ASN K 51 " ideal model delta sigma weight residual 121.54 127.67 -6.13 1.91e+00 2.74e-01 1.03e+01 ... (remaining 36199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 16334 21.57 - 43.13: 922 43.13 - 64.70: 135 64.70 - 86.26: 126 86.26 - 107.83: 51 Dihedral angle restraints: 17568 sinusoidal: 8697 harmonic: 8871 Sorted by residual: dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 88 " pdb=" CB CYS R 88 " ideal model delta sinusoidal sigma weight residual -86.00 -1.12 -84.88 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -1.14 -84.86 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual -86.00 -1.18 -84.82 1 1.00e+01 1.00e-02 8.73e+01 ... (remaining 17565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.397: 4317 0.397 - 0.794: 21 0.794 - 1.191: 15 1.191 - 1.588: 18 1.588 - 1.985: 3 Chirality restraints: 4374 Sorted by residual: chirality pdb=" C1 MAN p 6 " pdb=" O2 MAN p 5 " pdb=" C2 MAN p 6 " pdb=" O5 MAN p 6 " both_signs ideal model delta sigma weight residual False 2.40 0.41 1.99 2.00e-02 2.50e+03 9.85e+03 chirality pdb=" C1 MAN Z 6 " pdb=" O2 MAN Z 5 " pdb=" C2 MAN Z 6 " pdb=" O5 MAN Z 6 " both_signs ideal model delta sigma weight residual False 2.40 0.42 1.98 2.00e-02 2.50e+03 9.84e+03 chirality pdb=" C1 MAN h 6 " pdb=" O2 MAN h 5 " pdb=" C2 MAN h 6 " pdb=" O5 MAN h 6 " both_signs ideal model delta sigma weight residual False 2.40 0.42 1.98 2.00e-02 2.50e+03 9.81e+03 ... (remaining 4371 not shown) Planarity restraints: 4503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 79 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO I 80 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 80 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 80 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN P 79 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO P 80 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO P 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P 80 " -0.022 5.00e-02 4.00e+02 ... (remaining 4500 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 8218 2.84 - 3.35: 20373 3.35 - 3.87: 40835 3.87 - 4.38: 44681 4.38 - 4.90: 79689 Nonbonded interactions: 193796 Sorted by model distance: nonbonded pdb=" O GLN Q 5 " pdb=" OG SER Q 23 " model vdw 2.322 3.040 nonbonded pdb=" O GLN H 5 " pdb=" OG SER H 23 " model vdw 2.322 3.040 nonbonded pdb=" O GLN J 5 " pdb=" OG SER J 23 " model vdw 2.322 3.040 nonbonded pdb=" O VAL M 36 " pdb=" OG1 THR N 606 " model vdw 2.335 3.040 nonbonded pdb=" O VAL G 36 " pdb=" OG1 THR B 606 " model vdw 2.345 3.040 ... (remaining 193791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'o' } ncs_group { reference = chain 'V' selection = chain 'd' selection = chain 'l' } ncs_group { reference = chain 'W' selection = chain 'e' selection = chain 'm' } ncs_group { reference = chain 'X' selection = chain 'f' selection = chain 'n' } ncs_group { reference = chain 'Z' selection = chain 'h' selection = chain 'p' } 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: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 70.230 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.004 0.055 26655 Z= 0.259 Angle : 0.729 8.207 36204 Z= 0.348 Chirality : 0.135 1.985 4374 Planarity : 0.004 0.039 4440 Dihedral : 15.805 107.825 11739 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.01 % Allowed : 4.50 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.12), residues: 3021 helix: -4.59 (0.10), residues: 354 sheet: -1.82 (0.16), residues: 777 loop : -2.35 (0.12), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 50 HIS 0.003 0.001 HIS E 564 PHE 0.010 0.001 PHE M 53 TYR 0.009 0.001 TYR D 91 ARG 0.001 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 438 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8256 (pt0) cc_final: 0.8002 (pt0) REVERT: B 632 ASP cc_start: 0.8587 (t70) cc_final: 0.8087 (t0) REVERT: C 5 LEU cc_start: 0.8768 (tp) cc_final: 0.8386 (mm) REVERT: C 30 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7594 (mtm-85) REVERT: C 53 LYS cc_start: 0.9295 (ttmt) cc_final: 0.9058 (ttmm) REVERT: C 98 ASP cc_start: 0.8522 (m-30) cc_final: 0.8053 (t0) REVERT: D 77 ASN cc_start: 0.7880 (t0) cc_final: 0.7469 (t0) REVERT: H 3 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7658 (mm-40) REVERT: H 90 TYR cc_start: 0.7983 (m-10) cc_final: 0.7737 (m-10) REVERT: L 79 GLU cc_start: 0.8726 (tp30) cc_final: 0.8259 (tp30) REVERT: E 584 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7673 (mt-10) REVERT: E 632 ASP cc_start: 0.8603 (t70) cc_final: 