Starting phenix.real_space_refine on Fri Apr 12 07:09:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugp_26493/04_2024/7ugp_26493_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugp_26493/04_2024/7ugp_26493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugp_26493/04_2024/7ugp_26493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugp_26493/04_2024/7ugp_26493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugp_26493/04_2024/7ugp_26493_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugp_26493/04_2024/7ugp_26493_neut.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 146 5.16 5 C 15685 2.51 5 N 4284 2.21 5 O 4932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 474": "OD1" <-> "OD2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 429": "NH1" <-> "NH2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D GLU 621": "OE1" <-> "OE2" Residue "D GLU 654": "OE1" <-> "OE2" Residue "E GLU 584": "OE1" <-> "OE2" Residue "E GLU 654": "OE1" <-> "OE2" Residue "F GLU 584": "OE1" <-> "OE2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "M TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 53": "OD1" <-> "OD2" Residue "N TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 53": "OD1" <-> "OD2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 9": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "P TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 9": "NH1" <-> "NH2" Residue "Q ARG 20": "NH1" <-> "NH2" Residue "Q ARG 25": "NH1" <-> "NH2" Residue "Q TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q ASP 85": "OD1" <-> "OD2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 94": "NH1" <-> "NH2" Residue "Q PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 9": "NH1" <-> "NH2" Residue "R ARG 20": "NH1" <-> "NH2" Residue "R ARG 25": "NH1" <-> "NH2" Residue "R TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ASP 85": "OD1" <-> "OD2" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 94": "NH1" <-> "NH2" Residue "R PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 62": "OD1" <-> "OD2" Residue "J GLU 94": "OE1" <-> "OE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 62": "OD1" <-> "OD2" Residue "L GLU 94": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 25047 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3488 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 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: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3488 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 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: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3488 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 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: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} 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: "G" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} 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: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "K" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.56, per 1000 atoms: 0.50 Number of scatterers: 25047 At special positions: 0 Unit cell: (147.73, 157.289, 151.206, 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 146 16.00 O 4932 8.00 N 4284 7.00 C 15685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 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 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=2.02 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 126 " - pdb=" SG CYS B 196 " 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=1.73 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " 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=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " 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=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN V 4 " - " MAN V 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-4 " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA V 3 " - " MAN V 6 " " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 448 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 363 " " NAG A 608 " - " ASN A 234 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 160 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 448 " " NAG B 603 " - " ASN B 133 " " NAG B 604 " - " ASN B 276 " " NAG B 605 " - " ASN B 301 " " NAG B 606 " - " ASN B 392 " " NAG B 607 " - " ASN B 363 " " NAG B 608 " - " ASN B 234 " " NAG B 609 " - " ASN B 295 " " NAG B 610 " - " ASN B 160 " " NAG C 601 " - " ASN C 88 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 363 " " NAG C 607 " - " ASN C 234 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " 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 332 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN B 332 " " NAG W 1 " - " ASN B 156 " " NAG X 1 " - " ASN B 262 " " NAG Y 1 " - " ASN C 262 " " NAG Y 3 " - " ASN C 448 