Starting phenix.real_space_refine on Wed Mar 20 04:18:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6edu_9038/03_2024/6edu_9038.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6edu_9038/03_2024/6edu_9038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6edu_9038/03_2024/6edu_9038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6edu_9038/03_2024/6edu_9038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6edu_9038/03_2024/6edu_9038.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6edu_9038/03_2024/6edu_9038.pdb" } resolution = 4.06 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 141 5.16 5 C 16449 2.51 5 N 4350 2.21 5 O 5331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 419": "NH1" <-> "NH2" Residue "D TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "E ARG 419": "NH1" <-> "NH2" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 460": "NH1" <-> "NH2" Residue "F ARG 419": "NH1" <-> "NH2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 460": "NH1" <-> "NH2" Residue "J TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26271 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 884 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 884 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 884 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2989 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "E" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2989 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "F" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2989 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "G" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "J" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "K" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 802 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "L" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "M" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 802 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "N" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "O" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 802 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "P" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "S" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "U" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "u" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "v" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" C1 NAG t 1 " occ=0.69 ... (12 atoms not shown) pdb=" O7 NAG t 1 " occ=0.69 residue: pdb=" C1 NAG t 2 " occ=0.65 ... (12 atoms not shown) pdb=" O7 NAG t 2 " occ=0.65 residue: pdb=" C1 BMA t 3 " occ=0.92 ... (9 atoms not shown) pdb=" O6 BMA t 3 " occ=0.92 residue: pdb=" C1 MAN t 4 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN t 4 " occ=0.85 residue: pdb=" C1 MAN t 5 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN t 5 " occ=0.79 residue: pdb=" C1 MAN t 6 " occ=0.66 ... (9 atoms not shown) pdb=" O6 MAN t 6 " occ=0.66 residue: pdb=" C1 NAG u 1 " occ=0.69 ... (12 atoms not shown) pdb=" O7 NAG u 1 " occ=0.69 residue: pdb=" C1 NAG u 2 " occ=0.65 ... (12 atoms not shown) pdb=" O7 NAG u 2 " occ=0.65 residue: pdb=" C1 BMA u 3 " occ=0.92 ... (9 atoms not shown) pdb=" O6 BMA u 3 " occ=0.92 residue: pdb=" C1 MAN u 4 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN u 4 " occ=0.85 residue: pdb=" C1 MAN u 5 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN u 5 " occ=0.79 residue: pdb=" C1 MAN u 6 " occ=0.66 ... (9 atoms not shown) pdb=" O6 MAN u 6 " occ=0.66 ... (remaining 6 not shown) Time building chain proxies: 12.78, per 1000 atoms: 0.49 Number of scatterers: 26271 At special positions: 0 Unit cell: (162.44, 165.06, 132.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 5331 8.00 N 4350 7.00 C 16449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.52 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS D 501 " distance=2.13 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 F 501 " distance=1.89 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 E 501 " distance=2.09 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=2.50 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.01 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.26 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.01 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.07 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.01 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 84 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 90 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 99 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 89 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 99 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 89 " distance=2.04 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 Z 4 " - " MAN Z 5 " " MAN g 4 " - " MAN g 5 " " MAN n 4 " - " MAN n 5 " " MAN t 4 " - " MAN t 5 " " MAN t 5 " - " MAN t 6 " " MAN u 4 " - " MAN u 5 " " MAN u 5 " - " MAN u 6 " " MAN v 4 " - " MAN v 5 " " MAN v 5 " - " MAN v 6 " ALPHA1-3 " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " " BMA t 3 " - " MAN t 4 " " MAN t 7 " - " MAN t 8 " " BMA u 3 " - " MAN u 4 " " MAN u 7 " - " MAN u 8 " " BMA v 3 " - " MAN v 4 " " MAN v 7 " - " MAN v 8 