Starting phenix.real_space_refine on Mon Feb 19 19:53:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/02_2024/7ugo_26492_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/02_2024/7ugo_26492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/02_2024/7ugo_26492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/02_2024/7ugo_26492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/02_2024/7ugo_26492_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/02_2024/7ugo_26492_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 150 5.16 5 C 16029 2.51 5 N 4311 2.21 5 O 5100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 47": "OD1" <-> "OD2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 412": "OD1" <-> "OD2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C ASP 167": "OD1" <-> "OD2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 386": "OD1" <-> "OD2" Residue "C ARG 429": "NH1" <-> "NH2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D ASP 664": "OD1" <-> "OD2" Residue "E GLU 584": "OE1" <-> "OE2" Residue "E ASP 589": "OD1" <-> "OD2" Residue "F GLU 584": "OE1" <-> "OE2" Residue "F ASP 589": "OD1" <-> "OD2" Residue "F ASP 664": "OD1" <-> "OD2" Residue "M ASP 86": "OD1" <-> "OD2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 55": "OE1" <-> "OE2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 9": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 53": "OD1" <-> "OD2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "P ASP 85": "OD1" <-> "OD2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 9": "NH1" <-> "NH2" Residue "Q ARG 20": "NH1" <-> "NH2" Residue "Q TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 53": "OD1" <-> "OD2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q GLU 83": "OE1" <-> "OE2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 94": "NH1" <-> "NH2" Residue "Q PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 9": "NH1" <-> "NH2" Residue "R ARG 20": "NH1" <-> "NH2" Residue "R TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 53": "OD1" <-> "OD2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ASP 82": "OD1" <-> "OD2" Residue "R GLU 83": "OE1" <-> "OE2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 94": "NH1" <-> "NH2" Residue "R PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 66": "NH1" <-> "NH2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I ASP 86": "OD1" <-> "OD2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 56": "NH1" <-> "NH2" Residue "J PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J ASP 84": "OD1" <-> "OD2" Residue "J GLU 94": "OE1" <-> "OE2" Residue "J PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 56": "NH1" <-> "NH2" Residue "K PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K ASP 84": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L ASP 84": "OD1" <-> "OD2" Residue "L ASP 87": "OD1" <-> "OD2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25590 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3523 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 422} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3523 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 422} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3523 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 422} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "M" 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: "N" 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: "O" 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: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "Q" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "K" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "L" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "S" 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: "T" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'MAN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 106 Unusual residues: {'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'MAN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: "E" 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: "F" 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: 13.45, per 1000 atoms: 0.53 Number of scatterers: 25590 At special positions: 0 Unit cell: (155.04, 164.16, 157.32, 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 150 16.00 O 5100 8.00 N 4311 7.00 C 16029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " 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 A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " 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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM25337 C1 MAN A 607 49.714 112.559 76.927 1.00133.36 C !!! !!! HETATM24496 C6 BMA S 3 49.574 111.401 76.960 1.00 80.71 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Atom "HETATM25128 O5 MAN h 8 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-2 " MAN T 5 " - " MAN T 6 " " MAN X 1 " - " MAN X 2 " " MAN a 5 " - " MAN a 6 " " MAN e 1 " - " MAN e 2 " " MAN h 5 " - " MAN h 6 " " MAN h 8 " - " MAN h 9 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN e 1 " " MAN a 4 " - " MAN a 7 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 8 " " MAN h 4 " - " MAN h 7 " ALPHA1-6 " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 5 " " BMA a 3 " - " MAN a 4 " " MAN a 4 " - " MAN a 5 " " BMA g 3 " - " MAN C 606 " " BMA h 3 " - " MAN h 4 " " MAN h 4 " - " MAN h 5 " ALPHA2-6 " BMA Z 3 " - " MAN B 608 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " 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-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 448 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 160 " " NAG A 606 " - " ASN A 133 " " NAG B 602 " - " ASN B 88 " " NAG B 603 " - " ASN B 234 " " NAG B 604 " - " ASN B 448 " " NAG B 605 " - " ASN B 392 " " NAG B 606 " - " ASN B 160 " " NAG B 607 " - " ASN B 133 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 448 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 133 " " NAG C 607 " - " ASN C 160 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 701 " - " ASN F 637 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 363 " " NAG Y 1 " - " ASN A 156 " " NAG Z 1 " - " ASN B 262 " " NAG a 1 " - " ASN B 332 " " NAG b 1 " - " ASN B 301 " " NAG c 1 " - " ASN B 295 " " NAG d 1 " - " ASN B 363 " " NAG f 1 " - " ASN B 156 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 332 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 295 " " NAG k 1 " - " ASN C 363 " " NAG l 1 " - " ASN C 156 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.80 