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 156 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.59 Conformation dependent library (CDL) restraints added in 4.3 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5694 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 62 sheets defined 14.0% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.454A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.068A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'B' and resid 99 through 115 Processing helix chain 'B' and resid 334 through 353 Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.101A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.980A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.085A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'D' and resid 529 through 535 removed outlier: 3.845A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 546 removed outlier: 3.806A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 595 removed outlier: 3.879A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.715A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 658 Processing helix chain 'E' and resid 529 through 535 removed outlier: 4.144A pdb=" N MET E 535 " --> pdb=" O GLY E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 546 removed outlier: 3.923A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER E 546 " --> pdb=" O ARG E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 595 removed outlier: 3.862A pdb=" N ILE E 573 " --> pdb=" O THR E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.678A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 658 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 538 through 546 removed outlier: 4.007A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER F 546 " --> pdb=" O ARG F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 595 removed outlier: 3.905A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.751A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 659 Processing helix chain 'M' and resid 60 through 64 removed outlier: 3.547A pdb=" N ASN M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 100D through 100H removed outlier: 3.662A pdb=" N GLY M 100H" --> pdb=" O VAL M 100E" (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 64 removed outlier: 3.500A pdb=" N ASN N 64 " --> pdb=" O PRO N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 100D through 100H removed outlier: 3.569A pdb=" N GLY N 100H" --> pdb=" O VAL N 100E" (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.781A pdb=" N ASP G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.791A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.807A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.780A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR D 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS D 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.012A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.164A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.875A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.636A pdb=" N MET A 271 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.198A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 494 through 499 removed outlier: 3.547A pdb=" N ALA B 497 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS E 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 94 removed outlier: 4.022A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 154 through 162 Processing sheet with id=AB6, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.136A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 259 through 261 removed outlier: 5.863A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 12.047A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 12.217A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.752A pdb=" N LEU B 285 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.217A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 12.047A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 304 through 307 Processing sheet with id=AC2, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.182A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 499 removed outlier: 3.546A pdb=" N ALA C 497 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR F 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AC5, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.044A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AC7, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC8, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.130A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.784A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.425A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.054A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.738A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 285 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 