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " " BMA h 3 " - " MAN h 5 " " BMA o 3 " - " MAN o 5 " " BMA t 3 " - " MAN t 7 " " MAN t 7 " - " MAN t 9 " " BMA u 3 " - " MAN u 7 " " MAN u 7 " - " MAN u 9 " " BMA v 3 " - " MAN v 7 " " MAN v 7 " - " MAN v 9 " BETA1-4 " 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " 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 k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " 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 o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " NAG-ASN " NAG A 703 " - " ASN A 616 " " NAG B 701 " - " ASN B 616 " " NAG C 701 " - " ASN C 616 " " NAG D 601 " - " ASN D 88 " " NAG D 614 " - " ASN D 295 " " NAG D 615 " - " ASN D 332 " " NAG D 616 " - " ASN D 339 " " NAG D 617 " - " ASN D 355 " " NAG D 623 " - " ASN D 392 " " NAG D 624 " - " ASN D 397 " " NAG D 627 " - " ASN D 448 " " NAG E 601 " - " ASN E 88 " " NAG E 614 " - " ASN E 295 " " NAG E 615 " - " ASN E 332 " " NAG E 616 " - " ASN E 339 " " NAG E 617 " - " ASN E 355 " " NAG E 623 " - " ASN E 392 " " NAG E 624 " - " ASN E 397 " " NAG E 627 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 614 " - " ASN F 295 " " NAG F 615 " - " ASN F 332 " " NAG F 616 " - " ASN F 339 " " NAG F 617 " - " ASN F 355 " " NAG F 623 " - " ASN F 392 " " NAG F 624 " - " ASN F 397 " " NAG F 627 " - " ASN F 448 " " NAG V 1 " - " ASN A 637 " " NAG W 1 " - " ASN B 637 " " NAG X 1 " - " ASN C 637 " " NAG Y 1 " - " ASN D 241 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN D 276 " " NAG b 1 " - " ASN D 362 " " NAG c 1 " - " ASN D 386 " " NAG d 1 " - " ASN D 413 " " NAG e 1 " - " ASN D 197 " " NAG f 1 " - " ASN E 241 " " NAG g 1 " - " ASN E 262 " " NAG h 1 " - " ASN E 276 " " NAG i 1 " - " ASN E 362 " " NAG j 1 " - " ASN E 386 " " NAG k 1 " - " ASN E 413 " " NAG l 1 " - " ASN E 197 " " NAG m 1 " - " ASN F 241 " " NAG n 1 " - " ASN F 262 " " NAG o 1 " - " ASN F 276 " " NAG p 1 " - " ASN F 362 " " NAG q 1 " - " ASN F 386 " " NAG r 1 " - " ASN F 413 " " NAG s 1 " - " ASN F 197 " " NAG t 1 " - " ASN F 234 " " NAG u 1 " - " ASN D 234 " " NAG v 1 " - " ASN E 234 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.98 Conformation dependent library (CDL) restraints added in 4.8 seconds 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5946 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 64 sheets defined 14.1% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.886A pdb=" N PHE A 522 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 519 through 523' Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 565 through 595 removed outlier: 3.918A pdb=" N THR A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 4.083A pdb=" N TRP A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'B' and resid 519 through 523 removed outlier: 3.886A pdb=" N PHE B 522 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 519 through 523' Processing helix chain 'B' and resid 529 through 544 Processing helix chain 'B' and resid 565 through 595 removed outlier: 3.918A pdb=" N THR B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.083A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 652 Processing helix chain 'C' and resid 519 through 523 removed outlier: 3.886A pdb=" N PHE C 522 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 519 through 523' Processing helix chain 'C' and resid 529 through 544 Processing helix chain 'C' and resid 565 through 595 removed outlier: 3.918A pdb=" N THR C 569 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 573 " --> pdb=" O THR C 569 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 576 " --> pdb=" O GLY C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 removed outlier: 4.082A pdb=" N TRP C 631 " --> pdb=" O THR C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 652 Processing helix chain 'D' and resid 68 through 74 removed outlier: 3.902A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.545A pdb=" N ASP D 113 " --> pdb=" O ILE D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 352 Processing helix chain 'D' and resid 368 through 372 removed outlier: 4.188A pdb=" N VAL D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 372' Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.785A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 74 removed outlier: 3.903A pdb=" N HIS E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 113 removed outlier: 3.546A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 352 Processing helix chain 'E' and resid 368 through 372 removed outlier: 4.188A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 372' Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.785A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 74 removed outlier: 3.903A pdb=" N HIS F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 removed outlier: 3.545A pdb=" N ASP F 113 " --> pdb=" O ILE F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 352 Processing helix chain 'F' and resid 368 through 372 removed outlier: 4.188A pdb=" N VAL F 372 " --> pdb=" O ASP F 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 368 through 372' Processing helix chain 'F' and resid 476 through 481 removed outlier: 3.785A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 63 removed outlier: 4.004A pdb=" N ASP G 63 