0.8161 (t0) REVERT: F 5 LEU cc_start: 0.8781 (tp) cc_final: 0.8392 (mm) REVERT: F 13 LYS cc_start: 0.8594 (mttm) cc_final: 0.8111 (mmtt) REVERT: F 31 ASP cc_start: 0.8934 (m-30) cc_final: 0.8714 (m-30) REVERT: F 53 LYS cc_start: 0.9313 (ttmt) cc_final: 0.9042 (ttmm) REVERT: F 98 ASP cc_start: 0.8446 (m-30) cc_final: 0.7997 (t0) REVERT: I 58 VAL cc_start: 0.8818 (t) cc_final: 0.8547 (p) REVERT: I 77 ASN cc_start: 0.7731 (t0) cc_final: 0.7203 (t0) REVERT: K 79 GLU cc_start: 0.8717 (tp30) cc_final: 0.8260 (tp30) REVERT: M 56 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8580 (t) REVERT: M 69 TRP cc_start: 0.7134 (m-90) cc_final: 0.6863 (m-90) REVERT: N 542 ARG cc_start: 0.8563 (ttm170) cc_final: 0.8324 (ttp-170) REVERT: N 568 LEU cc_start: 0.6607 (pp) cc_final: 0.6389 (mt) REVERT: N 632 ASP cc_start: 0.8618 (t70) cc_final: 0.8125 (t0) REVERT: O 5 LEU cc_start: 0.8843 (tp) cc_final: 0.8621 (mm) REVERT: O 30 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7733 (mtt90) REVERT: O 31 ASP cc_start: 0.8908 (m-30) cc_final: 0.8698 (m-30) REVERT: O 98 ASP cc_start: 0.8551 (m-30) cc_final: 0.8229 (t0) REVERT: P 55 GLU cc_start: 0.6771 (tp30) cc_final: 0.6522 (tp30) REVERT: P 77 ASN cc_start: 0.7635 (t0) cc_final: 0.7221 (t0) REVERT: Q 3 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7972 (mm-40) REVERT: Q 46 GLU cc_start: 0.8262 (tt0) cc_final: 0.7902 (tt0) REVERT: Q 86 ASP cc_start: 0.8196 (t0) cc_final: 0.7884 (t0) REVERT: Q 90 TYR cc_start: 0.7907 (m-10) cc_final: 0.7472 (m-10) REVERT: R 42 GLN cc_start: 0.8734 (tp40) cc_final: 0.8098 (mp10) REVERT: R 79 GLU cc_start: 0.8732 (tp30) cc_final: 0.8275 (tp30) outliers start: 27 outliers final: 3 residues processed: 458 average time/residue: 0.4834 time to fit residues: 317.4049 Evaluate side-chains 296 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain M residue 56 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 175 optimal weight: 0.5980 chunk 272 optimal weight: 0.3980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 GLN G 315 GLN G 328 GLN G 411 ASN B 590 GLN B 630 GLN C 62 GLN D 69 GLN H 1 GLN H 3 GLN H 31 ASN A 72 HIS A 103 GLN A 315 GLN A 328 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN A 425 ASN E 590 GLN E 630 GLN F 62 GLN I 3 GLN I 69 GLN J 1 GLN J 3 GLN J 31 ASN K 37 GLN M 103 GLN M 315 GLN M 328 GLN M 411 ASN N 590 GLN N 630 GLN O 62 GLN P 3 GLN P 69 GLN Q 1 GLN Q 3 GLN Q 31 ASN R 37 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26655 Z= 0.306 Angle : 0.608 9.408 36204 Z= 0.298 Chirality : 0.046 0.347 4374 Planarity : 0.004 0.065 4440 Dihedral : 11.514 89.564 6091 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.16 % Allowed : 9.86 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.13), residues: 3021 helix: -2.60 (0.20), residues: 384 sheet: -1.58 (0.15), residues: 933 loop : -2.04 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 69 HIS 0.002 0.001 HIS A 330 PHE 0.011 0.001 PHE G 53 TYR 0.012 0.001 TYR I 91 ARG 0.007 0.001 ARG J 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 290 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8701 (t70) cc_final: 0.8204 (t0) REVERT: C 30 ARG cc_start: 0.7994 (mtt90) cc_final: 0.7757 (mtt90) REVERT: C 53 LYS cc_start: 0.9365 (ttmt) cc_final: 0.9056 (ttmm) REVERT: C 98 ASP cc_start: 0.8561 (m-30) cc_final: 0.8044 (t0) REVERT: D 77 ASN cc_start: 0.8113 (t0) cc_final: 0.7767 (t0) REVERT: H 90 TYR cc_start: 0.7907 (m-10) cc_final: 0.7635 (m-10) REVERT: L 66 ASP cc_start: 0.7977 (t0) cc_final: 0.7289 (t0) REVERT: L 79 GLU cc_start: 0.8633 (tp30) cc_final: 0.8293 (tp30) REVERT: E 584 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7634 (mt-10) REVERT: E 632 ASP cc_start: 0.8684 (t70) cc_final: 0.8254 (t0) REVERT: F 53 LYS cc_start: 0.9382 (ttmt) cc_final: 0.9058 (ttmm) REVERT: F 98 ASP cc_start: 0.8521 (m-30) cc_final: 0.8040 (t0) REVERT: I 58 VAL cc_start: 0.8805 (t) cc_final: 0.8504 (p) REVERT: I 77 ASN cc_start: 0.7838 (t0) cc_final: 0.7613 (t0) REVERT: J 54 ARG cc_start: 0.8295 (mtt90) cc_final: 0.7877 (mmp80) REVERT: K 79 GLU cc_start: 0.8718 (tp30) cc_final: 0.8192 (tp30) REVERT: M 69 TRP cc_start: 0.7297 (m-90) cc_final: 0.6901 (m-90) REVERT: N 530 MET cc_start: 0.8902 (mtp) cc_final: 0.8609 (mtp) REVERT: N 632 ASP cc_start: 0.8712 (t70) cc_final: 0.8195 (t0) REVERT: O 84 SER cc_start: 0.9063 (m) cc_final: 0.8817 (t) REVERT: O 98 ASP cc_start: 0.8607 (m-30) cc_final: 0.8176 (t0) REVERT: P 55 GLU cc_start: 0.7129 (tp30) cc_final: 0.6769 (tp30) REVERT: P 77 ASN cc_start: 