11.054A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.425A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AD3, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.202A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.678A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP M 34 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.678A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER M 100O" --> pdb=" O ARG M 96 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY M 98 " --> pdb=" O TYR M 100M" (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 20 through 23 removed outlier: 4.077A pdb=" N VAL M 20 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.680A pdb=" N THR N 107 " --> pdb=" O TYR N 90 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.680A pdb=" N THR N 107 " --> pdb=" O TYR N 90 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER N 100O" --> pdb=" O ARG N 96 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE N 100K" --> pdb=" O ARG N 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 20 through 23 removed outlier: 3.985A pdb=" N VAL N 20 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.723A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP O 34 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.723A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY O 98 " --> pdb=" O TYR O 100M" (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE O 100K" --> pdb=" O ARG O 100 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 20 through 22 removed outlier: 4.110A pdb=" N VAL O 20 " --> pdb=" O LEU O 80 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.623A pdb=" N THR G 110 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.623A pdb=" N THR G 110 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR G 94 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.798A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.791A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE I 102 " --> pdb=" O THR I 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.791A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.704A pdb=" N ARG P 9 " --> pdb=" O ARG P 103 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR P 105 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 19 through 21 Processing sheet with id=AF8, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.861A pdb=" N ARG Q 9 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N THR Q 105 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 19 through 21 Processing sheet with id=AG1, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.742A pdb=" N ARG R 9 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR R 105 " --> pdb=" O ARG R 9 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'R' and resid 19 through 21 Processing sheet with id=AG3, first strand: chain 'J' and resid 19 through 22 removed outlier: 3.505A pdb=" N ILE J 20 " --> pdb=" O LEU J 75 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER J 74 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 47 through 48 removed outlier: 3.782A pdb=" N TYR J 38 " --> pdb=" O TYR J 89 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 19 through 20 removed outlier: 3.775A pdb=" N ILE K 20 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU K 75 " --> pdb=" O ILE K 20 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER K 74 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 47 through 48 removed outlier: 3.765A pdb=" N TYR K 38 " --> pdb=" O TYR K 89 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.751A pdb=" N ILE L 20 " --> pdb=" O LEU L 75 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU L 75 " --> pdb=" O ILE L 20 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 47 through 48 removed outlier: 3.513A pdb=" N GLN L 39 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2055 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: 9.60 Time building geometry restraints manager: 10.49 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: 7919 1.34 - 1.47: 6342 1.47 - 1.59: 11112 1.59 - 1.71: 9 1.71 - 1.83: 202 Bond restraints: 25584 Sorted by residual: bond pdb=" C1 MAN Z 4 " pdb=" O5 MAN Z 4 " ideal model delta sigma weight residual 1.399 1.513 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C1 MAN Z 4 " pdb=" C2 MAN Z 4 " ideal model delta sigma weight residual 1.526 1.640 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C1 BMA U 3 " pdb=" C2 BMA U 3 " ideal model delta sigma weight residual 1.519 1.598 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C1 NAG C 604 " pdb=" O5 NAG C 604 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 25579 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.77: 836 106.77 - 114.25: 14914 114.25 - 121.72: 12444 121.72 - 129.19: 6310 129.19 - 136.66: 255 Bond angle restraints: 34759 Sorted by residual: angle pdb=" C THR N 83 " pdb=" N PRO N 84 " pdb=" CA PRO N 84 " ideal model delta sigma weight residual 119.05 128.95 -9.90 1.11e+00 8.12e-01 7.96e+01 angle pdb=" C ASN A 188 " pdb=" N THR A 189 " pdb=" CA THR A 189 " ideal model delta sigma weight residual 122.61 133.37 -10.76 1.56e+00 4.11e-01 4.76e+01 angle pdb=" C LYS B 117 " pdb=" N PRO B 118 " pdb=" CA PRO B 118 " ideal model delta sigma weight residual 118.85 125.15 -6.30 1.09e+00 8.42e-01 3.34e+01 angle pdb=" C LYS C 117 " pdb=" N PRO C 118 " pdb=" CA PRO C 118 " ideal model delta sigma weight residual 118.85 124.99 -6.14 1.09e+00 8.42e-01 3.18e+01 angle pdb=" C GLU B 267 " pdb=" N GLU B 268 " pdb=" CA GLU B 268 " ideal model delta sigma weight residual 121.54 132.18 -10.64 1.91e+00 2.74e-01 3.10e+01 ... (remaining 34754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.50: 14896 22.50 - 45.00: 945 45.00 - 67.50: 149 67.50 - 90.00: 60 90.00 - 112.51: 32 Dihedral angle restraints: 16082 sinusoidal: 7196 harmonic: 8886 Sorted by residual: 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 93.00 162.59 -69.59 1 1.00e+01 1.00e-02 6.25e+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 -140.70 54.70 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CA CYS A 119 " pdb=" C CYS A 119 " pdb=" N VAL A 120 " pdb=" CA VAL A 120 " ideal model delta harmonic sigma weight residual -180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 16079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 3880 0.146 - 0.292: 139 0.292 - 0.439: 16 0.439 - 0.585: 7 0.585 - 0.731: 3 Chirality restraints: 4045 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN A 262 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C2 NAG Y 1 " pdb=" C1 NAG Y 1 " pdb=" C3 NAG Y 1 " pdb=" N2 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.49 -1.88 -0.61 2.00e-01 2.50e+01 9.27e+00 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C 262 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.76e+00 ... (remaining 4042 not shown) Planarity restraints: 4399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 49 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C TYR R 49 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR R 49 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN R 50 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 46 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C LEU R 46 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU R 46 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU R 47 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR O 83 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO O 84 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO O 84 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO O 84 " 0.040 5.00e-02 4.00e+02 ... (remaining 4396 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.65: 1 1.65 - 2.46: 99 2.46 - 3.27: 22781 3.27 - 4.09: 60984 4.09 - 4.90: 105978 Warning: very small nonbonded interaction distances. Nonbonded interactions: 189843 Sorted by model distance: nonbonded pdb=" CD2 TYR R 49 " pdb=" OD2 ASP R 53 " model vdw 0.835 3.340 nonbonded pdb=" CG TYR R 49 " pdb=" OD2 ASP R 53 " model vdw 1.782 3.260 nonbonded pdb=" CE2 TYR R 49 " pdb=" OD2 ASP R 53 " model vdw 1.888 3.340 nonbonded pdb=" CD2 TYR R 49 " pdb=" CG ASP R 53 " model vdw 1.915 3.570 nonbonded pdb=" O ALA E 526 " pdb=" CG2 THR E 627 " model vdw 2.020 3.460 ... (remaining 189838 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 601 through 609)) selection = (chain 'B' and (resid 32 through 506 or resid 601 through 609)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 523 through 529 or (resid 530 and (name N or name CA or na \ me C or name O or name CB )) or resid 531 through 664 or resid 701)) selection = (chain 'F' and (resid 523 through 529 or (resid 530 and (name N or name CA or na \ me C or name O or name CB )) or resid 531 through 664 or resid 701)) } 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' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 108)) selection = (chain 'Q' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 108)) selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'V' selection = chain 'Z' } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'U' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.470 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: 10.860 Check model and map are aligned: 0.340 Set scattering table: 0.250 Process input model: 65.850 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 25584 Z= 0.420 Angle : 0.995 12.097 34759 Z= 0.544 Chirality : 0.070 0.731 4045 Planarity : 0.007 0.073 4358 Dihedral : 16.081 112.506 10283 Min Nonbonded Distance : 0.835 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.52 % Allowed : 8.43 % Favored : 91.