Conformation dependent library (CDL) restraints added in 4.4 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 52 sheets defined 14.1% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.557A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.815A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.560A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.828A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 127 " --> pdb=" O PRO B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'B' and resid 194 through 198 removed outlier: 4.129A pdb=" N ASN B 197 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.563A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.809A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 127' Processing helix chain 'C' and resid 194 through 198 removed outlier: 4.123A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.676A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 537 No H-bonds generated for 'chain 'D' and resid 535 through 537' Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.360A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 597 removed outlier: 3.514A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 removed outlier: 3.572A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.574A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.576A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 535 through 537 No H-bonds generated for 'chain 'E' and resid 535 through 537' Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.370A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 597 removed outlier: 3.509A pdb=" N ILE E 573 " --> pdb=" O THR E 569 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN E 575 " --> pdb=" O TRP E 571 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU E 587 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN E 590 " --> pdb=" O TYR E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 removed outlier: 3.624A pdb=" N ILE E 622 " --> pdb=" O ASN E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 removed outlier: 3.575A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 664 removed outlier: 3.590A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP E 664 " --> pdb=" O LEU E 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 535 through 541 removed outlier: 5.791A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 539 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 597 removed outlier: 3.521A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU F 587 " --> pdb=" O VAL F 583 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.621A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.567A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.797A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 4.153A pdb=" N THR M 87 " --> pdb=" O PRO M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 4.143A pdb=" N THR N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 100D through 100H removed outlier: 3.515A pdb=" N PHE N 100G" --> pdb=" O VAL N 100D" (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 4.125A pdb=" N THR O 87 " --> pdb=" O PRO O 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'J' and resid 25 through 30 removed outlier: 3.683A pdb=" N VAL J 29 " --> pdb=" O THR J 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 30 Processing helix chain 'L' and resid 25 through 30 Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 499 removed outlier: 4.704A pdb=" N LEU A 34 " --> pdb=" O TRP D 610 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 36 " --> pdb=" O VAL D 608 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N VAL A 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR D 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.540A pdb=" N LYS A 46 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 245 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 132 removed outlier: 3.519A pdb=" N GLN A 130 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 158 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.881A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.716A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.069A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.121A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.015A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 298 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 469 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 499 removed outlier: 4.606A pdb=" N LEU B 34 " --> pdb=" O TRP E 610 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 36 " --> pdb=" O VAL E 608 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL E 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL B 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N THR E 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.560A pdb=" N LYS B 46 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 245 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 132 removed outlier: 3.514A pdb=" N GLN B 130 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 158 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AB3, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.866A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 322 removed outlier: 7.018A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE B 322 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN B 301 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.087A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 469 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 499 removed outlier: 4.701A pdb=" N LEU C 34 " --> pdb=" O TRP F 610 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.543A pdb=" N LYS C 46 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 245 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 130 through 133 removed outlier: 4.329A pdb=" N GLN C 130 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 158 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.781A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.064A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.101A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 469 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AC2, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AC3, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.773A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.780A pdb=" N LEU M 78 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.020A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR M 50 " --> pdb=" O THR M 58 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR M 58 