0.7624 (t0) cc_final: 0.7258 (t0) REVERT: Q 46 GLU cc_start: 0.8388 (tt0) cc_final: 0.8021 (tt0) REVERT: Q 90 TYR cc_start: 0.7805 (m-10) cc_final: 0.7475 (m-10) REVERT: R 42 GLN cc_start: 0.8697 (tp40) cc_final: 0.8053 (mp10) REVERT: R 79 GLU cc_start: 0.8735 (tp30) cc_final: 0.8202 (tp30) outliers start: 31 outliers final: 20 residues processed: 316 average time/residue: 0.4249 time to fit residues: 202.2488 Evaluate side-chains 293 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 273 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 226 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 294 optimal weight: 0.0770 chunk 243 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 218 optimal weight: 0.5980 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN P 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26655 Z= 0.204 Angle : 0.537 9.683 36204 Z= 0.263 Chirality : 0.044 0.281 4374 Planarity : 0.004 0.050 4440 Dihedral : 9.637 84.639 6087 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.09 % Allowed : 12.49 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.14), residues: 3021 helix: -1.54 (0.25), residues: 381 sheet: -1.14 (0.16), residues: 897 loop : -1.77 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 69 HIS 0.001 0.001 HIS A 330 PHE 0.009 0.001 PHE M 53 TYR 0.008 0.001 TYR L 87 ARG 0.007 0.001 ARG I 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 288 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7083 (m-90) cc_final: 0.6521 (m-90) REVERT: B 632 ASP cc_start: 0.8716 (t70) cc_final: 0.8237 (t0) REVERT: C 30 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7765 (mtt90) REVERT: C 53 LYS cc_start: 0.9375 (ttmt) cc_final: 0.9050 (ttmm) REVERT: C 98 ASP cc_start: 0.8572 (m-30) cc_final: 0.8022 (t0) REVERT: D 77 ASN cc_start: 0.8186 (t0) cc_final: 0.7853 (t0) REVERT: H 54 ARG cc_start: 0.8257 (mtt90) cc_final: 0.7887 (mmp80) REVERT: H 90 TYR cc_start: 0.7885 (m-10) cc_final: 0.7618 (m-10) REVERT: L 66 ASP cc_start: 0.8041 (t0) cc_final: 0.7456 (t0) REVERT: L 79 GLU cc_start: 0.8644 (tp30) cc_final: 0.8308 (tp30) REVERT: A 377 ASN cc_start: 0.8897 (t0) cc_final: 0.8645 (t0) REVERT: E 584 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7586 (mt-10) REVERT: E 632 ASP cc_start: 0.8673 (t70) cc_final: 0.8238 (t0) REVERT: F 53 LYS cc_start: 0.9398 (ttmt) cc_final: 0.9047 (ttmm) REVERT: F 98 ASP cc_start: 0.8504 (m-30) cc_final: 0.8000 (t0) REVERT: I 58 VAL cc_start: 0.8772 (t) cc_final: 0.8454 (p) REVERT: I 77 ASN cc_start: 0.8021 (t0) cc_final: 0.7694 (t0) REVERT: J 54 ARG cc_start: 0.8370 (mtt90) cc_final: 0.7957 (mmp80) REVERT: K 66 ASP cc_start: 0.8077 (t0) cc_final: 0.7637 (t0) REVERT: K 70 ARG cc_start: 0.7262 (mmm160) cc_final: 0.6810 (mmp-170) REVERT: K 79 GLU cc_start: 0.8716 (tp30) cc_final: 0.8184 (tp30) REVERT: M 69 TRP cc_start: 0.7266 (m-90) cc_final: 0.6847 (m-90) REVERT: N 632 ASP cc_start: 0.8675 (t70) cc_final: 0.8146 (t0) REVERT: O 80 MET cc_start: 0.8990 (tmm) cc_final: 0.8601 (tmm) REVERT: O 84 SER cc_start: 0.9116 (m) cc_final: 0.8868 (t) REVERT: O 98 ASP cc_start: 0.8560 (m-30) cc_final: 0.8034 (t0) REVERT: P 55 GLU cc_start: 0.7531 (tp30) cc_final: 0.7177 (tp30) REVERT: P 77 ASN cc_start: 0.7690 (t0) cc_final: 0.7418 (t0) REVERT: Q 32 TYR cc_start: 0.8163 (m-10) cc_final: 0.7908 (m-10) REVERT: Q 46 GLU cc_start: 0.8429 (tt0) cc_final: 0.8165 (tt0) REVERT: Q 90 TYR cc_start: 0.7896 (m-10) cc_final: 0.7536 (m-10) REVERT: Q 97 ARG cc_start: 0.8820 (tmm-80) cc_final: 0.8009 (ttp80) REVERT: R 79 GLU cc_start: 0.8740 (tp30) cc_final: 0.8185 (tp30) outliers start: 29 outliers final: 25 residues processed: 310 average time/residue: 0.4194 time to fit residues: 197.0598 Evaluate side-chains 297 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 272 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 31 ASP Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.0470 chunk 205 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 273 optimal weight: 0.5980 chunk 289 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 259 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26655 Z= 0.143 Angle : 0.509 9.726 36204 Z= 0.247 Chirality : 0.043 0.264 4374 Planarity : 0.003 0.040 4440 Dihedral : 8.295 83.493 6087 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.69 % Allowed : 12.64 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.14), residues: 3021 helix: -0.91 (0.27), residues: 381 sheet: -0.75 (0.16), residues: 891 loop : -1.60 