Starting phenix.real_space_refine on Tue Dec 12 22:16:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/12_2023/6okp_20100.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/12_2023/6okp_20100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/12_2023/6okp_20100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/12_2023/6okp_20100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/12_2023/6okp_20100.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/12_2023/6okp_20100.pdb" } resolution = 3.28 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= 0.005 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 121 5.16 5 C 14261 2.51 5 N 3750 2.21 5 O 4725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L ARG 25": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 94": "NH1" <-> "NH2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 94": "NH1" <-> "NH2" Residue "N ARG 93": "NH1" <-> "NH2" Residue "O PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "P ARG 93": "NH1" <-> "NH2" Residue "Q ARG 94": "NH1" <-> "NH2" Residue "R ARG 93": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 22857 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 960 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "B" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 960 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 960 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "D" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3569 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3559 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3569 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "L" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "M" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1019 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "O" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1019 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "Q" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1019 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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: 6 Unresolved non-hydrogen chiralities: 3 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 7 Chain: "a" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 7 Chain: "h" 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: 6 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 7 Chain: "j" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 7 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" 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: "n" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: "q" 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: "r" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 9 Chain: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 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: "E" 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: "F" 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 Time building chain proxies: 11.47, per 1000 atoms: 0.50 Number of scatterers: 22857 At special positions: 0 Unit cell: (154.78, 166.77, 166.77, 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 121 16.00 O 4725 8.00 N 3750 7.00 C 14261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS D 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.01 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.02 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.01 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN H 5 " - " MAN H 6 " " MAN g 4 " - " MAN g 5 " " MAN h 4 " - " MAN h 5 " " MAN r 5 " - " MAN r 6 " " MAN s 5 " - " MAN s 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " " BMA H 3 " - " MAN H 8 " " MAN H 4 " - " MAN H 7 " " MAN H 8 " - " MAN H 9 " " BMA I 3 " - " MAN I 7 " " MAN I 4 " - " MAN I 5 " " BMA Z 3 " - " MAN Z 7 " " MAN Z 4 " - " MAN Z 5 " " BMA g 3 " - " MAN g 4 " " MAN g 6 " - " MAN g 7 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 7 " " MAN i 4 " - " MAN i 5 " " BMA j 3 " - " MAN j 7 " " MAN j 4 " - " MAN j 5 " " BMA r 3 " - " MAN r 8 " " MAN r 4 " - " MAN r 7 " " MAN r 8 " - " MAN r 9 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 7 " " MAN s 8 " - " MAN s 9 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " " MAN G 6 " - " MAN G 8 " " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 6 " " BMA g 3 " - " MAN g 6 " " BMA h 3 " - " MAN h 6 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 6 " " BMA j 3 " - " MAN j 4 " " MAN j 4 " - " MAN j 6 " " BMA r 3 " - " MAN r 4 " " MAN r 4 " - " MAN r 5 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 701 " - " ASN A 616 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 616 " " NAG C 702 " - " ASN C 637 " " NAG D 627 " - " ASN D 301 " " NAG D 631 " - " ASN D 88 " " NAG D 632 " - " ASN D 241 " " NAG D 635 " - " ASN D 276 " " NAG D 636 " - " ASN D 339 " " NAG D 640 " - " ASN D 396 " " NAG D 647 " - " ASN D 413 " " NAG D 648 " - " ASN D 355 " " NAG D 649 " - " ASN D 197 " " NAG E 610 " - " ASN E 301 " " NAG E 614 " - " ASN E 88 " " NAG E 615 " - " ASN E 241 " " NAG E 618 " - " ASN E 276 " " NAG E 619 " - " ASN E 339 " " NAG E 623 " - " ASN E 396 " " NAG E 630 " - " ASN E 413 " " NAG E 631 " - " ASN E 355 " " NAG E 639 " - " ASN E 197 " " NAG F 617 " - " ASN F 301 " " NAG F 621 " - " ASN F 88 " " NAG F 622 " - " ASN F 241 " " NAG F 625 " - " ASN F 276 " " NAG F 626 " - " ASN F 339 " " NAG F 630 " - " ASN F 396 " " NAG F 637 " - " ASN F 413 " " NAG F 638 " - " ASN F 355 " " NAG F 639 " - " ASN F 197 " " NAG G 1 " - " ASN D 295 " " NAG H 1 " - " ASN D 262 " " NAG I 1 " - " ASN D 448 " " NAG J 1 " - " ASN D 332 " " NAG S 1 " - " ASN D 160 " " NAG T 1 " - " ASN D 234 " " NAG U 1 " - " ASN D 392 " " NAG V 1 " - " ASN D 362 " " NAG W 1 " - " ASN D 386 " " NAG X 1 " - " ASN D 156 " " NAG Y 1 " - " ASN E 295 " " NAG Z 1 " - " ASN E 448 " " NAG a 1 " - " ASN E 160 " " NAG b 1 " - " ASN E 234 " " NAG c 1 " - " ASN E 392 " " NAG d 1 " - " ASN E 362 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 332 " " NAG h 1 " - " ASN E 137 " " NAG i 1 " - " ASN F 295 " " NAG j 1 " - " ASN F 448 " " NAG k 1 " - " ASN F 332 " " NAG l 1 " - " ASN F 160 " " NAG m 1 " - " ASN F 234 " " NAG n 1 " - " ASN F 392 " " NAG o 1 " - " ASN F 362 " " NAG p 1 " - " ASN F 386 " " NAG q 1 " - " ASN F 156 " " NAG r 1 " - " ASN E 262 " " NAG s 1 " - " ASN F 262 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.80 Conformation dependent library (CDL) restraints added in 4.1 seconds 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 54 sheets defined 14.1% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 571 through 595 removed outlier: 3.734A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 638 through 648 Processing helix chain 'A' and resid 651 through 663 removed outlier: 3.715A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 595 removed outlier: 3.733A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 651 through 663 removed outlier: 3.715A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 595 removed outlier: 3.733A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 595 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 628 through 635 Processing helix chain 'C' and resid 638 through 648 Processing helix chain 'C' and resid 651 through 663 removed outlier: 3.714A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 663 " --> pdb=" O GLU C 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 110 removed outlier: 3.611A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.626A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 353 removed outlier: 3.526A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS D 348 " --> pdb=" O GLN D 344 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.519A pdb=" N ASN D 478 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.298A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.650A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.621A pdb=" N TRP E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS E 348 " --> pdb=" O GLN E 344 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.580A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 373' Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'F' and resid 98 through 112 removed outlier: 4.308A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.971A pdb=" N GLU F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR F 341 " --> pdb=" O ARG F 337 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL F 346 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA F 347 " --> pdb=" O GLY F 343 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 348 " --> pdb=" O GLN F 344 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU F 351 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 353 " --> pdb=" O LEU F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.443A pdb=" N GLY F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 481 removed outlier: 3.759A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.868A pdb=" N ASN K 31 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR K 32 " --> pdb=" O MET K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.673A pdb=" N THR K 87 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 100D through 100H removed outlier: 3.638A pdb=" N PHE K 100G" --> pdb=" O VAL K 100D" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.353A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 65 No H-bonds generated for 'chain 'M' and resid 63 through 65' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 63 through 65 No H-bonds generated for 'chain 'Q' and resid 63 through 65' Processing helix chain 'Q' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.529A pdb=" N CYS A 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N TYR D 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR A 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL D 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL A 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.435A pdb=" N CYS B 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N TYR E 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR B 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N VAL E 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL B 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 603 through 609 removed outlier: 5.608A pdb=" N VAL F 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.550A pdb=" N ALA D 224 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AA7, first strand: chain 'D' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'D' and resid 292 through 293 Processing sheet with id=AA9, first strand: chain 'D' and resid 320 through 322 removed outlier: 5.344A pdb=" N ASP D 321A" --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 307 through 308 Processing sheet with id=AB2, first strand: chain 'D' and resid 394 through 395 removed outlier: 6.474A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.617A pdb=" N GLU D 381 " --> pdb=" O CYS D 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.518A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AB7, first strand: chain 'E' and resid 120 through 121 removed outlier: 4.026A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB9, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 260 removed outlier: 6.732A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 