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 79 removed outlier: 3.735A pdb=" N SER G 79 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 63 removed outlier: 4.004A pdb=" N ASP H 63 " --> pdb=" O SER H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 removed outlier: 3.734A pdb=" N SER H 79 " --> pdb=" O ILE H 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 63 removed outlier: 4.004A pdb=" N ASP I 63 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 79 removed outlier: 3.735A pdb=" N SER I 79 " --> pdb=" O ILE I 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 62 No H-bonds generated for 'chain 'K' and resid 60 through 62' Processing helix chain 'M' and resid 60 through 62 No H-bonds generated for 'chain 'M' and resid 60 through 62' Processing helix chain 'O' and resid 60 through 62 No H-bonds generated for 'chain 'O' and resid 60 through 62' Processing helix chain 'P' and resid 106 through 110 removed outlier: 3.902A pdb=" N SER P 109 " --> pdb=" O ASP P 106 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY P 110 " --> pdb=" O LYS P 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 106 through 110' Processing helix chain 'R' and resid 106 through 110 removed outlier: 3.902A pdb=" N SER R 109 " --> pdb=" O ASP R 106 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY R 110 " --> pdb=" O LYS R 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 106 through 110' Processing helix chain 'T' and resid 106 through 110 removed outlier: 3.902A pdb=" N SER T 109 " --> pdb=" O ASP T 106 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY T 110 " --> pdb=" O LYS T 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 106 through 110' Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 605 removed outlier: 3.626A pdb=" N CYS B 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL F 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 603 through 605 removed outlier: 3.733A pdb=" N CYS C 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AA4, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.753A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.601A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS D 239 " --> pdb=" O GLU D 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 198 through 202 Processing sheet with id=AA7, first strand: chain 'D' and resid 260 through 261 removed outlier: 6.595A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.480A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 260 through 261 removed outlier: 6.595A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.480A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLN D 417 " --> pdb=" O ASN D 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.820A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.754A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.602A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS E 239 " --> pdb=" O GLU E 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 198 through 202 Processing sheet with id=AB4, first strand: chain 'E' and resid 158 through 160 Processing sheet with id=AB5, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.594A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.478A pdb=" N VAL E 292 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.594A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.478A pdb=" N VAL E 292 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLN E 417 " --> pdb=" O ASN E 386 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 357 through 359 removed outlier: 6.820A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.753A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 91 through 92 removed outlier: 3.601A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS F 239 " --> pdb=" O GLU F 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 198 through 202 Processing sheet with id=AC2, first strand: chain 'F' and resid 260 through 261 removed outlier: 6.594A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.479A pdb=" N VAL F 292 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 260 through 261 removed outlier: 6.594A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.479A pdb=" N VAL F 292 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLN F 417 " --> pdb=" O ASN F 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 357 through 359 removed outlier: 6.819A pdb=" N THR F 357 " --> pdb=" O GLU F 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC6, first strand: chain 'G' and resid 12 through 17 Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AC8, first strand: chain 'H' and resid 12 through 17 Processing sheet with id=AC9, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AD1, first strand: chain 'I' and resid 12 through 17 Processing sheet with id=AD2, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.562A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP J 73 " --> pdb=" O THR J 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.713A pdb=" N VAL J 121 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA J 92 " --> pdb=" O VAL J 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.713A pdb=" N VAL J 121 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA J 92 " --> pdb=" O VAL J 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.220A pdb=" N