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 69 HIS 0.002 0.000 HIS K 38 PHE 0.006 0.001 PHE M 53 TYR 0.008 0.001 TYR F 90 ARG 0.008 0.000 ARG I 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 297 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7114 (m-90) cc_final: 0.6685 (m-90) REVERT: B 632 ASP cc_start: 0.8687 (t70) cc_final: 0.8223 (t0) REVERT: C 53 LYS cc_start: 0.9379 (ttmt) cc_final: 0.9074 (ttmm) REVERT: C 98 ASP cc_start: 0.8586 (m-30) cc_final: 0.8017 (t0) REVERT: D 77 ASN cc_start: 0.8255 (t0) cc_final: 0.7920 (t0) REVERT: H 54 ARG cc_start: 0.8266 (mtt90) cc_final: 0.7864 (mmp80) REVERT: H 90 TYR cc_start: 0.7836 (m-10) cc_final: 0.7514 (m-10) REVERT: L 66 ASP cc_start: 0.8069 (t0) cc_final: 0.7866 (t0) REVERT: L 79 GLU cc_start: 0.8648 (tp30) cc_final: 0.8300 (tp30) REVERT: A 161 MET cc_start: 0.8231 (tpt) cc_final: 0.7977 (mmm) REVERT: E 584 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7646 (mt-10) REVERT: E 632 ASP cc_start: 0.8616 (t70) cc_final: 0.8211 (t0) REVERT: F 53 LYS cc_start: 0.9414 (ttmt) cc_final: 0.9067 (ttmm) REVERT: F 98 ASP cc_start: 0.8483 (m-30) cc_final: 0.7928 (t0) REVERT: I 5 THR cc_start: 0.7492 (m) cc_final: 0.7242 (p) REVERT: I 58 VAL cc_start: 0.8746 (t) cc_final: 0.8425 (p) REVERT: I 77 ASN cc_start: 0.8133 (t0) cc_final: 0.7823 (t0) REVERT: J 54 ARG cc_start: 0.8347 (mtt90) cc_final: 0.8021 (mmp80) REVERT: K 66 ASP cc_start: 0.8076 (t0) cc_final: 0.7659 (t0) REVERT: K 70 ARG cc_start: 0.7144 (mmm160) cc_final: 0.6723 (mmp-170) REVERT: K 79 GLU cc_start: 0.8716 (tp30) cc_final: 0.8179 (tp30) REVERT: M 69 TRP cc_start: 0.7201 (m-90) cc_final: 0.6848 (m-90) REVERT: M 377 ASN cc_start: 0.8801 (t0) cc_final: 0.8601 (t0) REVERT: N 632 ASP cc_start: 0.8619 (t70) cc_final: 0.8088 (t0) REVERT: O 30 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7792 (mtt90) REVERT: O 98 ASP cc_start: 0.8563 (m-30) cc_final: 0.8032 (t0) REVERT: P 55 GLU cc_start: 0.7609 (tp30) cc_final: 0.7256 (tp30) REVERT: Q 32 TYR cc_start: 0.8228 (m-10) cc_final: 0.7779 (m-10) REVERT: Q 46 GLU cc_start: 0.8431 (tt0) cc_final: 0.8187 (tt0) REVERT: Q 86 ASP cc_start: 0.8185 (t0) cc_final: 0.7984 (t0) REVERT: Q 90 TYR cc_start: 0.7867 (m-10) cc_final: 0.7447 (m-10) REVERT: Q 97 ARG cc_start: 0.8743 (tmm-80) cc_final: 0.7875 (ttp80) REVERT: R 20 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7853 (mpp80) REVERT: R 66 ASP cc_start: 0.8144 (t0) cc_final: 0.7924 (t0) REVERT: R 70 ARG cc_start: 0.7463 (mmm160) cc_final: 0.7257 (mmp-170) REVERT: R 79 GLU cc_start: 0.8754 (tp30) cc_final: 0.8189 (tp30) outliers start: 45 outliers final: 31 residues processed: 335 average time/residue: 0.4128 time to fit residues: 210.9347 Evaluate side-chains 305 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 273 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.0470 chunk 164 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 247 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26655 Z= 0.202 Angle : 0.530 9.911 36204 Z= 0.258 Chirality : 0.044 0.285 4374 Planarity : 0.003 0.036 4440 Dihedral : 7.989 83.128 6087 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.84 % Allowed : 13.84 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 3021 helix: -0.56 (0.27), residues: 381 sheet: -0.53 (0.17), residues: 891 loop : -1.53 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 69 HIS 0.002 0.000 HIS M 330 PHE 0.010 0.001 PHE M 53 TYR 0.010 0.001 TYR D 91 ARG 0.009 0.000 ARG M 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 281 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7089 (m-90) cc_final: 0.6707 (m-90) REVERT: G 205 CYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7232 (m) REVERT: B 626 MET cc_start: 0.8075 (ttm) cc_final: 0.7827 (mtt) REVERT: B 632 ASP cc_start: 0.8728 (t70) cc_final: 0.8283 (t0) REVERT: C 53 LYS cc_start: 0.9385 (ttmt) cc_final: 0.9074 (ttmm) REVERT: C 98 ASP cc_start: 0.8545 (m-30) cc_final: 0.7877 (t0) REVERT: D 77 ASN cc_start: 0.8292 (t0) cc_final: 0.7839 (t0) REVERT: H 54 ARG cc_start: 0.8290 (mtt90) cc_final: 0.7986 (mmp80) REVERT: H 90 TYR cc_start: 0.7800 (m-10) cc_final: 0.7477 (m-10) REVERT: L 66 ASP cc_start: 0.8169 (t0) cc_final: 0.7590 (t0) REVERT: L 79 GLU cc_start: 0.8646 (tp30) cc_final: 0.8295 (tp30) REVERT: E 584 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7643 (mt-10) REVERT: E 632 ASP cc_start: 0.8619 (t70) cc_final: 0.8162 (t0) REVERT: F 53 LYS cc_start: 0.9428 (ttmt) cc_final: 0.9046 (ttmm) REVERT: F 98 ASP cc_start: 0.8523 (m-30) cc_final: 