322 through 323 removed outlier: 4.335A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AC4, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.626A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.642A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.543A pdb=" N ALA F 224 " --> pdb=" O VAL F 489 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.899A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.733A pdb=" N THR F 357 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE F 468 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AD3, first strand: chain 'F' and resid 297 through 298 removed outlier: 3.712A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 302 through 304 removed outlier: 5.060A pdb=" N ASP F 321A" --> pdb=" O THR F 303 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 307 through 308 Processing sheet with id=AD6, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.513A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.623A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL K 109 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 88 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR K 33 " --> pdb=" O ALA K 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.623A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL K 109 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 88 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER K 100O" --> pdb=" O ARG K 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 67 through 68 Processing sheet with id=AE2, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AE3, first strand: chain 'L' and resid 44 through 46 removed outlier: 3.701A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.573A pdb=" N GLN M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.612A pdb=" N ALA M 93 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP M 34 " --> pdb=" O PHE M 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.387A pdb=" N LEU N 11 " --> pdb=" O GLU N 102 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA N 34 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG N 45 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.573A pdb=" N GLN O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.612A pdb=" N ALA O 93 " --> pdb=" O SER O 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.387A pdb=" N LEU P 11 " --> pdb=" O GLU P 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN P 89 " --> pdb=" O ALA P 34 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA P 34 " --> pdb=" O GLN P 89 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 4 through 7 removed outlier: 3.573A pdb=" N GLN Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.611A pdb=" N ALA Q 93 " --> pdb=" O SER Q 35 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TRP Q 34 " --> pdb=" O PHE Q 50 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.388A pdb=" N LEU R 11 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN R 89 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA R 34 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG R 45 " --> pdb=" O GLN R 37 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.79 Time building geometry restraints manager: 11.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6778 1.34 - 1.46: 5637 1.46 - 1.58: 10743 1.58 - 1.70: 5 1.70 - 1.82: 160 Bond restraints: 23323 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG E 614 " pdb=" O5 NAG E 614 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 MAN j 6 " pdb=" C2 MAN j 6 " ideal model delta sigma weight residual 1.526 1.593 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 MAN I 6 " pdb=" C2 MAN I 6 " ideal model delta sigma weight residual 1.526 1.590 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C3 MAN i 4 " pdb=" O3 MAN i 4 " ideal model delta sigma weight residual 1.408 1.472 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 23318 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.53: 504 105.53 - 112.87: 13154 112.87 - 120.20: 8483 120.20 - 127.53: 9250 127.53 - 134.87: 313 Bond angle restraints: 31704 Sorted by residual: angle pdb=" N ASN F 332 " pdb=" CA ASN F 332 " pdb=" C ASN F 332 " ideal model delta sigma weight residual 111.02 119.54 -8.52 1.25e+00 6.40e-01 4.64e+01 angle pdb=" C GLU D 411 " pdb=" N GLN D 412 " pdb=" CA GLN D 412 " ideal model delta sigma weight residual 121.54 133.48 -11.94 1.91e+00 2.74e-01 3.91e+01 angle pdb=" C PRO D 407 " pdb=" N THR D 408 " pdb=" CA THR D 408 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.25e+01 angle pdb=" CA LEU F 116 " pdb=" CB LEU F 116 " pdb=" CG LEU F 116 " ideal model delta sigma weight residual 116.30 133.17 -16.87 3.50e+00 8.16e-02 2.32e+01 angle pdb=" C PRO F 407 " pdb=" N THR F 408 " pdb=" CA THR F 408 " ideal model delta sigma weight residual 126.45 134.87 -8.42 1.77e+00 3.19e-01 2.26e+01 ... (remaining 31699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 13722 16.22 - 32.43: 668 32.43 - 48.65: 192 48.65 - 64.87: 110 64.87 - 81.08: 16 Dihedral angle restraints: 14708 sinusoidal: 7080 harmonic: 7628 Sorted by residual: dihedral pdb=" CA ASP O 101 " pdb=" C ASP O 101 " pdb=" N PRO O 102 " pdb=" CA PRO O 102 " ideal model delta harmonic sigma weight residual -180.00 -119.65 -60.35 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA ASP Q 101 " pdb=" C ASP Q 101 " pdb=" N PRO Q 102 " pdb=" CA PRO Q 102 " ideal model delta harmonic sigma weight residual -180.00 -119.68 -60.32 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA ASP M 101 " pdb=" C ASP M 101 " pdb=" N PRO M 102 " pdb=" CA PRO M 102 " ideal model delta harmonic sigma weight residual -180.00 -119.69 -60.31 0 5.00e+00 4.00e-02 1.45e+02 ... (remaining 14705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.259: 3971 0.259 - 0.518: 25 0.518 - 0.777: 3 0.777 - 1.036: 1 1.036 - 1.295: 2 Chirality restraints: 4002 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN D 392 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.11 -1.29 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN E 392 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.19 -1.21 2.00e-01 2.50e+01 3.64e+01 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN E 386 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.70e+01 ... (remaining 3999 not shown) Planarity restraints: 3887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG r 2 " -0.040 2.00e-02 2.50e+03 3.32e-02 1.37e+01 pdb=" C7 NAG r 2 " 0.007 2.00e-02 2.50e+03 pdb=" C8 NAG r 2 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG r 2 " 0.054 2.00e-02 2.50e+03 pdb=" O7 NAG r 2 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP M 101 " 0.055 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO M 102 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO M 102 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 102 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP O 101 " -0.055 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO O 102 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO O 102 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO O 102 " -0.046 5.00e-02 4.00e+02 ... (remaining 3884 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3110 2.76 - 3.29: 19609 3.29 - 3.83: 34443 3.83 - 4.36: 39237 4.36 - 4.90: 69517 Nonbonded interactions: 165916 Sorted by model distance: nonbonded pdb=" O TRP F 69 " pdb=" OG1 THR F 71 " model vdw 2.222 2.440 nonbonded pdb=" O TRP E 69 " pdb=" OG1 THR E 71 " model vdw 2.245 2.440 nonbonded pdb=" OD1 ASP Q 100B" pdb=" O6 NAG s 1 " model vdw 2.258 2.440 nonbonded pdb=" OG SER D 447 " pdb=" O7 NAG H 1 " model vdw 2.276 2.440 nonbonded pdb=" O PRO E 369 " pdb=" OG1 THR E 373 " model vdw 2.294 2.440 ... (remaining 165911 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 32 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 152 through 505 or resid 627 through 649)) selection = chain 'E' selection = (chain 'F' and (resid 32 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 152 through 505 or resid 617 through 639)) } ncs_group { reference = (chain 'G' and resid 5 through 8) selection = (chain 'H' and resid 6 through 9) selection = (chain 'I' and resid 4 through 7) selection = (chain 'Z' and resid 4 through 7) selection = (chain 'g' and resid 4 through 7) selection = (chain 'i' and resid 4 through 7) selection = (chain 'j' and resid 4 through 7) selection = (chain 'r' and resid 6 through 9) selection = (chain 's' and resid 6 through 9) } ncs_group { reference = chain 'J' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'a' selection = chain 'c' selection = chain 'l' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 6.620 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 62.110 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.009 0.090 23323 Z= 0.579 Angle : 1.228 16.875 31704 Z= 0.611 Chirality : 0.079 1.295 4002 Planarity : 0.008 0.085 3823 Dihedral : 11.655 81.081 9731 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.09 % Favored : 88.60 % Rotamer: Outliers : 0.57 % Allowed : 2.62 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.48 % 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: -3.85 (0.14), residues: 2614 helix: -2.87 (0.21), residues: 301 sheet: -1.54 (0.17), residues: 835 loop : -3.23 (0.13), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP Q 103 HIS 0.012 0.002 HIS M 100G PHE 0.035 0.005 PHE O 100A TYR 0.033 0.003 TYR M 52 ARG 0.021 0.001 ARG F 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 602 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 613 average time/residue: 0.4009 time to fit residues: 360.3102 Evaluate side-chains 337 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 336 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1875 time to fit residues: 3.4405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 236 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN A 658 GLN B 650 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN D 98 ASN D 114 GLN D 397 ASN E 66 HIS E 98 ASN E 114 GLN E 397 ASN ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN F 114 GLN F 325 ASN F 397 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN R 6 GLN R 49 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 23323 Z= 0.338 Angle : 0.867 12.207 31704 Z= 0.424 Chirality : 0.057 0.815 4002 Planarity : 0.006 0.086 3823 Dihedral : 10.578 59.180 4860 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.76 % Favored : 90.09 % Rotamer: Outliers : 2.92 % Allowed : 10.85 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.32 % 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: -3.14 (0.15), residues: 2614 helix: -1.46 (0.27), residues: 342 sheet: -0.93 (0.19), residues: 795 loop : -3.04 (0.13), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 395 HIS 0.010 0.002 HIS R 49 PHE 0.030 0.003 PHE P 71 TYR 0.020 0.002 TYR M 52 ARG 0.006 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 354 time to evaluate : 2.571 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 outliers start: 67 outliers final: 40 residues processed: 398 average time/residue: 0.3786 time to fit residues: 224.7720 Evaluate side-chains 357 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 317 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2050 time to fit residues: 18.2509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 