Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 14:55:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/04_2023/7ugo_26492_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/04_2023/7ugo_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_26492/04_2023/7ugo_26492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/04_2023/7ugo_26492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/04_2023/7ugo_26492_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugo_26492/04_2023/7ugo_26492_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 12.74, per 1000 atoms: 0.50 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: 11.97 Conformation dependent library (CDL) restraints added in 3.9 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: 1.64 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: 8.79 Time building geometry restraints manager: 12.71 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 - 17.84: 13684 17.84 - 35.68: 1023 35.68 - 53.52: 162 53.52 - 71.36: 23 71.36 - 89.19: 18 Dihedral angle restraints: 14910 sinusoidal: 5910 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 14907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.944: 4164 0.944 - 1.887: 5 1.887 - 2.831: 4 2.831 - 3.774: 6 3.774 - 4.718: 7 Chirality restraints: 4186 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 4183 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.980 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 64.840 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.410 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: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.710 ------------------------------------------------------------------------------- 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 4186 Planarity : 0.004 0.207 4401 Dihedral : 12.557 89.195 9018 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 % 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 *********************** 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 : 3.152 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 outliers start: 4 outliers final: 1 residues processed: 723 average time/residue: 0.4342 time to fit residues: 466.3630 Evaluate side-chains 520 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 519 time to evaluate : 2.989 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2088 time to fit residues: 4.4507 ------------------------------------------------------------------------------- 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: 10.0000 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: 7.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN L 39 GLN L 81 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 26130 Z= 0.160 Angle : 0.605 13.109 35478 Z= 0.289 Chirality : 0.046 0.477 4186 Planarity : 0.003 0.049 4401 Dihedral : 3.882 33.300 3387 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 0.11 % 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: -0.49 (0.29), residues: 342 sheet: -1.11 (0.16), residues: 909 loop : -2.78 (0.12), residues: 1821 *********************** 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 623 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 620 time to evaluate : 3.034 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 outliers start: 3 outliers final: 0 residues processed: 623 average time/residue: 0.3926 time to fit residues: 378.0071 Evaluate side-chains 512 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 2.905 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7914 ------------------------------------------------------------------------------- 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: 0.9990 chunk 85 optimal weight: 0.0370 chunk 229 optimal weight: 0.1980 chunk 187 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 275 optimal weight: 30.0000 chunk 297 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 overall best weight: 1.2464 ------------------------------------------------------------------------------- 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 C 293 GLN C 302 ASN C 374 HIS ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN M 60 ASN N 60 ASN O 60 ASN Q 26 GLN Q 38 HIS Q 52 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 26130 Z= 0.188 Angle : 0.564 10.459 35478 Z= 0.280 Chirality : 0.044 0.423 4186 Planarity : 0.004 0.059 4401 Dihedral : 4.009 32.508 3387 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.04 % 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: -0.01 (0.31), residues: 327 sheet: -0.86 (0.16), residues: 930 loop : -2.52 (0.13), residues: 1815 *********************** 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 609 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 608 time to evaluate : 3.102 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 outliers start: 1 outliers final: 0 residues processed: 609 average time/residue: 0.3933 time to fit residues: 369.2290 Evaluate side-chains 485 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 3.149 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2534 ------------------------------------------------------------------------------- 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: 8.9990 chunk 207 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 185 optimal weight: 8.9990 chunk 276 optimal weight: 20.0000 chunk 292 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 A 302 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN D 591 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN M 60 ASN N 60 ASN N 76 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 26130 Z= 0.399 Angle : 0.731 11.189 35478 Z= 0.361 Chirality : 0.050 0.493 4186 Planarity : 0.005 0.188 4401 Dihedral : 4.854 35.753 3387 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 0.07 % 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: 0.06 (0.30), residues: 315 sheet: -0.75 (0.16), residues: 1029 loop : -2.68 (0.13), residues: 1728 *********************** 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 578 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 576 time to evaluate : 3.171 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 outliers start: 2 outliers final: 0 residues processed: 578 average time/residue: 0.3888 time to fit residues: 346.1448 Evaluate side-chains 471 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 2.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9887 ------------------------------------------------------------------------------- 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: 5.9990 chunk 166 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 218 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 249 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 262 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** 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** N 60 ASN ** O 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 HIS Q 26 GLN Q 89 HIS R 26 GLN R 89 HIS H 64 GLN J 6 GLN K 6 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 26130 Z= 0.189 Angle : 0.599 11.117 35478 Z= 0.301 Chirality : 0.045 0.407 4186 Planarity : 0.005 0.194 4401 Dihedral : 4.535 35.120 3387 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.04 % 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: 0.12 (0.30), residues: 321 sheet: -0.65 (0.16), residues: 987 loop : -2.52 (0.13), residues: 1764 *********************** 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 603 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 602 time to evaluate : 2.820 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 outliers start: 1 outliers final: 0 residues processed: 602 average time/residue: 0.4064 time to fit residues: 381.5502 Evaluate side-chains 477 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 3.025 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3667 ------------------------------------------------------------------------------- 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: 2.9990 chunk 263 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 