0.7943 (t0) REVERT: I 5 THR cc_start: 0.7541 (m) cc_final: 0.7254 (p) REVERT: I 58 VAL cc_start: 0.8702 (t) cc_final: 0.8360 (p) REVERT: J 54 ARG cc_start: 0.8372 (mtt90) cc_final: 0.8025 (mmp80) REVERT: K 66 ASP cc_start: 0.8169 (t0) cc_final: 0.7733 (t0) REVERT: K 70 ARG cc_start: 0.7126 (mmm160) cc_final: 0.6683 (mmp-170) REVERT: K 79 GLU cc_start: 0.8708 (tp30) cc_final: 0.8168 (tp30) REVERT: M 69 TRP cc_start: 0.7273 (m-90) cc_final: 0.6844 (m-90) REVERT: M 205 CYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7215 (m) REVERT: N 530 MET cc_start: 0.8546 (mtt) cc_final: 0.8267 (mtt) REVERT: N 632 ASP cc_start: 0.8695 (t70) cc_final: 0.8168 (t0) REVERT: O 30 ARG cc_start: 0.8033 (mtt90) cc_final: 0.7813 (mtt90) REVERT: O 98 ASP cc_start: 0.8575 (m-30) cc_final: 0.8029 (t0) REVERT: P 55 GLU cc_start: 0.7795 (tp30) cc_final: 0.7383 (tp30) REVERT: P 58 VAL cc_start: 0.8631 (t) cc_final: 0.8236 (p) REVERT: Q 27 ASP cc_start: 0.6677 (t0) cc_final: 0.6474 (t0) REVERT: Q 46 GLU cc_start: 0.8459 (tt0) cc_final: 0.8212 (tt0) REVERT: Q 86 ASP cc_start: 0.8380 (t0) cc_final: 0.8028 (t0) REVERT: Q 90 TYR cc_start: 0.7834 (m-10) cc_final: 0.7411 (m-10) REVERT: Q 97 ARG cc_start: 0.8831 (tmm-80) cc_final: 0.7943 (ttp80) REVERT: R 20 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7825 (mpp80) REVERT: R 26 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7875 (mm-40) REVERT: R 79 GLU cc_start: 0.8741 (tp30) cc_final: 0.8175 (tp30) outliers start: 49 outliers final: 35 residues processed: 320 average time/residue: 0.4075 time to fit residues: 200.2292 Evaluate side-chains 309 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 271 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain N residue 626 MET Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 10.0000 chunk 261 optimal weight: 0.0370 chunk 57 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 152 optimal weight: 0.5980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26655 Z= 0.155 Angle : 0.514 9.784 36204 Z= 0.250 Chirality : 0.043 0.270 4374 Planarity : 0.003 0.037 4440 Dihedral : 7.586 81.473 6087 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.02 % Allowed : 14.10 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.15), residues: 3021 helix: -0.22 (0.28), residues: 381 sheet: -0.30 (0.17), residues: 885 loop : -1.43 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 69 HIS 0.001 0.000 HIS A 374 PHE 0.009 0.001 PHE F 73 TYR 0.010 0.001 TYR J 32 ARG 0.010 0.000 ARG M 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 286 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7076 (m-90) cc_final: 0.6760 (m-90) REVERT: B 626 MET cc_start: 0.7999 (ttm) cc_final: 0.7748 (mtt) REVERT: B 632 ASP cc_start: 0.8715 (t70) cc_final: 0.8274 (t0) REVERT: C 53 LYS cc_start: 0.9388 (ttmt) cc_final: 0.9074 (ttmm) REVERT: C 98 ASP cc_start: 0.8560 (m-30) cc_final: 0.7874 (t0) REVERT: D 77 ASN cc_start: 0.8254 (t0) cc_final: 0.7859 (t0) REVERT: H 54 ARG cc_start: 0.8265 (mtt90) cc_final: 0.7992 (mmp80) REVERT: H 90 TYR cc_start: 0.7777 (m-10) cc_final: 0.7481 (m-10) REVERT: L 79 GLU cc_start: 0.8642 (tp30) cc_final: 0.8283 (tp30) REVERT: A 377 ASN cc_start: 0.8926 (t0) cc_final: 0.8654 (t0) REVERT: A 475 MET cc_start: 0.8084 (mmm) cc_final: 0.7865 (mmt) REVERT: E 584 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7716 (mt-10) REVERT: E 632 ASP cc_start: 0.8433 (t70) cc_final: 0.7966 (t0) REVERT: F 53 LYS cc_start: 0.9434 (ttmt) cc_final: 0.9074 (ttmm) REVERT: F 98 ASP cc_start: 0.8545 (m-30) cc_final: 0.7918 (t0) REVERT: I 5 THR cc_start: 0.7535 (m) cc_final: 0.7291 (p) REVERT: I 58 VAL cc_start: 0.8654 (t) cc_final: 0.8316 (p) REVERT: J 54 ARG cc_start: 0.8405 (mtt90) cc_final: 0.8053 (mmp80) REVERT: K 66 ASP cc_start: 0.8204 (t0) cc_final: 0.7771 (t0) REVERT: K 70 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6619 (mmp-170) REVERT: K 79 GLU cc_start: 0.8703 (tp30) cc_final: 0.8161 (tp30) REVERT: M 69 TRP cc_start: 0.7252 (m-90) cc_final: 0.6917 (m-90) REVERT: N 632 ASP cc_start: 0.8685 (t70) cc_final: 0.8168 (t0) REVERT: O 30 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7773 (mtt90) REVERT: O 98 ASP cc_start: 0.8561 (m-30) cc_final: 0.8005 (t0) REVERT: P 55 GLU cc_start: 0.7842 (tp30) cc_final: 0.7542 (tp30) REVERT: P 58 VAL cc_start: 0.8613 (t) cc_final: 0.8213 (p) REVERT: P 77 ASN cc_start: 0.7541 (t0) cc_final: 0.7217 (t0) REVERT: Q 32 TYR cc_start: 0.8358 (m-10) cc_final: 0.7953 (m-10) REVERT: Q 46 GLU cc_start: 0.8462 (tt0) cc_final: 