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.12), residues: 3036 helix: -3.82 (0.12), residues: 336 sheet: -2.47 (0.15), residues: 900 loop : -3.14 (0.11), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 628 HIS 0.012 0.001 HIS C 66 PHE 0.019 0.002 PHE A 159 TYR 0.013 0.001 TYR M 100B ARG 0.004 0.000 ARG D 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 374 time to evaluate : 2.595 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: B 191 TYR cc_start: 0.8069 (m-80) cc_final: 0.7829 (m-80) REVERT: B 475 MET cc_start: 0.6523 (mpp) cc_final: 0.5949 (mmt) REVERT: C 189 THR cc_start: 0.4330 (OUTLIER) cc_final: 0.4068 (t) REVERT: M 100 TYR cc_start: 0.8224 (m-80) cc_final: 0.8019 (m-10) REVERT: N 90 TYR cc_start: 0.8516 (m-80) cc_final: 0.8110 (m-80) REVERT: O 31 ASN cc_start: 0.6014 (t0) cc_final: 0.5752 (p0) REVERT: O 90 TYR cc_start: 0.8426 (m-80) cc_final: 0.8182 (m-80) REVERT: O 100 MET cc_start: 0.6872 (mpp) cc_final: 0.6534 (mpp) REVERT: G 98 LEU cc_start: 0.8746 (mt) cc_final: 0.8402 (mt) REVERT: H 98 LEU cc_start: 0.8516 (mt) cc_final: 0.8226 (mt) REVERT: I 98 LEU cc_start: 0.8755 (mt) cc_final: 0.8385 (mt) REVERT: P 85 ASP cc_start: 0.7293 (t0) cc_final: 0.7092 (t0) REVERT: P 86 TYR cc_start: 0.6881 (m-80) cc_final: 0.6680 (m-80) REVERT: R 85 ASP cc_start: 0.7125 (t0) cc_final: 0.6894 (t0) REVERT: R 86 TYR cc_start: 0.7049 (m-80) cc_final: 0.6814 (m-80) REVERT: K 18 VAL cc_start: 0.3362 (m) cc_final: 0.3091 (p) REVERT: K 68 LYS cc_start: 0.2774 (mtpt) cc_final: 0.2280 (tptt) REVERT: L 68 LYS cc_start: 0.3785 (mttt) cc_final: 0.2885 (tptm) outliers start: 14 outliers final: 3 residues processed: 388 average time/residue: 0.4551 time to fit residues: 259.9045 Evaluate side-chains 196 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 2.919 ------------------------------------------------------------------------------- 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: 10.0000 chunk 229 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 176 optimal weight: 7.9990 chunk 275 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 103 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS B 99 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 64 ASN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN G 6 GLN H 6 GLN I 6 GLN P 50 ASN P 51 ASN Q 38 HIS Q 51 ASN R 34 GLN R 38 HIS R 51 ASN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 81 GLN L 33 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 25584 Z= 0.526 Angle : 0.920 14.307 34759 Z= 0.457 Chirality : 0.058 0.473 4045 Planarity : 0.006 0.064 4358 Dihedral : 12.265 118.675 4706 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 0.67 % Allowed : 8.80 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.13), residues: 3036 helix: -0.79 (0.24), residues: 354 sheet: -2.53 (0.15), residues: 966 loop : -2.89 (0.12), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 631 HIS 0.008 0.002 HIS A 330 PHE 0.026 0.003 PHE C 53 TYR 0.026 0.002 TYR H 27 ARG 0.015 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 208 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.8014 (p0) REVERT: M 80 LEU cc_start: 0.7028 (tp) cc_final: 0.6698 (tt) REVERT: N 3 GLN cc_start: 0.6467 (tp40) cc_final: 0.5735 (pp30) REVERT: O 27 ASP cc_start: 0.5812 (p0) cc_final: 0.5580 (p0) REVERT: K 49 MET cc_start: 0.7727 (mmm) cc_final: 0.7345 (tpp) REVERT: K 62 ASP cc_start: 0.6878 (t0) cc_final: 0.6517 (t0) REVERT: K 68 LYS cc_start: 0.3192 (mtpt) cc_final: 0.2896 (tptt) REVERT: L 68 LYS cc_start: 0.4259 (mttt) cc_final: 0.3192 (tptt) outliers start: 18 outliers final: 13 residues processed: 226 average time/residue: 0.4190 time to fit residues: 146.0772 Evaluate side-chains 169 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 2.888 ------------------------------------------------------------------------------- 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: 6.9990 chunk 85 optimal weight: 0.7980 chunk 229 optimal weight: 8.9990 chunk 187 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 275 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 273 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS B 425 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 279 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN ** Q 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN Q 51 ASN ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 40 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25584 Z= 0.266 Angle : 0.693 11.295 34759 Z= 0.339 Chirality : 0.052 0.497 4045 Planarity : 0.004 0.056 4358 Dihedral : 10.922 115.044 4706 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.14), residues: 3036 helix: 0.44 (0.27), residues: 354 sheet: -2.31 (0.15), residues: 930 loop : -2.73 (0.12), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 47 HIS 0.007 0.001 HIS A 374 PHE 0.016 0.002 PHE B 376 TYR 0.018 0.001 TYR L 34 ARG 0.003 0.000 ARG P 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 475 MET cc_start: 0.7937 (ptp) cc_final: 0.7719 (ptp) REVERT: F 530 MET cc_start: 0.7268 (mmt) cc_final: 0.6966 (mmt) REVERT: M 80 LEU cc_start: 0.6866 (tp) cc_final: 0.6659 (tt) REVERT: N 3 GLN cc_start: 0.6335 (tp40) cc_final: 0.5619 (pp30) REVERT: N 53 ASP cc_start: 0.7167 (t0) cc_final: 0.6876 (t0) REVERT: O 3 GLN cc_start: 0.5471 (pp30) cc_final: 0.5211 (pp30) REVERT: O 27 ASP cc_start: 0.5761 (p0) cc_final: 0.5504 (p0) REVERT: O 47 TRP cc_start: 0.6992 (t60) cc_final: 0.6686 (t-100) REVERT: O 100 MET cc_start: 0.6971 (mpp) cc_final: 0.6253 (mpp) REVERT: K 62 ASP cc_start: 0.6889 (t0) cc_final: 0.6467 (t0) REVERT: K 68 LYS cc_start: 0.3388 (mtpt) cc_final: 0.2991 (tptt) REVERT: L 62 ASP cc_start: 0.6875 (t0) cc_final: 0.6243 (t0) REVERT: L 68 LYS cc_start: 0.4038 (mttt) cc_final: 0.3093 (tptt) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.4081 time to fit residues: 138.8242 Evaluate side-chains 159 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.879 ------------------------------------------------------------------------------- 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: 0.6980 chunk 207 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 185 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS B 103 GLN B 258 GLN B 302 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 103 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 279 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN P 51 ASN ** Q 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 25584 Z= 0.361 Angle : 0.746 11.135 34759 Z= 0.366 Chirality : 0.053 0.444 4045 Planarity : 0.004 0.058 4358 Dihedral : 10.664 119.573 4706 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.14), residues: 3036 helix: 0.84 (0.28), residues: 354 sheet: -2.29 (0.15), residues: 924 loop : -2.65 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 69 HIS 0.018 0.001 HIS Q 89 PHE 0.022 0.002 PHE M 100J TYR 0.019 0.002 TYR H 27 ARG 0.008 0.001 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 475 MET cc_start: 0.8250 (ptp) cc_final: 0.7731 (ptp) REVERT: M 80 LEU cc_start: 0.6772 (tp) cc_final: 0.6542 (tt) REVERT: N 46 GLU cc_start: 0.5768 (pm20) cc_final: 0.5506 (pm20) REVERT: O 3 GLN cc_start: 0.5353 (pp30) cc_final: 0.5102 (pp30) REVERT: O 27 ASP cc_start: 0.5959 (p0) cc_final: 0.5626 (p0) REVERT: O 100 MET cc_start: 0.6848 (mpp) cc_final: 0.6629 (mpp) REVERT: J 62 ASP cc_start: 0.7166 (t70) cc_final: 0.6372 (t0) REVERT: K 49 MET cc_start: 0.7498 (tpt) cc_final: 0.6969 (tpp) REVERT: K 62 ASP cc_start: 0.7040 (t0) cc_final: 0.6616 (t0) REVERT: K 68 LYS cc_start: 0.3841 (mtpt) cc_final: 0.3160 (tptt) REVERT: L 62 ASP cc_start: 0.7236 (t0) cc_final: 0.6746 (t0) REVERT: L 68 LYS cc_start: 0.4160 (mttt) cc_final: 0.3056 (tptt) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.3920 time to fit residues: 123.8338 Evaluate side-chains 153 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.837 ------------------------------------------------------------------------------- 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: 7.9990 chunk 166 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 218 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 249 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS F 577 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN Q 51 ASN L 41 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25584 Z= 0.224 Angle : 0.653 11.355 34759 Z= 0.317 Chirality : 0.051 0.460 4045 Planarity : 0.004 0.049 4358 Dihedral : 9.976 116.063 4706 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.14), residues: 3036 helix: 1.08 (0.28), residues: 360 sheet: -2.06 (0.16), residues: 864 loop : -2.45 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 47 HIS 0.012 0.001 HIS R 89 PHE 0.024 0.001 PHE I 100F TYR 0.011 0.001 TYR H 27 ARG 0.006 0.000 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 MET cc_start: 0.8185 (ptp) cc_final: 0.7586 (ptp) REVERT: N 53 ASP cc_start: 0.7145 (t0) cc_final: 0.6813 (t0) REVERT: N 81 LYS cc_start: 0.7887 (mmpt) cc_final: 0.7260 (mttp) REVERT: O 3 GLN cc_start: 0.5459 (pp30) cc_final: 0.5213 (pp30) REVERT: O 27 ASP cc_start: 0.5897 (p0) cc_final: 0.5487 (p0) REVERT: O 100 MET cc_start: 0.6852 (mpp) cc_final: 0.6617 (mpp) REVERT: J 62 ASP cc_start: 0.7118 (t70) cc_final: 0.6238 (t0) REVERT: K 68 LYS cc_start: 0.3702 (mtpt) cc_final: 0.3089 (tptt) REVERT: L 49 MET cc_start: 0.7890 (mmm) cc_final: 0.7085 (tpp) REVERT: L 62 ASP cc_start: 0.7179 (t0) cc_final: 0.6746 (t0) REVERT: L 68 LYS cc_start: 0.4123 (mttt) cc_final: 0.3015 (tptt) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.4096 time to fit residues: 143.3333 Evaluate side-chains 157 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.989 ------------------------------------------------------------------------------- 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: 7.9990 chunk 263 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 293 optimal weight: 0.6980 chunk 243 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 0.0970 chunk 153 optimal weight: 5.9990 overall best weight: 2.