171 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 243 optimal weight: 0.9980 chunk 135 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 258 GLN A 293 GLN B 114 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN D 577 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Q 26 GLN R 26 GLN R 38 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8106 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 26130 Z= 0.179 Angle : 0.575 10.826 35478 Z= 0.292 Chirality : 0.044 0.392 4186 Planarity : 0.004 0.035 4401 Dihedral : 4.483 40.335 3387 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer Outliers : 0.11 % 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: -2.19 (0.14), residues: 3072 helix: 0.32 (0.31), residues: 321 sheet: -0.61 (0.16), residues: 987 loop : -2.42 (0.13), residues: 1764 *********************** 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 592 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 589 time to evaluate : 2.961 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 outliers start: 3 outliers final: 0 residues processed: 592 average time/residue: 0.3692 time to fit residues: 342.5935 Evaluate side-chains 477 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 2.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7610 ------------------------------------------------------------------------------- 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: 5.9990 chunk 165 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 292 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN N 60 ASN Q 26 GLN R 26 GLN R 38 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 39 GLN L 6 GLN L 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 26130 Z= 0.266 Angle : 0.617 10.722 35478 Z= 0.312 Chirality : 0.045 0.384 4186 Planarity : 0.004 0.044 4401 Dihedral : 4.640 37.903 3387 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer Outliers : 0.04 % 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: -2.21 (0.14), residues: 3072 helix: 0.26 (0.30), residues: 321 sheet: -0.58 (0.16), residues: 1002 loop : -2.46 (0.13), residues: 1749 *********************** 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 590 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 589 time to evaluate : 2.838 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 outliers start: 1 outliers final: 0 residues processed: 590 average time/residue: 0.3744 time to fit residues: 347.3911 Evaluate side-chains 478 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 2.984 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9341 ------------------------------------------------------------------------------- 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: 7.9990 chunk 116 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 144 optimal weight: 0.0020 chunk 27 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 114 GLN B 258 GLN B 293 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN Q 26 GLN R 26 GLN R 38 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 26130 Z= 0.162 Angle : 0.570 10.562 35478 Z= 0.291 Chirality : 0.043 0.380 4186 Planarity : 0.004 0.036 4401 Dihedral : 4.506 35.894 3387 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.04 % 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: -2.09 (0.14), residues: 3072 helix: 0.32 (0.30), residues: 330 sheet: -0.50 (0.16), residues: 981 loop : -2.37 (0.13), residues: 1761 *********************** 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 587 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 586 time to evaluate : 3.336 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 outliers start: 1 outliers final: 0 residues processed: 587 average time/residue: 0.3869 time to fit residues: 358.3320 Evaluate side-chains 478 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0341 ------------------------------------------------------------------------------- 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: 0.4980 chunk 279 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 213 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 245 optimal weight: 0.0670 chunk 257 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- 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 A 293 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN M 60 ASN Q 26 GLN R 26 GLN R 38 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 39 GLN L 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 26130 Z= 0.172 Angle : 0.570 10.484 35478 Z= 0.291 Chirality : 0.044 0.380 4186 Planarity : 0.004 0.037 4401 Dihedral : 4.476 35.272 3387 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 0.07 % 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: -2.02 (0.14), residues: 3072 helix: 0.51 (0.30), residues: 312 sheet: -0.55 (0.17), residues: 957 loop : -2.23 (0.13), residues: 1803 *********************** 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 587 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 585 time to evaluate : 3.060 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 outliers start: 2 outliers final: 1 residues processed: 586 average time/residue: 0.3720 time to fit residues: 344.0215 Evaluate side-chains 482 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 481 time to evaluate : 3.045 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2673 time to fit residues: 4.6109 ------------------------------------------------------------------------------- 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: 6.9990 chunk 287 optimal weight: 0.8980 chunk 175 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 chunk 200 optimal weight: 0.5980 chunk 301 optimal weight: 10.0000 chunk 277 optimal weight: 0.0070 chunk 240 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 293 GLN B 114 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN D 650 GLN F 630 GLN M 60 ASN N 60 ASN O 60 ASN Q 26 GLN R 26 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2836 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= 0.174 Angle : 0.570 10.331 35478 Z= 0.290 Chirality : 0.044 0.377 4186 Planarity : 0.004 0.036 4401 Dihedral : 4.462 38.045 3387 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.04 % 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: -1.94 (0.14), residues: 3072 helix: 0.53 (0.30), residues: 312 sheet: -0.50 (0.17), residues: 960 loop : -2.17 (0.13), residues: 1800 ********************** 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 581 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 580 time to evaluate : 3.029 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 outliers start: 1 outliers final: 0 residues processed: 581 average time/residue: 0.3771 time to fit residues: 346.8650 Evaluate side-chains 481 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 3.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7284 ------------------------------------------------------------------------------- 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: 20.0000 chunk 256 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 293 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN M 60 ASN N 60 ASN Q 26 GLN R 26 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111796 restraints weight = 46082.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.112189 restraints weight = 35613.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111954 restraints weight = 42128.256| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 26130 Z= 0.276 Angle : 0.639 10.213 35478 Z= 0.324 Chirality : 0.045 0.377 4186 Planarity : 0.004 0.040 4401 Dihedral : 4.745 37.956 3387 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 0.07 % 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: -2.03 (0.14), residues: 3072 helix: 0.13 (0.30), residues: 324 sheet: -0.48 (0.16), residues: 1002 loop : -2.27 (0.13), residues: 1746 =============================================================================== Job complete usr+sys time: 6115.97 seconds wall clock time: 111 minutes 44.31 seconds (6704.31 seconds total)