0.8192 (tt0) REVERT: Q 86 ASP cc_start: 0.8436 (t0) cc_final: 0.8028 (t0) REVERT: Q 90 TYR cc_start: 0.7803 (m-10) cc_final: 0.7421 (m-10) REVERT: Q 97 ARG cc_start: 0.8788 (tmm-80) cc_final: 0.7903 (ttp80) REVERT: R 20 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7790 (mpp80) REVERT: R 26 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7872 (mm-40) REVERT: R 79 GLU cc_start: 0.8728 (tp30) cc_final: 0.8185 (tp30) outliers start: 54 outliers final: 45 residues processed: 328 average time/residue: 0.4014 time to fit residues: 203.6409 Evaluate side-chains 321 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 275 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 7 TYR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 620 SER Chi-restraints excluded: chain N residue 626 MET Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 7 TYR Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** M 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26655 Z= 0.247 Angle : 0.559 10.030 36204 Z= 0.273 Chirality : 0.044 0.303 4374 Planarity : 0.003 0.049 4440 Dihedral : 7.598 81.798 6087 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.59 % Allowed : 14.36 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 3021 helix: -0.06 (0.28), residues: 381 sheet: -0.26 (0.17), residues: 939 loop : -1.34 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 69 HIS 0.002 0.001 HIS G 72 PHE 0.011 0.001 PHE I 87 TYR 0.012 0.001 TYR D 91 ARG 0.009 0.001 ARG M 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 269 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7181 (m-90) cc_final: 0.6826 (m-90) REVERT: G 205 CYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7231 (m) REVERT: B 626 MET cc_start: 0.8067 (ttm) cc_final: 0.7809 (mtt) REVERT: B 632 ASP cc_start: 0.8822 (t70) cc_final: 0.8382 (t0) REVERT: C 53 LYS cc_start: 0.9398 (ttmt) cc_final: 0.9079 (ttmm) REVERT: C 98 ASP cc_start: 0.8560 (m-30) cc_final: 0.7826 (t0) REVERT: D 58 VAL cc_start: 0.8588 (t) cc_final: 0.8198 (p) REVERT: D 77 ASN cc_start: 0.8329 (t0) cc_final: 0.7988 (t0) REVERT: H 54 ARG cc_start: 0.8380 (mtt90) cc_final: 0.7964 (mmp80) REVERT: H 90 TYR cc_start: 0.7839 (m-10) cc_final: 0.7574 (m-10) REVERT: L 79 GLU cc_start: 0.8617 (tp30) cc_final: 0.8195 (tp30) REVERT: A 377 ASN cc_start: 0.8944 (t0) cc_final: 0.8730 (t0) REVERT: E 632 ASP cc_start: 0.8483 (t70) cc_final: 0.8026 (t0) REVERT: F 98 ASP cc_start: 0.8559 (m-30) cc_final: 0.7900 (t0) REVERT: I 5 THR cc_start: 0.7627 (m) cc_final: 0.7326 (p) REVERT: I 58 VAL cc_start: 0.8706 (t) cc_final: 0.8393 (p) REVERT: J 6 GLU cc_start: 0.7686 (pt0) cc_final: 0.7403 (pt0) REVERT: K 70 ARG cc_start: 0.7044 (mmm160) cc_final: 0.6684 (mmp-170) REVERT: K 79 GLU cc_start: 0.8652 (tp30) cc_final: 0.8145 (tp30) REVERT: M 69 TRP cc_start: 0.7242 (m-90) cc_final: 0.6887 (m-90) REVERT: M 205 CYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7154 (m) REVERT: N 632 ASP cc_start: 0.8720 (t70) cc_final: 0.8192 (t0) REVERT: O 84 SER cc_start: 0.9178 (m) cc_final: 0.8916 (t) REVERT: O 98 ASP cc_start: 0.8588 (m-30) cc_final: 0.7993 (t0) REVERT: P 55 GLU cc_start: 0.7973 (tp30) cc_final: 0.7711 (tp30) REVERT: P 58 VAL cc_start: 0.8611 (t) cc_final: 0.8213 (p) REVERT: P 77 ASN cc_start: 0.7832 (t0) cc_final: 0.7523 (t0) REVERT: Q 32 TYR cc_start: 0.8465 (m-10) cc_final: 0.8251 (m-10) REVERT: Q 46 GLU cc_start: 0.8481 (tt0) cc_final: 0.8216 (tt0) REVERT: Q 86 ASP cc_start: 0.8508 (t0) cc_final: 0.8084 (t0) REVERT: Q 90 TYR cc_start: 0.7932 (m-10) cc_final: 0.7601 (m-10) REVERT: Q 97 ARG cc_start: 0.8923 (tmm-80) cc_final: 0.8221 (ttp80) REVERT: R 20 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7432 (mpp80) REVERT: R 79 GLU cc_start: 0.8712 (tp30) cc_final: 0.8172 (tp30) outliers start: 69 outliers final: 57 residues processed: 325 average time/residue: 0.3934 time to fit residues: 197.4499 Evaluate side-chains 323 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 263 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 7 TYR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 620 SER Chi-restraints excluded: chain N residue 626 MET Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 7 TYR Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 172 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26655 Z= 0.289 Angle : 0.585 10.086 36204 Z= 0.286 Chirality : 0.044 0.311 4374 Planarity : 0.004 0.048 4440 Dihedral : 7.694 82.169 6087 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.55 % Allowed : 