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS B 258 GLN C 72 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS M 3 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25584 Z= 0.283 Angle : 0.683 11.113 34759 Z= 0.333 Chirality : 0.051 0.458 4045 Planarity : 0.004 0.056 4358 Dihedral : 9.989 119.418 4706 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.14), residues: 3036 helix: 1.53 (0.29), residues: 342 sheet: -1.99 (0.17), residues: 864 loop : -2.43 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 47 HIS 0.004 0.001 HIS A 330 PHE 0.014 0.002 PHE C 391 TYR 0.034 0.001 TYR L 88 ARG 0.006 0.000 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 606 THR cc_start: 0.8289 (p) cc_final: 0.8007 (p) REVERT: F 535 MET cc_start: 0.5549 (mpp) cc_final: 0.5330 (mpp) REVERT: N 81 LYS cc_start: 0.7971 (mmpt) cc_final: 0.7254 (mttp) REVERT: O 27 ASP cc_start: 0.6025 (p0) cc_final: 0.5581 (p0) REVERT: O 100 MET cc_start: 0.6828 (mpp) cc_final: 0.6628 (mpp) REVERT: J 62 ASP cc_start: 0.7075 (t70) cc_final: 0.6366 (t0) REVERT: K 68 LYS cc_start: 0.3795 (mtpt) cc_final: 0.3049 (tptt) REVERT: L 49 MET cc_start: 0.8070 (mmm) cc_final: 0.7634 (mmm) REVERT: L 62 ASP cc_start: 0.7354 (t0) cc_final: 0.6906 (t0) REVERT: L 68 LYS cc_start: 0.4172 (mttt) cc_final: 0.2978 (tptt) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.3802 time to fit residues: 120.0097 Evaluate side-chains 151 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.879 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 246 optimal weight: 0.6980 chunk 163 optimal weight: 20.0000 chunk 292 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 134 optimal weight: 0.0050 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 348 GLN M 3 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25584 Z= 0.205 Angle : 0.650 13.884 34759 Z= 0.315 Chirality : 0.050 0.467 4045 Planarity : 0.004 0.048 4358 Dihedral : 9.700 117.143 4706 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.07 % Allowed : 1.12 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.15), residues: 3036 helix: 1.64 (0.28), residues: 342 sheet: -1.89 (0.17), residues: 864 loop : -2.35 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 47 HIS 0.002 0.001 HIS A 330 PHE 0.013 0.001 PHE B 376 TYR 0.011 0.001 TYR H 27 ARG 0.006 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 606 THR cc_start: 0.8177 (p) cc_final: 0.7960 (p) REVERT: F 535 MET cc_start: 0.5493 (mpp) cc_final: 0.5292 (mpp) REVERT: N 38 ARG cc_start: 0.7395 (tmm-80) cc_final: 0.6862 (tmm-80) REVERT: N 54 ARG cc_start: 0.6700 (mtm-85) cc_final: 0.6425 (ptt-90) REVERT: N 81 LYS cc_start: 0.7833 (mmpt) cc_final: 0.7426 (mttp) REVERT: O 27 ASP cc_start: 0.6049 (p0) cc_final: 0.5621 (p0) REVERT: O 81 LYS cc_start: 0.7913 (mppt) cc_final: 0.7644 (mmtt) REVERT: O 100 MET cc_start: 0.6685 (mpp) cc_final: 0.6476 (mpp) REVERT: J 62 ASP cc_start: 0.7010 (t70) cc_final: 0.6294 (t0) REVERT: K 68 LYS cc_start: 0.4037 (mtpt) cc_final: 0.3279 (tptt) REVERT: K 88 TYR cc_start: 0.5511 (m-80) cc_final: 0.4603 (m-80) REVERT: L 62 ASP cc_start: 0.7368 (t0) cc_final: 0.6924 (t0) REVERT: L 68 LYS cc_start: 0.4086 (mttt) cc_final: 0.2968 (tptt) outliers start: 2 outliers final: 0 residues processed: 199 average time/residue: 0.3665 time to fit residues: 116.5761 Evaluate side-chains 155 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.965 ------------------------------------------------------------------------------- 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: 4.9990 chunk 116 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN H 32 HIS ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25584 Z= 0.309 Angle : 0.709 16.406 34759 Z= 0.345 Chirality : 0.052 0.468 4045 Planarity : 0.004 0.051 4358 Dihedral : 9.896 120.525 4706 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.15), residues: 3036 helix: 1.53 (0.29), residues: 342 sheet: -1.88 (0.17), residues: 876 loop : -2.38 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 47 HIS 0.003 0.001 HIS B 330 PHE 0.013 0.002 PHE C 391 TYR 0.022 0.001 TYR L 88 ARG 0.006 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 606 THR cc_start: 0.8288 (p) cc_final: 0.8082 (p) REVERT: N 38 ARG cc_start: 0.7270 (tmm-80) cc_final: 0.6777 (tmm-80) REVERT: N 81 LYS cc_start: 0.7843 (mmpt) cc_final: 0.7294 (mttp) REVERT: O 27 ASP cc_start: 0.6165 (p0) cc_final: 0.5761 (p0) REVERT: O 81 LYS cc_start: 0.7943 (mppt) cc_final: 0.7653 (mmtt) REVERT: O 100 MET cc_start: 0.6759 (mpp) cc_final: 0.6504 (mpp) REVERT: J 62 ASP cc_start: 0.6952 (t70) cc_final: 0.6374 (t0) REVERT: K 68 LYS cc_start: 0.3978 (mtpt) cc_final: 0.3187 (tptt) REVERT: K 88 TYR cc_start: 0.5392 (m-80) cc_final: 0.5153 (m-80) REVERT: L 62 ASP cc_start: 0.7314 (t0) cc_final: 0.6871 (t0) REVERT: L 68 LYS cc_start: 0.4104 (mttt) cc_final: 0.2905 (tptt) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.3736 time to fit residues: 112.7044 Evaluate side-chains 153 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.898 ------------------------------------------------------------------------------- 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: 6.9990 chunk 279 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 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 72 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS B 258 GLN C 72 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25584 Z= 0.307 Angle : 0.713 14.305 34759 Z= 0.348 Chirality : 0.052 0.481 4045 Planarity : 0.004 0.049 4358 Dihedral : 9.877 119.975 4706 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.04 % Allowed : 0.79 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.15), residues: 3036 helix: 1.51 (0.29), residues: 342 sheet: -1.86 (0.17), residues: 876 loop : -2.38 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP F 631 HIS 0.005 0.001 HIS C 330 PHE 0.019 0.002 PHE L 64 TYR 0.018 0.001 TYR H 27 ARG 0.005 0.001 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 606 THR cc_start: 0.8257 (p) cc_final: 0.8057 (p) REVERT: N 54 ARG cc_start: 0.6898 (mtm-85) cc_final: 0.6619 (ptt-90) REVERT: N 81 LYS cc_start: 0.7899 (mmpt) cc_final: 0.7291 (mttp) REVERT: O 27 ASP cc_start: 0.6274 (p0) cc_final: 0.5811 (p0) REVERT: O 81 LYS cc_start: 0.7963 (mppt) cc_final: 0.7575 (mmtt) REVERT: O 100 MET cc_start: 0.6709 (mpp) cc_final: 0.6466 (mpp) REVERT: J 62 ASP cc_start: 0.7080 (t70) cc_final: 0.6497 (t0) REVERT: K 68 LYS cc_start: 0.3900 (mtpt) cc_final: 0.3235 (tptt) REVERT: K 88 TYR cc_start: 0.5427 (m-80) cc_final: 0.4752 (m-80) REVERT: L 62 ASP cc_start: 0.7175 (t0) cc_final: 0.6884 (t0) REVERT: L 68 LYS cc_start: 0.4110 (mttt) cc_final: 0.2936 (tptt) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.3885 time to fit residues: 117.3827 Evaluate side-chains 148 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.900 ------------------------------------------------------------------------------- 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: 4.9990 chunk 287 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 301 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25584 Z= 0.217 Angle : 0.663 13.200 34759 Z= 0.322 Chirality : 0.051 0.477 4045 Planarity : 0.004 0.047 4358 Dihedral : 9.595 118.487 4706 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.07 % Allowed : 0.26 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.15), residues: 3036 helix: 1.68 (0.29), residues: 342 sheet: -1.75 (0.17), residues: 876 loop : -2.29 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 631 HIS 0.003 0.001 HIS A 330 PHE 0.015 0.001 PHE C 391 TYR 0.014 0.001 TYR H 27 ARG 0.006 0.000 ARG N 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 606 THR cc_start: 0.8221 (p) cc_final: 0.8013 (p) REVERT: M 27 ASP cc_start: 0.6248 (p0) cc_final: 0.5738 (p0) REVERT: M 38 ARG cc_start: 0.6185 (ptt90) cc_final: 0.5964 (ptt90) REVERT: N 54 ARG cc_start: 0.6828 (mtm-85) cc_final: 0.6599 (ptt-90) REVERT: O 27 ASP cc_start: 0.6280 (p0) cc_final: 0.5814 (p0) REVERT: O 81 LYS cc_start: 0.7959 (mppt) cc_final: 0.7605 (mmtt) REVERT: O 100 MET cc_start: 0.6671 (mpp) cc_final: 0.6425 (mpp) REVERT: J 62 ASP cc_start: 0.7045 (t70) cc_final: 0.6501 (t0) REVERT: K 49 MET cc_start: 0.7848 (tpt) cc_final: 0.7536 (tpt) REVERT: L 62 ASP cc_start: 0.7183 (t0) cc_final: 0.6884 (t0) REVERT: L 68 LYS cc_start: 0.4116 (mttt) cc_final: 0.2958 (tptt) outliers start: 2 outliers final: 2 residues processed: 195 average time/residue: 0.3657 time to fit residues: 115.3900 Evaluate side-chains 156 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 2.865 ------------------------------------------------------------------------------- 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: 6.9990 chunk 256 optimal weight: 0.0000 chunk 73 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 247 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS B 72 HIS B 99 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 HIS ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.074933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.059263 restraints weight = 96905.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058892 restraints weight = 90855.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058730 restraints weight = 90643.162| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25584 Z= 0.188 Angle : 0.644 11.668 34759 Z= 0.312 Chirality : 0.050 0.479 4045 Planarity : 0.004 0.047 4358 Dihedral : 9.368 117.415 4706 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.04 % Allowed : 0.22 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.15), residues: 3036 helix: 1.86 (0.29), residues: 345 sheet: -1.71 (0.17), residues: 915 loop : -2.19 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP F 631 HIS 0.004 0.001 HIS B 330 PHE 0.013 0.001 PHE B 376 TYR 0.025 0.001 TYR K 88 ARG 0.004 0.000 ARG N 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4321.93 seconds wall clock time: 81 minutes 28.36 seconds (4888.36 seconds total)