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.020A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'N' and resid 58 through 59 removed outlier: 4.652A pdb=" N THR N 58 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR N 50 " --> pdb=" O THR N 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE N 48 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 58 through 59 removed outlier: 4.652A pdb=" N THR N 58 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR N 50 " --> pdb=" O THR N 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE N 48 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 67 through 72 Processing sheet with id=AD2, first strand: chain 'O' and resid 3 through 7 removed outlier: 4.161A pdb=" N LEU O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.005A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE O 48 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR O 50 " --> pdb=" O THR O 58 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR O 58 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.005A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.415A pdb=" N LEU P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 20 through 22 Processing sheet with id=AD7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.332A pdb=" N LEU Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 19 through 22 removed outlier: 3.534A pdb=" N ALA Q 19 " --> pdb=" O ILE Q 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.189A pdb=" N LEU R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.574A pdb=" N ALA R 19 " --> pdb=" O ILE R 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 5 removed outlier: 4.406A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS G 22 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 3 through 5 removed outlier: 4.406A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS G 22 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.366A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.453A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.453A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.385A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 3 through 5 removed outlier: 4.421A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS I 22 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 5 removed outlier: 4.421A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS I 22 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.369A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 9 through 10 removed outlier: 6.222A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 18 through 21 Processing sheet with id=AF4, first strand: chain 'K' and resid 9 through 10 removed outlier: 6.973A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 18 through 22 removed outlier: 3.528A pdb=" N CYS K 22 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA K 73 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.239A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 18 through 22 removed outlier: 3.527A pdb=" N CYS L 22 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA L 73 " --> pdb=" O CYS L 22 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 1845 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: 8.44 Time building geometry restraints manager: 11.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8095 1.34 - 1.47: 6687 1.47 - 1.59: 11138 1.59 - 1.71: 0 1.71 - 1.83: 210 Bond restraints: 26130 Sorted by residual: bond pdb=" N SER C 158 " pdb=" CA SER C 158 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N VAL A 172 " pdb=" CA VAL A 172 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N GLN A 170 " pdb=" CA GLN A 170 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.21e-02 6.83e+03 7.66e+00 bond pdb=" N LYS A 171 " pdb=" CA LYS A 171 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.19e+00 bond pdb=" N PHE C 159 " pdb=" CA PHE C 159 " ideal model delta sigma weight residual 1.455 1.479 -0.025 1.29e-02 6.01e+03 3.72e+00 ... (remaining 26125 not shown) Histogram of bond angle deviations from ideal: 98.97 - 105.98: 539 105.98 - 112.99: 14746 112.99 - 120.00: 8123 120.00 - 127.00: 11723 127.00 - 134.01: 347 Bond angle restraints: 35478 Sorted by residual: angle pdb=" N ASN C 160 " pdb=" CA ASN C 160 " pdb=" C ASN C 160 " ideal model delta sigma weight residual 111.28 120.15 -8.87 1.09e+00 8.42e-01 6.63e+01 angle pdb=" N PHE C 159 " pdb=" CA PHE C 159 " pdb=" C PHE C 159 " ideal model delta sigma weight residual 109.24 119.12 -9.88 1.51e+00 4.39e-01 4.28e+01 angle pdb=" N ASP C 167 " pdb=" CA ASP C 167 " pdb=" C ASP C 167 " ideal model delta sigma weight residual 111.36 116.75 -5.39 1.09e+00 8.42e-01 2.44e+01 angle pdb=" CA SER C 158 " pdb=" C SER C 158 " pdb=" N PHE C 159 " ideal model delta sigma weight residual 116.29 122.70 -6.41 1.30e+00 5.92e-01 2.43e+01 angle pdb=" N LEU C 165 " pdb=" CA LEU C 165 " pdb=" C LEU C 165 " ideal model delta sigma weight residual 109.96 103.46 6.50 1.50e+00 4.44e-01 1.88e+01 ... (remaining 35473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 15701 24.08 - 48.16: 712 48.16 - 72.24: 148 72.24 - 96.32: 68 96.32 - 120.40: 48 Dihedral angle restraints: 16677 sinusoidal: 7677 harmonic: 9000 Sorted by residual: dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -158.09 72.09 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -157.36 71.36 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -157.16 71.16 1 1.00e+01 1.00e-02 6.50e+01 ... (remaining 16674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.944: 4164 0.944 - 1.887: 6 1.887 - 2.831: 4 2.831 - 3.774: 6 3.774 - 4.718: 7 Chirality restraints: 4187 Sorted by residual: chirality pdb=" C1 MAN e 2 " pdb=" O2 MAN e 1 " pdb=" C2 MAN e 2 " pdb=" O5 MAN e 2 " both_signs ideal model delta sigma weight residual False 2.40 -2.32 4.72 2.00e-02 2.50e+03 5.56e+04 chirality pdb=" C1 MAN h 9 " pdb=" O2 MAN h 8 " pdb=" C2 MAN h 9 " pdb=" O5 MAN h 9 " both_signs ideal model delta sigma weight residual False 2.40 -2.31 4.71 2.00e-02 2.50e+03 5.56e+04 chirality pdb=" C1 MAN g 4 " pdb=" O3 BMA g 3 " pdb=" C2 MAN g 4 " pdb=" O5 MAN g 4 " both_signs ideal model delta sigma weight residual False 2.40 -2.31 4.71 2.00e-02 2.50e+03 5.56e+04 ... (remaining 4184 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 607 " 0.248 2.00e-02 2.50e+03 2.07e-01 5.38e+02 pdb=" C7 NAG C 607 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG C 607 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG C 607 " -0.346 2.00e-02 2.50e+03 pdb=" O7 NAG C 607 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 160 " 