GLN D 80 ASN D 132 ASN D 203 GLN D 374 HIS E 66 HIS E 80 ASN E 308 HIS ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 23323 Z= 0.399 Angle : 0.892 13.078 31704 Z= 0.434 Chirality : 0.057 0.806 4002 Planarity : 0.006 0.083 3823 Dihedral : 10.126 59.978 4860 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.67 % Favored : 88.10 % Rotamer: Outliers : 3.10 % Allowed : 12.73 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.36 % 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: -2.86 (0.15), residues: 2614 helix: -0.84 (0.28), residues: 319 sheet: -0.78 (0.19), residues: 782 loop : -2.91 (0.13), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 96 HIS 0.007 0.002 HIS R 38 PHE 0.025 0.003 PHE P 71 TYR 0.028 0.002 TYR F 191 ARG 0.009 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 329 time to evaluate : 2.330 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 outliers start: 71 outliers final: 33 residues processed: 381 average time/residue: 0.4177 time to fit residues: 239.8352 Evaluate side-chains 340 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 307 time to evaluate : 2.188 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.2071 time to fit residues: 16.0109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 4.9990 chunk 177 optimal weight: 40.0000 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 237 optimal weight: 30.0000 chunk 251 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 224 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN E 80 ASN E 99 ASN E 114 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 23323 Z= 0.199 Angle : 0.738 10.697 31704 Z= 0.359 Chirality : 0.052 0.711 4002 Planarity : 0.005 0.085 3823 Dihedral : 9.592 58.728 4860 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.03 % Favored : 90.86 % Rotamer: Outliers : 2.09 % Allowed : 13.91 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.20 % 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: -2.47 (0.16), residues: 2614 helix: -0.26 (0.29), residues: 316 sheet: -0.48 (0.20), residues: 764 loop : -2.70 (0.14), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 96 HIS 0.005 0.001 HIS N 49 PHE 0.026 0.002 PHE O 50 TYR 0.023 0.001 TYR E 191 ARG 0.007 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 338 time to evaluate : 2.664 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 outliers start: 48 outliers final: 18 residues processed: 370 average time/residue: 0.4033 time to fit residues: 223.0981 Evaluate side-chains 329 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 311 time to evaluate : 2.423 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.2091 time to fit residues: 10.2829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 214 optimal weight: 0.1980 chunk 173 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 462 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 23323 Z= 0.474 Angle : 0.916 14.022 31704 Z= 0.441 Chirality : 0.059 0.763 4002 Planarity : 0.006 0.088 3823 Dihedral : 9.815 59.752 4860 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.97 % Favored : 87.83 % Rotamer: Outliers : 2.83 % Allowed : 14.52 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.20 % 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: -2.64 (0.15), residues: 2614 helix: -0.41 (0.29), residues: 319 sheet: -0.72 (0.20), residues: 766 loop : -2.75 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 96 HIS 0.007 0.002 HIS A 564 PHE 0.031 0.003 PHE M 100A TYR 0.025 0.002 TYR E 39 ARG 0.013 0.001 ARG R 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 314 time to evaluate : 2.536 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 outliers start: 65 outliers final: 40 residues processed: 354 average time/residue: 0.4021 time to fit residues: 211.5858 Evaluate side-chains 343 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 303 time to evaluate : 2.585 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2229 time to fit residues: 19.3208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 251 optimal weight: 10.0000 chunk 208 optimal weight: 0.0980 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23323 Z= 0.205 Angle : 0.743 12.807 31704 Z= 0.361 Chirality : 0.053 0.692 4002 Planarity : 0.005 0.089 3823 Dihedral : 9.459 59.556 4860 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.84 % Favored : 91.01 % Rotamer: Outliers : 1.35 % Allowed : 15.43 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.16 % 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: -2.36 (0.16), residues: 2614 helix: -0.03 (0.29), residues: 319 sheet: -0.46 (0.20), residues: 766 loop : -2.65 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 96 HIS 0.005 0.001 HIS N 49 PHE 0.025 0.002 PHE M 100A TYR 0.025 0.001 TYR E 191 ARG 0.011 0.000 ARG O 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 320 time to evaluate : 2.482 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 outliers start: 31 outliers final: 11 residues processed: 339 average time/residue: 0.4113 time to fit residues: 207.5024 Evaluate side-chains 315 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 304 time to evaluate : 2.386 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2813 time to fit residues: 8.1855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 2.9990 chunk 28 optimal weight: 0.0070 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 190 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23323 Z= 0.209 Angle : 0.737 14.791 31704 Z= 0.354 Chirality : 0.053 0.734 4002 Planarity : 0.005 0.090 3823 Dihedral : 9.222 59.931 4860 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.06 % Favored : 89.79 % Rotamer: Outliers : 1.18 % Allowed : 16.30 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.16 % 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: -2.25 (0.16), residues: 2614 helix: 0.21 (0.30), residues: 319 sheet: -0.49 (0.19), residues: 784 loop : -2.57 (0.14), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 96 HIS 0.005 0.001 HIS N 38 PHE 0.025 0.002 PHE O 50 TYR 0.023 0.001 TYR F 191 ARG 0.009 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 319 time to evaluate : 2.698 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 outliers start: 27 outliers final: 14 residues processed: 334 average time/residue: 0.4103 time to fit residues: 203.7040 Evaluate side-chains 318 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 304 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2112 time to fit residues: 9.2234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 170 optimal weight: 40.0000 chunk 123 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23323 Z= 0.333 Angle : 0.820 15.839 31704 Z= 0.395 Chirality : 0.055 0.673 4002 Planarity : 0.005 0.093 3823 Dihedral : 9.352 59.982 4860 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.17 % Favored : 88.68 % Rotamer: Outliers : 0.96 % Allowed : 16.74 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % 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: -2.33 (0.16), residues: 2614 helix: -0.01 (0.29), residues: 326 sheet: -0.54 (0.19), residues: 784 loop : -2.59 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP O 47 HIS 0.006 0.002 HIS E 330 PHE 0.030 0.003 PHE M 100A TYR 0.027 0.002 TYR F 191 ARG 0.010 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 308 time to evaluate : 2.439 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 outliers start: 22 outliers final: 10 residues processed: 321 average time/residue: 0.4098 time to fit residues: 195.4921 Evaluate side-chains 312 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 302 time to evaluate : 2.671 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2444 time to fit residues: 7.9678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 211 optimal weight: 0.0170 chunk 220 optimal weight: 7.9990 chunk 232 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 190 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23323 Z= 0.170 Angle : 0.712 15.086 31704 Z= 0.341 Chirality : 0.051 0.569 4002 Planarity : 0.005 0.096 3823 Dihedral : 9.230 58.638 4860 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.45 % Favored : 91.43 % Rotamer: Outliers : 0.35 % Allowed : 17.39 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.08 % 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: -2.08 (0.16), residues: 2614 helix: 0.38 (0.30), residues: 320 sheet: -0.34 (0.20), residues: 775 loop : -2.48 (0.14), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 96 HIS 0.005 0.001 HIS N 49 PHE 0.030 0.002 PHE P 71 TYR 0.024 0.001 TYR O 52 ARG 0.008 0.000 ARG O 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 318 time to evaluate : 2.282 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 outliers start: 8 outliers final: 7 residues processed: 323 average time/residue: 0.4238 time to fit residues: 204.8907 Evaluate side-chains 306 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 299 time to evaluate : 2.410 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2269 time to fit residues: 6.4431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.6980 chunk 246 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 259 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23323 Z= 0.310 Angle : 0.824 26.811 31704 Z= 0.391 Chirality : 0.066 2.299 4002 Planarity : 0.005 0.097 3823 Dihedral : 9.900 141.781 4860 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.75 % Favored : 89.10 % Rotamer: Outliers : 0.31 % Allowed : 18.18 % Favored : 81.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % 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: -2.17 (0.16), residues: 2614 helix: 0.25 (0.30), residues: 325 sheet: -0.42 (0.19), residues: 798 loop : -2.54 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP O 47 HIS 0.005 0.002 HIS E 330 PHE 0.035 0.002 PHE P 71 TYR 0.028 0.001 TYR F 191 ARG 0.018 0.001 ARG D 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 304 time to evaluate : 2.658 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 outliers start: 7 outliers final: 3 residues processed: 307 average time/residue: 0.4091 time to fit residues: 186.6234 Evaluate side-chains 303 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 300 time to evaluate : 2.445 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2135 time to fit residues: 4.4687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.160263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120802 restraints weight = 34440.420| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 4.22 r_work: 0.3123 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23323 Z= 0.232 Angle : 0.757 14.742 31704 Z= 0.365 Chirality : 0.054 0.705 4002 Planarity : 0.005 0.097 3823 Dihedral : 9.689 117.190 4860 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.91 % Favored : 89.94 % Rotamer: Outliers : 0.39 % Allowed : 18.27 % Favored : 81.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2614 helix: 0.46 (0.30), residues: 316 sheet: -0.45 (0.19), residues: 793 loop : -2.46 (0.14), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP O 47 HIS 0.005 0.001 HIS E 330 PHE 0.037 0.002 PHE P 71 TYR 0.025 0.001 TYR F 191 ARG 0.009 0.000 ARG O 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5139.24 seconds wall clock time: 94 minutes 32.77 seconds (5672.77 seconds total)