VAL K 11 " --> pdb=" O THR K 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.615A pdb=" N CYS K 23 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 47 through 50 removed outlier: 6.549A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 3 through 6 removed outlier: 3.563A pdb=" N THR L 78 " --> pdb=" O ASP L 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP L 73 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR L 71 " --> pdb=" O TYR L 80 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.712A pdb=" N VAL L 121 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA L 92 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP L 36 " --> pdb=" O MET L 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.712A pdb=" N VAL L 121 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA L 92 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.220A pdb=" N VAL M 11 " --> pdb=" O THR M 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'M' and resid 19 through 24 removed outlier: 3.614A pdb=" N CYS M 23 " --> pdb=" O ALA M 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 47 through 50 removed outlier: 6.549A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.563A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.713A pdb=" N VAL N 121 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA N 92 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.713A pdb=" N VAL N 121 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA N 92 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.220A pdb=" N VAL O 11 " --> pdb=" O THR O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'O' and resid 19 through 24 removed outlier: 3.615A pdb=" N CYS O 23 " --> pdb=" O ALA O 73 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 47 through 50 removed outlier: 6.548A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AF3, first strand: chain 'P' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP P 53 " --> pdb=" O LYS P 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP P 37 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN P 51 " --> pdb=" O VAL P 35 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL P 35 " --> pdb=" O GLN P 51 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP P 53 " --> pdb=" O TYR P 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR P 33 " --> pdb=" O TRP P 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR P 101 " --> pdb=" O SER P 121 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP P 53 " --> pdb=" O LYS P 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP P 37 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN P 51 " --> pdb=" O VAL P 35 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL P 35 " --> pdb=" O GLN P 51 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP P 53 " --> pdb=" O TYR P 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR P 33 " --> pdb=" O TRP P 53 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 112 through 113 Processing sheet with id=AF6, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'Q' and resid 54 through 55 removed outlier: 6.474A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AF9, first strand: chain 'R' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP R 53 " --> pdb=" O LYS R 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP R 37 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN R 51 " --> pdb=" O VAL R 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL R 35 " --> pdb=" O GLN R 51 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP R 53 " --> pdb=" O TYR R 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR R 33 " --> pdb=" O TRP R 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR R 101 " --> pdb=" O SER R 121 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP R 53 " --> pdb=" O LYS R 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP R 37 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN R 51 " --> pdb=" O VAL R 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL R 35 " --> pdb=" O GLN R 51 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP R 53 " --> pdb=" O TYR R 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR R 33 " --> pdb=" O TRP R 53 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'R' and resid 112 through 113 Processing sheet with id=AG3, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'S' and resid 54 through 55 removed outlier: 6.474A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 5 through 6 Processing sheet with id=AG6, first strand: chain 'T' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP T 53 " --> pdb=" O LYS T 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP T 37 " --> pdb=" O ILE T 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN T 51 " --> pdb=" O VAL T 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL T 35 " --> pdb=" O GLN T 51 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP T 53 " --> pdb=" O TYR T 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR T 33 " --> pdb=" O TRP T 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR T 101 " --> pdb=" O SER T 121 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP T 53 " --> pdb=" O LYS T 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP T 37 " --> pdb=" O ILE T 