0.150 2.00e-02 2.50e+03 1.59e-01 3.16e+02 pdb=" CG ASN C 160 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 160 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN C 160 " -0.249 2.00e-02 2.50e+03 pdb=" C1 NAG C 607 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 157 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C CYS C 157 " -0.038 2.00e-02 2.50e+03 pdb=" O CYS C 157 " 0.014 2.00e-02 2.50e+03 pdb=" N SER C 158 " 0.013 2.00e-02 2.50e+03 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.75: 7 1.75 - 2.54: 189 2.54 - 3.33: 28547 3.33 - 4.11: 54529 4.11 - 4.90: 96666 Warning: very small nonbonded interaction distances. Nonbonded interactions: 179938 Sorted by model distance: nonbonded pdb=" O2 MAN T 4 " pdb=" O5 MAN T 7 " model vdw 0.965 2.440 nonbonded pdb=" C6 BMA S 3 " pdb=" C1 MAN A 607 " model vdw 1.167 3.870 nonbonded pdb=" O2 MAN T 4 " pdb=" C1 MAN T 7 " model vdw 1.399 3.470 nonbonded pdb=" O3 MAN T 4 " pdb=" C2 MAN T 7 " model vdw 1.408 3.470 nonbonded pdb=" O3 MAN T 4 " pdb=" C1 MAN T 7 " model vdw 1.659 3.470 ... (remaining 179933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 506 or resid 602 through 605)) selection = (chain 'B' and (resid 32 through 506 or resid 602 through 605)) selection = (chain 'C' and (resid 32 through 506 or resid 602 through 605)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'g' } ncs_group { reference = chain 'T' selection = chain 'a' } ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'X' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.020 Extract box with map and model: 5.160 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 65.610 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 0.041 26130 Z= 0.235 Angle : 0.638 9.884 35478 Z= 0.341 Chirality : 0.250 4.718 4187 Planarity : 0.004 0.207 4401 Dihedral : 16.021 120.404 10785 Min Nonbonded Distance : 0.965 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.13), residues: 3072 helix: -1.18 (0.27), residues: 342 sheet: -1.70 (0.15), residues: 984 loop : -3.15 (0.12), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 45 HIS 0.004 0.001 HIS A 66 PHE 0.007 0.001 PHE L 64 TYR 0.013 0.001 TYR K 51 ARG 0.002 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 722 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8721 (tpp) cc_final: 0.8064 (tpt) REVERT: A 195 ASN cc_start: 0.7842 (p0) cc_final: 0.7321 (p0) REVERT: A 474 ASP cc_start: 0.7776 (p0) cc_final: 0.7537 (p0) REVERT: B 125 LEU cc_start: 0.9289 (tp) cc_final: 0.9048 (tp) REVERT: B 161 MET cc_start: 0.8806 (tpp) cc_final: 0.8463 (tpp) REVERT: B 474 ASP cc_start: 0.7695 (p0) cc_final: 0.7415 (p0) REVERT: C 125 LEU cc_start: 0.9289 (tp) cc_final: 0.9004 (tp) REVERT: C 474 ASP cc_start: 0.7605 (p0) cc_final: 0.7214 (p0) REVERT: C 475 MET cc_start: 0.8292 (ptt) cc_final: 0.8047 (ptt) REVERT: D 630 GLN cc_start: 0.7875 (pt0) cc_final: 0.7595 (pt0) REVERT: E 540 GLN cc_start: 0.8428 (mp10) cc_final: 0.8222 (mp10) REVERT: F 540 GLN cc_start: 0.8531 (mp10) cc_final: 0.8080 (mp10) REVERT: F 542 ARG cc_start: 0.8464 (ptt-90) cc_final: 0.8255 (ptt90) REVERT: F 653 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7640 (mt0) REVERT: M 29 MET cc_start: 0.4488 (pmm) cc_final: 0.4265 (pmm) REVERT: M 91 TYR cc_start: 0.7262 (m-80) cc_final: 0.6963 (m-10) REVERT: M 100 MET cc_start: 0.7748 (mpp) cc_final: 0.7516 (mtm) REVERT: M 103 TRP cc_start: 0.8169 (m100) cc_final: 0.7879 (m-10) REVERT: N 21 THR cc_start: 0.8763 (m) cc_final: 0.8478 (t) REVERT: N 29 MET cc_start: 0.4731 (pmm) cc_final: 0.4358 (pmm) REVERT: N 91 TYR cc_start: 0.7416 (m-80) cc_final: 0.7057 (m-10) REVERT: N 96 ARG cc_start: 0.9050 (ttp-110) cc_final: 0.8752 (ttp-110) REVERT: N 103 TRP cc_start: 0.8207 (m100) cc_final: 0.7961 (m-10) REVERT: O 29 MET cc_start: 0.4748 (pmm) cc_final: 0.4403 (pmm) REVERT: O 100 TYR cc_start: 0.8588 (p90) cc_final: 0.8342 (p90) REVERT: P 31 ARG cc_start: 0.6787 (ttp-110) cc_final: 0.6428 (ttp-110) REVERT: P 83 GLU cc_start: 0.7986 (tt0) cc_final: 0.7330 (tt0) REVERT: Q 38 HIS cc_start: 0.7198 (t70) cc_final: 0.6971 (t70) REVERT: G 34 MET cc_start: 0.8496 (ttp) cc_final: 0.8161 (ttp) REVERT: G 82 LEU cc_start: 0.8658 (tp) cc_final: 0.8425 (tp) REVERT: H 34 MET cc_start: 0.8368 (ttp) cc_final: 0.8108 (ttm) REVERT: I 34 MET cc_start: 0.8372 (ttp) cc_final: 0.8062 (ttp) REVERT: I 86 ASP cc_start: 0.6459 (t0) cc_final: 0.5871 (t0) REVERT: J 47 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8625 (ttpt) REVERT: J 102 LEU cc_start: 0.7894 (tt) cc_final: 0.7551 (tt) REVERT: K 47 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8783 (ttpt) REVERT: L 38 TYR cc_start: 0.8009 (m-80) cc_final: 0.7685 (m-80) REVERT: L 41 HIS cc_start: 0.7729 (m90) cc_final: 0.7227 (m90) REVERT: L 47 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8301 (ttpt) REVERT: L 102 LEU cc_start: 0.8125 (tt) cc_final: 0.7464 (tt) outliers start: 4 outliers final: 1 residues processed: 723 average time/residue: 0.4283 time to fit residues: 463.3491 Evaluate side-chains 526 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 525 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 0.2980 chunk 229 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 237 optimal weight: 0.7980 chunk 91 optimal weight: 0.0030 chunk 144 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 275 optimal weight: 20.0000 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 258 GLN A 283 ASN A 293 GLN A 478 ASN B 186AASN B 283 ASN B 293 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186AASN C 283 ASN C 293 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN M 60 ASN N 60 ASN N 64 ASN O 1 GLN O 60 ASN Q 52 GLN R 26 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 41 HIS J 81 GLN K 39 GLN K 81 GLN L 39 GLN L 81 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26130 Z= 0.161 Angle : 0.599 12.651 35478 Z= 0.287 Chirality : 0.047 0.500 4187 Planarity : 0.003 0.049 4401 Dihedral : 15.180 104.772 5154 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.11 % Allowed : 4.19 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.89 (0.14), residues: 3072 helix: -0.48 (0.29), residues: 342 sheet: -1.11 (0.16), residues: 909 loop : -2.78 (0.12), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP M 36 HIS 0.004 0.001 HIS B 66 PHE 0.031 0.001 PHE C 159 TYR 0.015 0.001 TYR D 638 ARG 0.005 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 624 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8694 (t0) REVERT: A 97 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7586 (mtmm) REVERT: A 161 MET cc_start: 0.8665 (tpp) cc_final: 0.8348 (tpp) REVERT: A 195 ASN cc_start: 0.7898 (p0) cc_final: 0.7433 (p0) REVERT: A 474 ASP cc_start: 0.7796 (p0) cc_final: 0.7583 (p0) REVERT: B 125 LEU cc_start: 0.9275 (tp) cc_final: 0.9030 (tp) REVERT: B 161 MET cc_start: 0.8782 (tpp) cc_final: 0.8412 (tpp) REVERT: B 452 LEU cc_start: 0.9031 (mt) cc_final: 0.8774 (mp) REVERT: B 475 MET cc_start: 0.8533 (ptt) cc_final: 0.8290 (ptt) REVERT: C 125 LEU cc_start: 0.9260 (tp) cc_final: 0.8917 (tp) REVERT: C 178 LYS cc_start: 0.8616 (tptt) cc_final: 0.8397 (tptt) REVERT: C 434 MET cc_start: 0.9041 (ttm) cc_final: 0.8491 (ttm) REVERT: C 474 ASP cc_start: 0.7529 (p0) cc_final: 0.7325 (p0) REVERT: D 540 GLN cc_start: 0.8198 (mp10) cc_final: 0.7948 (mp10) REVERT: D 630 GLN cc_start: 0.7717 (pt0) cc_final: 0.6552 (tp-100) REVERT: D 634 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6076 (mt-10) REVERT: E 540 GLN cc_start: 0.8490 (mp10) cc_final: 0.8277 (mp10) REVERT: E 630 GLN cc_start: 0.7647 (pt0) cc_final: 0.7120 (pt0) REVERT: E 647 GLU cc_start: 0.8131 (pt0) cc_final: 0.7883 (pt0) REVERT: E 650 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7700 (mm-40) REVERT: F 540 GLN cc_start: 0.8493 (mp10) cc_final: 0.8040 (mp10) REVERT: F 653 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7635 (mt0) REVERT: M 91 TYR cc_start: 0.7257 (m-80) cc_final: 0.7019 (m-10) REVERT: M 100 GLU cc_start: 0.8071 (mp0) cc_final: 0.7630 (mp0) REVERT: M 103 TRP cc_start: 0.8213 (m100) cc_final: 0.7959 (m-10) REVERT: N 21 THR cc_start: 0.8759 (m) cc_final: 0.8530 (t) REVERT: N 91 TYR cc_start: 0.7664 (m-80) cc_final: 0.7308 (m-10) REVERT: N 96 ARG cc_start: 0.9010 (ttp-110) cc_final: 0.8723 (ttp-110) REVERT: N 100 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6923 (mm-30) REVERT: N 103 TRP cc_start: 0.8229 (m100) cc_final: 0.8006 (m-10) REVERT: O 29 MET cc_start: 0.4723 (pmm) cc_final: 0.4246 (pmm) REVERT: O 69 ILE cc_start: 0.7772 (tp) cc_final: 0.7373 (tp) REVERT: O 100 TYR cc_start: 0.8608 (p90) cc_final: 0.8393 (p90) REVERT: R 54 ARG cc_start: 0.7516 (mpp80) cc_final: 0.7276 (mtm180) REVERT: G 79 TYR cc_start: 0.9130 (m-80) cc_final: 0.8922 (m-80) REVERT: G 82 LEU cc_start: 0.8563 (tp) cc_final: 0.8317 (tp) REVERT: H 34 MET cc_start: 0.8273 (ttp) cc_final: 0.8068 (ttm) REVERT: I 34 MET cc_start: 0.8307 (ttp) cc_final: 0.8026 (ttp) REVERT: I 86 ASP cc_start: 0.6572 (t0) cc_final: 0.6067 (t0) REVERT: J 38 TYR cc_start: 0.8670 (m-80) cc_final: 0.7866 (m-80) REVERT: K 47 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8627 (ttpp) REVERT: L 38 TYR cc_start: 0.8093 (m-80) cc_final: 0.7680 (m-80) REVERT: L 47 LYS cc_start: 0.8945 (ttpp) cc_final: 0.8664 (ttpt) outliers start: 3 outliers final: 0 residues processed: 627 average time/residue: 0.3719 time to fit residues: 360.8488 Evaluate side-chains 524 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 523 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 275 optimal weight: 30.0000 chunk 297 optimal weight: 0.0270 chunk 245 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 293 GLN B 293 GLN B 302 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN C 302 ASN C 374 HIS ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN M 60 ASN N 60 ASN O 60 ASN P 38 HIS Q 26 GLN Q 52 GLN R 26 GLN I 58 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 41 HIS L 39 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26130 Z= 0.199 Angle : 0.580 11.113 35478 Z= 0.283 Chirality : 0.045 0.372 4187 Planarity : 0.004 0.055 4401 Dihedral : 13.063 111.343 5154 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.49 (0.14), residues: 3072 helix: -0.07 (0.30), residues: 327 sheet: -0.86 (0.16), residues: 930 loop : -2.52 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP O 36 HIS 0.005 0.001 HIS C 66 PHE 0.010 0.001 PHE A 93 TYR 0.019 0.001 TYR D 638 ARG 0.006 0.000 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 611 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8825 (tpp) cc_final: 0.8005 (tpp) REVERT: A 161 MET cc_start: 0.8683 (tpp) cc_final: 0.8441 (tpp) REVERT: B 125 LEU cc_start: 0.9230 (tp) cc_final: 0.8988 (tp) REVERT: B 161 MET cc_start: 0.8841 (tpp) cc_final: 0.8432 (tpp) REVERT: C 125 LEU cc_start: 0.9253 (tp) cc_final: 0.8927 (tp) REVERT: C 153 GLU cc_start: 0.8794 (tp30) cc_final: 0.8453 (tp30) REVERT: C 434 MET cc_start: 0.9004 (ttm) cc_final: 0.8405 (ttm) REVERT: E 650 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7614 (mm-40) REVERT: F 540 GLN cc_start: 0.8596 (mp10) cc_final: 0.8149 (mp10) REVERT: M 69 ILE cc_start: 0.7625 (tp) cc_final: 0.7337 (tp) REVERT: M 91 TYR cc_start: 0.7305 (m-80) cc_final: 0.6915 (m-10) REVERT: N 96 ARG cc_start: 0.8959 (ttp-110) cc_final: 0.8711 (ttp-110) REVERT: N 100 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6807 (mm-30) REVERT: N 103 TRP cc_start: 0.8290 (m100) cc_final: 0.8067 (m-10) REVERT: O 69 ILE cc_start: 0.7709 (tp) cc_final: 0.7252 (tp) REVERT: O 100 TYR cc_start: 0.8695 (p90) cc_final: 0.8464 (p90) REVERT: P 46 LEU cc_start: 0.8983 (pt) cc_final: 0.8766 (pt) REVERT: R 90 MET cc_start: 0.8649 (tpp) cc_final: 0.8409 (tpp) REVERT: H 34 MET cc_start: 0.8316 (ttp) cc_final: 0.8053 (ttm) REVERT: I 34 MET cc_start: 0.8261 (ttp) cc_final: 0.8058 (ttp) REVERT: I 86 ASP cc_start: 0.6659 (t0) cc_final: 0.6125 (t0) REVERT: J 38 TYR cc_start: 0.8774 (m-80) cc_final: 0.7926 (m-80) REVERT: K 47 LYS cc_start: 0.8909 (ttpp) cc_final: 0.8648 (ttpt) REVERT: K 102 LEU cc_start: 0.7783 (tt) cc_final: 0.7502 (tt) REVERT: L 38 TYR cc_start: 0.8120 (m-80) cc_final: 0.7634 (m-80) REVERT: L 47 LYS cc_start: 0.9006 (ttpp) cc_final: 0.8593 (ttpt) outliers start: 1 outliers final: 0 residues processed: 612 average time/residue: 0.3818 time to fit residues: 362.2106 Evaluate side-chains 492 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 144 optimal weight: 0.0060 chunk 262 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 293 GLN A 302 ASN B 293 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN M 60 ASN N 60 ASN P 89 HIS Q 26 GLN Q 38 HIS Q 52 GLN R 26 GLN J 6 GLN J 39 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26130 Z= 0.255 Angle : 0.617 11.186 35478 Z= 0.302 Chirality : 0.046 0.351 4187 Planarity : 0.005 0.209 4401 Dihedral : 11.444 113.964 5154 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.04 % Allowed : 5.12 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 3072 helix: 0.17 (0.31), residues: 321 sheet: -0.70 (0.16), residues: 1011 loop : -2.50 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP M 36 HIS 0.008 0.001 HIS Q 38 PHE 0.022 0.002 PHE J 64 TYR 0.031 0.002 TYR F 638 ARG 0.024 0.000 