14.89 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 3021 helix: 0.03 (0.28), residues: 381 sheet: -0.16 (0.17), residues: 924 loop : -1.37 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 69 HIS 0.002 0.001 HIS A 249 PHE 0.015 0.001 PHE O 73 TYR 0.013 0.001 TYR D 91 ARG 0.008 0.001 ARG M 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 266 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7160 (m-90) cc_final: 0.6868 (m-90) REVERT: B 632 ASP cc_start: 0.8849 (t70) cc_final: 0.8403 (t0) REVERT: C 53 LYS cc_start: 0.9409 (ttmt) cc_final: 0.9066 (ttmm) REVERT: C 98 ASP cc_start: 0.8561 (m-30) cc_final: 0.7800 (t0) REVERT: D 77 ASN cc_start: 0.8350 (t0) cc_final: 0.8065 (t0) REVERT: H 90 TYR cc_start: 0.7887 (m-10) cc_final: 0.7599 (m-10) REVERT: L 79 GLU cc_start: 0.8568 (tp30) cc_final: 0.8143 (tp30) REVERT: A 377 ASN cc_start: 0.8922 (t0) cc_final: 0.8706 (t0) REVERT: E 632 ASP cc_start: 0.8497 (t70) cc_final: 0.8045 (t0) REVERT: F 84 SER cc_start: 0.9139 (m) cc_final: 0.8902 (t) REVERT: F 98 ASP cc_start: 0.8584 (m-30) cc_final: 0.7830 (t0) REVERT: I 1 ASP cc_start: 0.8129 (p0) cc_final: 0.7872 (p0) REVERT: I 5 THR cc_start: 0.7725 (m) cc_final: 0.7383 (p) REVERT: I 58 VAL cc_start: 0.8709 (t) cc_final: 0.8405 (p) REVERT: J 86 ASP cc_start: 0.8284 (t0) cc_final: 0.8078 (t0) REVERT: K 26 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7272 (mm-40) REVERT: K 79 GLU cc_start: 0.8626 (tp30) cc_final: 0.8123 (tp30) REVERT: M 69 TRP cc_start: 0.7248 (m-90) cc_final: 0.6878 (m-90) REVERT: N 632 ASP cc_start: 0.8719 (t70) cc_final: 0.8190 (t0) REVERT: O 84 SER cc_start: 0.9225 (m) cc_final: 0.8964 (t) REVERT: O 98 ASP cc_start: 0.8569 (m-30) cc_final: 0.7923 (t0) REVERT: P 77 ASN cc_start: 0.8124 (t0) cc_final: 0.7880 (t0) REVERT: Q 5 GLN cc_start: 0.9341 (tp-100) cc_final: 0.9086 (tp-100) REVERT: Q 32 TYR cc_start: 0.8408 (m-10) cc_final: 0.8138 (m-10) REVERT: Q 86 ASP cc_start: 0.8510 (t0) cc_final: 0.8090 (t0) REVERT: Q 90 TYR cc_start: 0.7948 (m-10) cc_final: 0.7599 (m-10) REVERT: R 20 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7442 (mpp80) REVERT: R 79 GLU cc_start: 0.8693 (tp30) cc_final: 0.8162 (tp30) outliers start: 68 outliers final: 57 residues processed: 322 average time/residue: 0.3886 time to fit residues: 192.4062 Evaluate side-chains 312 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 254 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 620 SER Chi-restraints excluded: chain N residue 626 MET Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 31 ASP Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 269 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26655 Z= 0.235 Angle : 0.577 11.656 36204 Z= 0.279 Chirality : 0.044 0.297 4374 Planarity : 0.004 0.073 4440 Dihedral : 7.593 81.377 6087 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.17 % Allowed : 15.90 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3021 helix: 0.19 (0.29), residues: 381 sheet: -0.08 (0.18), residues: 912 loop : -1.32 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 69 HIS 0.002 0.001 HIS A 72 PHE 0.010 0.001 PHE I 87 TYR 0.009 0.001 TYR D 91 ARG 0.010 0.001 ARG I 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 262 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7131 (m-90) cc_final: 0.6885 (m-90) REVERT: B 632 ASP cc_start: 0.8836 (t70) cc_final: 0.8370 (t0) REVERT: C 23 GLU cc_start: 0.7468 (mp0) cc_final: 0.7208 (mp0) REVERT: C 53 LYS cc_start: 0.9407 (ttmt) cc_final: 0.9070 (ttmm) REVERT: C 98 ASP cc_start: 0.8555 (m-30) cc_final: 0.7788 (t0) REVERT: H 5 GLN cc_start: 0.9289 (tp-100) cc_final: 0.9086 (tp-100) REVERT: H 90 TYR cc_start: 0.7893 (m-10) cc_final: 0.7686 (m-10) REVERT: L 79 GLU cc_start: 0.8580 (tp30) cc_final: 0.8152 (tp30) REVERT: A 475 MET cc_start: 0.8333 (mmm) cc_final: 0.7918 (mmt) REVERT: E 632 ASP cc_start: 0.8434 (t70) cc_final: 0.7977 (t0) REVERT: F 84 SER cc_start: 0.9144 (m) cc_final: 0.8891 (t) REVERT: F 98 ASP cc_start: 0.8577 (m-30) cc_final: 0.7896 (t0) REVERT: I 1 ASP cc_start: 0.8127 (p0) cc_final: 0.7885 (p0) REVERT: I 5 THR cc_start: 0.7719 (m) cc_final: 0.7395 (p) REVERT: J 5 GLN cc_start: 0.9247 (tp-100) cc_final: 0.8971 (tp-100) REVERT: J 54 ARG cc_start: 0.8407 (mmp80) cc_final: 0.7978 (ptp90) REVERT: K 79 GLU cc_start: 0.8620 (tp30) cc_final: 0.8119 (tp30) REVERT: M 69 TRP cc_start: 0.7173 (m-90) cc_final: 0.6848 (m-90) REVERT: N 632 ASP cc_start: 0.8699 (t70) cc_final: 0.8175 (t0) REVERT: O 84 SER cc_start: 0.9219 (m) cc_final: 