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 583 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8723 (tpp) cc_final: 0.8102 (tpp) REVERT: A 161 MET cc_start: 0.8696 (tpp) cc_final: 0.8370 (tpp) REVERT: B 35 TRP cc_start: 0.7326 (m-90) cc_final: 0.7108 (m-90) REVERT: B 125 LEU cc_start: 0.9239 (tp) cc_final: 0.8970 (tp) REVERT: B 161 MET cc_start: 0.8863 (tpp) cc_final: 0.8550 (tpp) REVERT: B 475 MET cc_start: 0.8567 (ptt) cc_final: 0.8345 (ptt) REVERT: C 125 LEU cc_start: 0.9287 (tp) cc_final: 0.8992 (tp) REVERT: C 153 GLU cc_start: 0.8836 (tp30) cc_final: 0.8560 (tp30) REVERT: C 434 MET cc_start: 0.8923 (ttm) cc_final: 0.8327 (ttm) REVERT: C 474 ASP cc_start: 0.7255 (p0) cc_final: 0.7016 (p0) REVERT: F 540 GLN cc_start: 0.8634 (mp10) cc_final: 0.8261 (mp10) REVERT: M 91 TYR cc_start: 0.7096 (m-80) cc_final: 0.6745 (m-10) REVERT: M 100 GLU cc_start: 0.8030 (mp0) cc_final: 0.7653 (mp0) REVERT: N 96 ARG cc_start: 0.8941 (ttp-110) cc_final: 0.8655 (ttp-110) REVERT: N 100 GLU cc_start: 0.7578 (mm-30) cc_final: 0.6857 (mm-30) REVERT: N 103 TRP cc_start: 0.8383 (m100) cc_final: 0.8066 (m-10) REVERT: P 46 LEU cc_start: 0.8915 (pt) cc_final: 0.8714 (pt) REVERT: G 34 MET cc_start: 0.8268 (ttp) cc_final: 0.7889 (ttm) REVERT: G 82 LEU cc_start: 0.8761 (tp) cc_final: 0.8360 (tp) REVERT: H 34 MET cc_start: 0.8348 (ttp) cc_final: 0.8063 (ttm) REVERT: H 86 ASP cc_start: 0.6984 (t0) cc_final: 0.6439 (t0) REVERT: I 86 ASP cc_start: 0.6806 (t0) cc_final: 0.6264 (t0) REVERT: J 38 TYR cc_start: 0.8661 (m-80) cc_final: 0.7787 (m-80) REVERT: J 48 LEU cc_start: 0.8468 (tp) cc_final: 0.8162 (tp) REVERT: K 47 LYS cc_start: 0.9097 (ttpp) cc_final: 0.8763 (ttpt) REVERT: L 38 TYR cc_start: 0.8191 (m-80) cc_final: 0.7748 (m-10) REVERT: L 47 LYS cc_start: 0.9053 (ttpp) cc_final: 0.8797 (ttpt) outliers start: 1 outliers final: 0 residues processed: 584 average time/residue: 0.3638 time to fit residues: 331.1672 Evaluate side-chains 483 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 149 optimal weight: 0.0470 chunk 262 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 258 GLN A 293 GLN B 293 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN P 26 GLN Q 26 GLN Q 50 ASN Q 52 GLN Q 89 HIS R 26 GLN R 89 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 6 GLN L 39 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26130 Z= 0.291 Angle : 0.640 10.702 35478 Z= 0.319 Chirality : 0.046 0.326 4187 Planarity : 0.005 0.190 4401 Dihedral : 10.357 112.142 5154 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.27 (0.14), residues: 3072 helix: 0.17 (0.30), residues: 321 sheet: -0.70 (0.16), residues: 1032 loop : -2.45 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 36 HIS 0.007 0.001 HIS C 216 PHE 0.022 0.002 PHE J 64 TYR 0.029 0.002 TYR F 638 ARG 0.022 0.001 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 590 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8674 (tpp) cc_final: 0.8432 (tpp) REVERT: B 125 LEU cc_start: 0.9281 (tp) cc_final: 0.8738 (tt) REVERT: B 161 MET cc_start: 0.8856 (tpp) cc_final: 0.8574 (tpp) REVERT: B 307 ILE cc_start: 0.8687 (pt) cc_final: 0.8373 (pt) REVERT: C 125 LEU cc_start: 0.9290 (tp) cc_final: 0.8986 (tp) REVERT: C 163 THR cc_start: 0.8269 (m) cc_final: 0.7959 (t) REVERT: C 434 MET cc_start: 0.8877 (ttm) cc_final: 0.8447 (ttm) REVERT: E 626 MET cc_start: 0.7321 (tpp) cc_final: 0.7091 (tpp) REVERT: E 653 GLN cc_start: 0.8171 (mt0) cc_final: 0.7845 (mm-40) REVERT: F 540 GLN cc_start: 0.8714 (mp10) cc_final: 0.8304 (mp10) REVERT: N 96 ARG cc_start: 0.8982 (ttp-110) cc_final: 0.8655 (ttp-110) REVERT: N 103 TRP cc_start: 0.8333 (m100) cc_final: 0.8092 (m-10) REVERT: P 26 GLN cc_start: 0.8636 (mm-40) cc_final: 0.7891 (mm-40) REVERT: P 35 TRP cc_start: 0.8627 (m100) cc_final: 0.8412 (m100) REVERT: P 46 LEU cc_start: 0.8856 (pt) cc_final: 0.8652 (pt) REVERT: P 90 MET cc_start: 0.8666 (tpp) cc_final: 0.8315 (ttt) REVERT: Q 31 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7642 (mtm110) REVERT: Q 79 GLU cc_start: 0.7618 (mp0) cc_final: 0.7407 (mp0) REVERT: R 66 ASP cc_start: 0.7955 (t0) cc_final: 0.7559 (t0) REVERT: G 34 MET cc_start: 0.8250 (ttp) cc_final: 0.7860 (ttm) REVERT: H 34 MET cc_start: 0.8409 (ttp) cc_final: 0.8138 (ttm) REVERT: H 86 ASP cc_start: 0.7148 (t0) cc_final: 0.6640 (t0) REVERT: I 81 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7485 (mm-30) REVERT: I 86 ASP cc_start: 0.7026 (t0) cc_final: 0.6362 (t0) REVERT: K 47 LYS cc_start: 0.9148 (ttpp) cc_final: 0.8805 (ttpt) REVERT: L 38 TYR cc_start: 0.8282 (m-80) cc_final: 0.7863 (m-10) REVERT: L 47 LYS cc_start: 0.9065 (ttpp) cc_final: 0.8623 (ttpt) outliers start: 1 outliers final: 1 residues processed: 590 average time/residue: 0.3980 time to fit residues: 363.4534 Evaluate side-chains 471 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 470 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 293 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 293 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Q 26 GLN Q 52 GLN R 26 GLN R 38 HIS H 64 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN K 6 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26130 Z= 0.195 Angle : 0.584 10.606 35478 Z= 0.294 Chirality : 0.045 0.321 4187 Planarity : 0.006 0.281 4401 Dihedral : 9.522 109.992 5154 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.18 (0.14), residues: 3072 helix: 0.30 (0.31), residues: 321 sheet: -0.63 (0.16), residues: 978 loop : -2.37 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 96 HIS 0.005 0.001 HIS P 89 PHE 0.021 0.001 PHE J 64 TYR 0.024 0.001 TYR F 638 ARG 0.014 0.000 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 598 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8357 (ptt) cc_final: 0.8079 (ttp) REVERT: B 35 TRP cc_start: 0.7525 (m100) cc_final: 0.7321 (m100) REVERT: B 125 LEU cc_start: 0.9243 (tp) cc_final: 0.8976 (tp) REVERT: B 161 MET cc_start: 0.8833 (tpp) cc_final: 0.8523 (tpp) REVERT: B 307 ILE cc_start: 0.8634 (pt) cc_final: 0.8326 (pt) REVERT: B 475 MET cc_start: 0.8612 (ptt) cc_final: 0.8367 (ptt) REVERT: C 125 LEU cc_start: 0.9265 (tp) cc_final: 0.8968 (tp) REVERT: C 163 THR cc_start: 0.8030 (m) cc_final: 0.7793 (t) REVERT: C 434 MET cc_start: 0.8836 (ttm) cc_final: 0.8233 (ttm) REVERT: D 630 GLN cc_start: 0.8018 (pt0) cc_final: 0.7788 (pt0) REVERT: E 647 GLU cc_start: 0.8169 (pt0) cc_final: 0.7911 (pt0) REVERT: F 540 GLN cc_start: 0.8662 (mp10) cc_final: 0.8276 (mp10) REVERT: F 626 MET cc_start: 0.7424 (tpp) cc_final: 0.7165 (tpp) REVERT: M 100 GLU cc_start: 0.8011 (mp0) cc_final: 0.7603 (mp0) REVERT: N 96 ARG cc_start: 0.8972 (ttp-110) cc_final: 0.8673 (ttp-110) REVERT: N 103 TRP cc_start: 0.8289 (m100) cc_final: 0.7982 (m-10) REVERT: O 69 ILE cc_start: 0.7901 (tp) cc_final: 0.7530 (tp) REVERT: O 100 TYR cc_start: 0.8821 (p90) cc_final: 0.8573 (p90) REVERT: Q 31 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7651 (mtm110) REVERT: G 82 LEU cc_start: 0.8756 (tp) cc_final: 0.8342 (tp) REVERT: G 83 ARG cc_start: 0.6898 (mmt90) cc_final: 0.6484 (mpt-90) REVERT: H 34 MET cc_start: 0.8300 (ttp) cc_final: 0.8012 (ttm) REVERT: H 86 ASP cc_start: 0.7080 (t0) cc_final: 0.6559 (t0) REVERT: I 86 ASP cc_start: 0.6896 (t0) cc_final: 0.6281 (t0) REVERT: J 38 TYR cc_start: 0.8723 (m-80) cc_final: 0.7950 (m-80) REVERT: J 71 ASN cc_start: 0.6392 (t0) cc_final: 0.6140 (t0) REVERT: K 47 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8810 (ttpt) REVERT: L 38 TYR cc_start: 0.8269 (m-80) cc_final: 0.7923 (m-10) REVERT: L 47 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8801 (ttpt) outliers start: 0 outliers final: 0 residues processed: 598 average time/residue: 0.3643 time to fit residues: 337.7198 Evaluate side-chains 492 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 287 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 GLN R 26 GLN R 38 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 6 GLN L 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26130 Z= 0.293 Angle : 0.650 10.527 35478 Z= 0.327 Chirality : 0.046 0.316 4187 Planarity : 0.005 0.169 4401 Dihedral : 9.245 110.467 5154 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.22 (0.14), residues: 3072 helix: 0.44 (0.30), residues: 315 sheet: -0.70 (0.16), residues: 1017 loop : -2.43 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 96 HIS 0.005 0.001 HIS C 66 PHE 0.019 0.002 PHE J 64 TYR 0.022 0.002 TYR F 638 ARG 0.014 0.001 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 591 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8538 (tpp) cc_final: 0.8203 (tpp) REVERT: B 35 TRP cc_start: 0.7734 (m100) cc_final: 0.7313 (m100) REVERT: B 125 LEU cc_start: 0.9308 (tp) cc_final: 0.8992 (tp) REVERT: B 161 MET cc_start: 0.8863 (tpp) cc_final: 0.8589 (tpp) REVERT: B 307 ILE cc_start: 0.8638 (pt) cc_final: 0.8345 (pt) REVERT: C 125 LEU cc_start: 0.9220 (tp) cc_final: 0.8897 (tp) REVERT: C 434 MET cc_start: 0.8808 (ttm) cc_final: 0.8247 (ttm) REVERT: M 100 GLU cc_start: 0.8066 (mp0) cc_final: 0.7685 (mp0) REVERT: N 96 ARG cc_start: 0.8920 (ttp-110) cc_final: 0.8596 (ttp-110) REVERT: N 103 TRP cc_start: 0.8433 (m100) cc_final: 0.7830 (m-10) REVERT: O 69 ILE cc_start: 0.8065 (tp) cc_final: 0.7642 (tp) REVERT: P 35 TRP cc_start: 0.8742 (m100) cc_final: 0.8481 (m100) REVERT: Q 31 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7757 (mtm110) REVERT: Q 79 GLU cc_start: 0.7667 (mp0) cc_final: 0.7466 (mp0) REVERT: H 34 MET cc_start: 0.8414 (ttp) cc_final: 0.8100 (ttm) REVERT: H 86 ASP cc_start: 0.7124 (t0) cc_final: 0.6720 (t0) REVERT: I 86 ASP cc_start: 0.7126 (t0) cc_final: 0.6483 (t0) REVERT: K 47 LYS cc_start: 0.9175 (ttpp) cc_final: 0.8574 (ttpt) REVERT: L 38 TYR cc_start: 0.8360 (m-80) cc_final: 0.7971 (m-10) REVERT: L 47 LYS cc_start: 0.9037 (ttpp) cc_final: 0.8673 (ttpt) outliers start: 0 outliers final: 0 residues processed: 591 average time/residue: 0.3771 time to fit residues: 345.5887 Evaluate side-chains 488 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 144 optimal weight: 0.0270 chunk 27 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 287 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN Q 26 GLN R 26 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26130 Z= 0.221 Angle : 0.600 10.558 35478 Z= 0.305 Chirality : 0.045 0.314 4187 Planarity : 0.004 0.125 4401 Dihedral : 9.071 111.059 5154 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.13 (0.14), residues: 3072 helix: 0.47 (0.30), residues: 321 sheet: -0.56 (0.16), residues: 981 loop : -2.39 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 47 HIS 0.005 0.001 HIS B 66 PHE 0.026 0.001 PHE R 95B TYR 0.033 0.001 TYR N 59 ARG 0.012 0.000 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 583 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8818 (tpp) cc_final: 0.7873 (tpp) REVERT: A 474 ASP cc_start: 0.7625 (p0) cc_final: 0.7392 (p0) REVERT: A 475 MET cc_start: 0.8368 (ptt) cc_final: 0.7993 (ttp) REVERT: B 35 TRP cc_start: 0.7634 (m100) cc_final: 0.6428 (m-10) REVERT: B 125 LEU cc_start: 0.9269 (tp) cc_final: 0.8993 (tp) REVERT: B 161 MET cc_start: 0.8837 (tpp) cc_final: 0.8531 (tpp) REVERT: B 307 ILE cc_start: 0.8616 (pt) cc_final: 0.8322 (pt) REVERT: C 125 LEU cc_start: 0.9269 (tp) cc_final: 0.8957 (tp) REVERT: C 434 MET cc_start: 0.8805 (ttm) cc_final: 0.8227 (ttm) REVERT: M 100 GLU cc_start: 0.8036 (mp0) cc_final: 0.7726 (mp0) REVERT: N 47 TRP cc_start: 0.8667 (t60) cc_final: 0.7854 (t60) REVERT: N 96 ARG cc_start: 0.8953 (ttp-110) cc_final: 0.8607 (ttp-110) REVERT: N 103 TRP cc_start: 0.8368 (m100) cc_final: 0.7917 (m-10) REVERT: P 35 TRP cc_start: 0.8759 (m100) cc_final: 0.8426 (m100) REVERT: P 36 TYR cc_start: 0.8481 (m-80) cc_final: 0.8116 (m-80) REVERT: P 46 LEU cc_start: 0.8904 (pt) cc_final: 0.8564 (pt) REVERT: R 66 ASP cc_start: 0.7843 (t0) cc_final: 0.7553 (t0) REVERT: H 34 MET cc_start: 0.8340 (ttp) cc_final: 0.8059 (ttm) REVERT: H 86 ASP cc_start: 0.7098 (t0) cc_final: 0.6585 (t0) REVERT: I 86 ASP cc_start: 0.7105 (t0) cc_final: 0.6536 (t0) REVERT: K 47 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8821 (ttpt) REVERT: L 38 TYR cc_start: 0.8335 (m-80) cc_final: 0.7985 (m-10) REVERT: L 47 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8833 (ttpt) outliers start: 0 outliers final: 0 residues processed: 583 average time/residue: 0.3819 time to fit residues: 343.9761 Evaluate side-chains 487 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 487 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 0.0670 chunk 279 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 272 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 213 optimal weight: 0.0770 chunk 83 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 257 optimal weight: 0.9990 chunk 271 optimal weight: 3.