0.8949 (t) REVERT: O 98 ASP cc_start: 0.8570 (m-30) cc_final: 0.7897 (t0) REVERT: P 77 ASN cc_start: 0.8085 (t0) cc_final: 0.7879 (t0) REVERT: Q 32 TYR cc_start: 0.8402 (m-10) cc_final: 0.8133 (m-10) REVERT: Q 86 ASP cc_start: 0.8524 (t0) cc_final: 0.8117 (t0) REVERT: Q 90 TYR cc_start: 0.7919 (m-10) cc_final: 0.7589 (m-10) REVERT: R 20 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7446 (mpp80) REVERT: R 79 GLU cc_start: 0.8681 (tp30) cc_final: 0.8155 (tp30) outliers start: 58 outliers final: 52 residues processed: 311 average time/residue: 0.4009 time to fit residues: 193.5210 Evaluate side-chains 304 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 251 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 3.9990 chunk 284 optimal weight: 0.8980 chunk 173 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 chunk 237 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 465 ASN A 377 ASN A 425 ASN A 465 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 26655 Z= 0.215 Angle : 0.695 59.196 36204 Z= 0.367 Chirality : 0.043 0.292 4374 Planarity : 0.004 0.071 4440 Dihedral : 7.604 81.345 6087 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.10 % Allowed : 16.27 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3021 helix: 0.22 (0.29), residues: 381 sheet: -0.07 (0.18), residues: 876 loop : -1.31 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 69 HIS 0.002 0.001 HIS A 72 PHE 0.009 0.001 PHE I 87 TYR 0.008 0.001 TYR D 91 ARG 0.013 0.000 ARG I 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 251 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7125 (m-90) cc_final: 0.6884 (m-90) REVERT: G 475 MET cc_start: 0.8107 (mmm) cc_final: 0.7885 (mmm) REVERT: B 632 ASP cc_start: 0.8834 (t70) cc_final: 0.8368 (t0) REVERT: C 53 LYS cc_start: 0.9404 (ttmt) cc_final: 0.9067 (ttmm) REVERT: C 98 ASP cc_start: 0.8550 (m-30) cc_final: 0.7783 (t0) REVERT: H 5 GLN cc_start: 0.9287 (tp-100) cc_final: 0.9077 (tp-100) REVERT: H 90 TYR cc_start: 0.7882 (m-10) cc_final: 0.7677 (m-10) REVERT: L 79 GLU cc_start: 0.8578 (tp30) cc_final: 0.8150 (tp30) REVERT: A 475 MET cc_start: 0.8335 (mmm) cc_final: 0.7928 (mmt) REVERT: E 632 ASP cc_start: 0.8435 (t70) cc_final: 0.7972 (t0) REVERT: F 84 SER cc_start: 0.9144 (m) cc_final: 0.8890 (t) REVERT: F 98 ASP cc_start: 0.8573 (m-30) cc_final: 0.7894 (t0) REVERT: I 1 ASP cc_start: 0.8124 (p0) cc_final: 0.7887 (p0) REVERT: I 5 THR cc_start: 0.7706 (m) cc_final: 0.7387 (p) REVERT: K 79 GLU cc_start: 0.8619 (tp30) cc_final: 0.8118 (tp30) REVERT: M 69 TRP cc_start: 0.7165 (m-90) cc_final: 0.6850 (m-90) REVERT: N 632 ASP cc_start: 0.8700 (t70) cc_final: 0.8176 (t0) REVERT: O 84 SER cc_start: 0.9217 (m) cc_final: 0.8947 (t) REVERT: O 98 ASP cc_start: 0.8570 (m-30) cc_final: 0.7882 (t0) REVERT: P 77 ASN cc_start: 0.8083 (t0) cc_final: 0.7875 (t0) REVERT: Q 32 TYR cc_start: 0.8398 (m-10) cc_final: 0.8132 (m-10) REVERT: Q 86 ASP cc_start: 0.8522 (t0) cc_final: 0.8113 (t0) REVERT: Q 90 TYR cc_start: 0.7916 (m-10) cc_final: 0.7587 (m-10) REVERT: R 20 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7445 (mpp80) REVERT: R 79 GLU cc_start: 0.8679 (tp30) cc_final: 0.8149 (tp30) outliers start: 56 outliers final: 53 residues processed: 299 average time/residue: 0.3872 time to fit residues: 178.9866 Evaluate side-chains 304 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 250 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.6980 chunk 253 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 244 optimal weight: 0.1980 chunk 30 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 GLN A 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.084694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.059044 restraints weight = 62477.567| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.40 r_work: 0.2816 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26655 Z= 0.178 Angle : 0.567 10.562 36204 Z= 0.276 Chirality : 0.043 0.283 4374 Planarity : 0.004 0.068 4440 Dihedral : 7.442 80.465 6087 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.95 % Allowed : 16.54 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 3021 helix: 0.36 (0.29), residues: 381 sheet: 0.03 (0.18), residues: 906 loop : -1.27 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 571 HIS 0.001 0.000 HIS M 105 PHE 0.011 0.001 PHE A 376 TYR 0.008 0.001 TYR D 91 ARG 0.010 0.000 ARG I 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5280.84 seconds wall clock time: 95 minutes 58.19 seconds (5758.19 seconds total)