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN R 26 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN K 6 GLN K 39 GLN L 6 GLN L 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26130 Z= 0.163 Angle : 0.586 10.551 35478 Z= 0.296 Chirality : 0.044 0.314 4187 Planarity : 0.005 0.262 4401 Dihedral : 8.778 115.674 5154 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.00 (0.14), residues: 3072 helix: 0.72 (0.31), residues: 312 sheet: -0.55 (0.16), residues: 975 loop : -2.26 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP O 103 HIS 0.005 0.001 HIS B 66 PHE 0.022 0.001 PHE R 95B TYR 0.022 0.001 TYR D 638 ARG 0.006 0.000 ARG E 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 593 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8638 (tpp) cc_final: 0.7756 (tpp) REVERT: A 474 ASP cc_start: 0.7624 (p0) cc_final: 0.7375 (p0) REVERT: A 475 MET cc_start: 0.8362 (ptt) cc_final: 0.8016 (ttp) REVERT: B 35 TRP cc_start: 0.7626 (m100) cc_final: 0.6406 (m-10) REVERT: B 125 LEU cc_start: 0.9288 (tp) cc_final: 0.9006 (tp) REVERT: B 161 MET cc_start: 0.8815 (tpp) cc_final: 0.8476 (tpp) REVERT: B 258 GLN cc_start: 0.8513 (mt0) cc_final: 0.8311 (mt0) REVERT: B 307 ILE cc_start: 0.8580 (pt) cc_final: 0.8318 (pt) REVERT: B 373 THR cc_start: 0.9267 (t) cc_final: 0.9017 (t) REVERT: B 475 MET cc_start: 0.8660 (ptt) cc_final: 0.8409 (ptt) REVERT: C 125 LEU cc_start: 0.9217 (tp) cc_final: 0.8895 (tp) REVERT: C 163 THR cc_start: 0.8264 (m) cc_final: 0.7923 (t) REVERT: C 434 MET cc_start: 0.8781 (ttm) cc_final: 0.8187 (ttm) REVERT: F 617 ARG cc_start: 0.7439 (mtt180) cc_final: 0.7188 (mtt180) REVERT: M 100 GLU cc_start: 0.8082 (mp0) cc_final: 0.7751 (mp0) REVERT: N 47 TRP cc_start: 0.8671 (t60) cc_final: 0.7834 (t60) REVERT: N 96 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8622 (ttp-110) REVERT: N 103 TRP cc_start: 0.8317 (m100) cc_final: 0.7965 (m-10) REVERT: P 30 SER cc_start: 0.8301 (m) cc_final: 0.8044 (m) REVERT: P 35 TRP cc_start: 0.8695 (m100) cc_final: 0.8414 (m100) REVERT: P 36 TYR cc_start: 0.8437 (m-80) cc_final: 0.8006 (m-80) REVERT: P 46 LEU cc_start: 0.8872 (pt) cc_final: 0.8523 (pt) REVERT: P 70 ARG cc_start: 0.8841 (tpp80) cc_final: 0.8618 (tpp80) REVERT: Q 79 GLU cc_start: 0.7694 (mp0) cc_final: 0.7416 (mp0) REVERT: G 83 ARG cc_start: 0.6851 (mmt90) cc_final: 0.6426 (mpt-90) REVERT: H 86 ASP cc_start: 0.7028 (t0) cc_final: 0.6525 (t0) REVERT: I 81 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7365 (mm-30) REVERT: I 86 ASP cc_start: 0.6977 (t0) cc_final: 0.6309 (t0) REVERT: J 38 TYR cc_start: 0.8843 (m-80) cc_final: 0.7716 (m-10) REVERT: K 47 LYS cc_start: 0.9137 (ttpp) cc_final: 0.8470 (ttpt) REVERT: L 38 TYR cc_start: 0.8085 (m-80) cc_final: 0.7696 (m-10) outliers start: 0 outliers final: 0 residues processed: 593 average time/residue: 0.3597 time to fit residues: 332.7801 Evaluate side-chains 499 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 0.4980 chunk 287 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 200 optimal weight: 9.9990 chunk 301 optimal weight: 0.3980 chunk 277 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN N 60 ASN Q 26 GLN R 26 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26130 Z= 0.169 Angle : 0.582 10.731 35478 Z= 0.293 Chirality : 0.044 0.311 4187 Planarity : 0.003 0.037 4401 Dihedral : 8.492 111.463 5154 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.89 (0.14), residues: 3072 helix: 0.90 (0.31), residues: 306 sheet: -0.48 (0.17), residues: 957 loop : -2.18 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP I 50 HIS 0.005 0.001 HIS C 66 PHE 0.022 0.001 PHE R 95B TYR 0.021 0.001 TYR D 638 ARG 0.017 0.000 ARG O 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 586 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8577 (tpp) cc_final: 0.7726 (tpp) REVERT: A 474 ASP cc_start: 0.7616 (p0) cc_final: 0.7403 (p0) REVERT: A 475 MET cc_start: 0.8384 (ptt) cc_final: 0.8026 (ttp) REVERT: B 35 TRP cc_start: 0.7557 (m100) cc_final: 0.6269 (m-10) REVERT: B 125 LEU cc_start: 0.9283 (tp) cc_final: 0.9001 (tp) REVERT: B 161 MET cc_start: 0.8791 (tpp) cc_final: 0.8390 (tpp) REVERT: B 258 GLN cc_start: 0.8575 (mt0) cc_final: 0.8362 (mt0) REVERT: B 307 ILE cc_start: 0.8603 (pt) cc_final: 0.8339 (pt) REVERT: B 475 MET cc_start: 0.8665 (ptt) cc_final: 0.8427 (ptt) REVERT: C 104 MET cc_start: 0.8805 (tpp) cc_final: 0.7666 (tpp) REVERT: C 125 LEU cc_start: 0.9216 (tp) cc_final: 0.8897 (tp) REVERT: C 163 THR cc_start: 0.8268 (m) cc_final: 0.7950 (t) REVERT: C 434 MET cc_start: 0.8786 (ttm) cc_final: 0.8177 (ttm) REVERT: E 650 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7423 (mm-40) REVERT: F 540 GLN cc_start: 0.8399 (mp10) cc_final: 0.8084 (mp10) REVERT: M 100 GLU cc_start: 0.8080 (mp0) cc_final: 0.7726 (mp0) REVERT: N 47 TRP cc_start: 0.8693 (t60) cc_final: 0.7802 (t60) REVERT: N 96 ARG cc_start: 0.8909 (ttp-110) cc_final: 0.8654 (ttp-110) REVERT: N 103 TRP cc_start: 0.8419 (m100) cc_final: 0.7920 (m-10) REVERT: O 100 TYR cc_start: 0.9008 (p90) cc_final: 0.8783 (p90) REVERT: P 30 SER cc_start: 0.8428 (m) cc_final: 0.8209 (m) REVERT: P 35 TRP cc_start: 0.8688 (m100) cc_final: 0.8427 (m100) REVERT: P 36 TYR cc_start: 0.8438 (m-80) cc_final: 0.8041 (m-80) REVERT: P 46 LEU cc_start: 0.8911 (pt) cc_final: 0.8574 (pt) REVERT: P 70 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8631 (tpp80) REVERT: R 66 ASP cc_start: 0.8015 (t0) cc_final: 0.7720 (t0) REVERT: H 86 ASP cc_start: 0.7032 (t0) cc_final: 0.6517 (t0) REVERT: I 86 ASP cc_start: 0.7028 (t0) cc_final: 0.6442 (t0) REVERT: J 38 TYR cc_start: 0.8839 (m-80) cc_final: 0.7795 (m-10) REVERT: K 47 LYS cc_start: 0.9217 (ttpp) cc_final: 0.8907 (ttpt) REVERT: L 38 TYR cc_start: 0.7915 (m-80) cc_final: 0.7380 (m-10) outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.3701 time to fit residues: 338.8863 Evaluate side-chains 499 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 114 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN M 60 ASN Q 26 GLN R 26 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 71 ASN K 6 GLN K 39 GLN L 6 GLN L 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109093 restraints weight = 45442.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.109146 restraints weight = 30583.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.109713 restraints weight = 33472.092| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 26130 Z= 0.401 Angle : 0.737 10.615 35478 Z= 0.370 Chirality : 0.049 0.322 4187 Planarity : 0.004 0.045 4401 Dihedral : 9.186 122.731 5154 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.04 % Allowed : 0.67 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.13 (0.14), residues: 3072 helix: 0.52 (0.30), residues: 306 sheet: -0.65 (0.16), residues: 1023 loop : -2.36 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP I 50 HIS 0.006 0.002 HIS R 89 PHE 0.023 0.002 PHE J 64 TYR 0.024 0.002 TYR C 435 ARG 0.010 0.001 ARG E 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6182.21 seconds wall clock time: 113 minutes 3.69 seconds (6783.69 seconds total)