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN T 51 " --> pdb=" O VAL T 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL T 35 " --> pdb=" O GLN T 51 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP T 53 " --> pdb=" O TYR T 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR T 33 " --> pdb=" O TRP T 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'T' and resid 112 through 113 Processing sheet with id=AG9, first strand: chain 'U' and resid 4 through 7 Processing sheet with id=AH1, first strand: chain 'U' and resid 54 through 55 removed outlier: 6.474A pdb=" N TRP U 36 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR U 50 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL U 34 " --> pdb=" O TYR U 50 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2226 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: 8.87 Time building geometry restraints manager: 12.74 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: 8010 1.34 - 1.47: 6866 1.47 - 1.59: 11722 1.59 - 1.72: 3 1.72 - 1.84: 189 Bond restraints: 26790 Sorted by residual: bond pdb=" C ALA E 204 " pdb=" N CYS E 205 " ideal model delta sigma weight residual 1.332 1.540 -0.208 1.14e-02 7.69e+03 3.33e+02 bond pdb=" C ALA F 204 " pdb=" N CYS F 205 " ideal model delta sigma weight residual 1.332 1.273 0.058 8.60e-03 1.35e+04 4.61e+01 bond pdb=" N THR F 163 " pdb=" CA THR F 163 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.29e-02 6.01e+03 1.48e+01 bond pdb=" N THR D 163 " pdb=" CA THR D 163 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.46e+01 bond pdb=" N THR E 163 " pdb=" CA THR E 163 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.46e+01 ... (remaining 26785 not shown) Histogram of bond angle deviations from ideal: 79.26 - 94.95: 4 94.95 - 110.64: 9023 110.64 - 126.33: 26797 126.33 - 142.02: 603 142.02 - 157.71: 2 Bond angle restraints: 36429 Sorted by residual: angle pdb=" O ALA F 204 " pdb=" C ALA F 204 " pdb=" N CYS F 205 " ideal model delta sigma weight residual 122.65 157.71 -35.06 1.22e+00 6.72e-01 8.26e+02 angle pdb=" C ALA F 204 " pdb=" N CYS F 205 " pdb=" CA CYS F 205 " ideal model delta sigma weight residual 122.00 90.97 31.03 1.08e+00 8.57e-01 8.26e+02 angle pdb=" CA ALA F 204 " pdb=" C ALA F 204 " pdb=" N CYS F 205 " ideal model delta sigma weight residual 115.29 79.26 36.03 1.44e+00 4.82e-01 6.26e+02 angle pdb=" O ALA E 204 " pdb=" C ALA E 204 " pdb=" N CYS E 205 " ideal model delta sigma weight residual 122.65 152.88 -30.23 1.22e+00 6.72e-01 6.14e+02 angle pdb=" CA ALA E 204 " pdb=" C ALA E 204 " pdb=" N CYS E 205 " ideal model delta sigma weight residual 115.29 85.42 29.87 1.44e+00 4.82e-01 4.30e+02 ... (remaining 36424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 16390 21.53 - 43.06: 747 43.06 - 64.60: 156 64.60 - 86.13: 82 86.13 - 107.66: 49 Dihedral angle restraints: 17424 sinusoidal: 8154 harmonic: 9270 Sorted by residual: dihedral pdb=" C THR D 163 " pdb=" N THR D 163 " pdb=" CA THR D 163 " pdb=" CB THR D 163 " ideal model delta harmonic sigma weight residual -122.00 -150.22 28.22 0 2.50e+00 1.60e-01 1.27e+02 dihedral pdb=" C THR E 163 " pdb=" N THR E 163 " pdb=" CA THR E 163 " pdb=" CB THR E 163 " ideal model delta harmonic sigma weight residual -122.00 -150.18 28.18 0 2.50e+00 1.60e-01 1.27e+02 dihedral pdb=" C THR F 163 " pdb=" N THR F 163 " pdb=" CA THR F 163 " pdb=" CB THR F 163 " ideal model delta harmonic sigma weight residual -122.00 -150.11 28.11 0 2.50e+00 1.60e-01 1.26e+02 ... (remaining 17421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 4416 0.209 - 0.418: 75 0.418 - 0.627: 6 0.627 - 0.836: 3 0.836 - 1.044: 3 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C1 NAG s 2 " pdb=" O4 NAG s 1 " pdb=" C2 NAG s 2 " pdb=" O5 NAG s 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.12e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.23e+02 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.08e+02 ... (remaining 4500 not shown) Planarity restraints: 4512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG l 2 " -0.346 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG l 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG l 2 " -0.141 2.00e-02 2.50e+03 pdb=" N2 NAG l 2 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG l 2 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG l 1 " -0.332 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG l 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG l 1 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG l 1 " 0.498 2.00e-02 2.50e+03 pdb=" O7 NAG l 1 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG s 2 " 0.140 2.00e-02 2.50e+03 1.16e-01 1.68e+02 pdb=" C7 NAG s 2 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG s 2 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG s 2 " -0.187 2.00e-02 2.50e+03 pdb=" O7 NAG s 2 " -0.019 2.00e-02 2.50e+03 ... (remaining 4509 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 2 1.97 - 2.71: 1152 2.71 - 3.44: 34295 3.44 - 4.17: 61018 4.17 - 4.90: 103216 Nonbonded interactions: 199683 Sorted by model distance: nonbonded pdb=" NZ LYS D 155 " pdb=" CB TYR D 177 " model vdw 1.242 3.520 nonbonded pdb=" OH TYR J 103 " pdb=" OD2 ASP K 52 " model vdw 1.783 2.440 nonbonded pdb=" O SER F 158 " pdb=" OG SER F 158 " model vdw 1.976 2.440 nonbonded pdb=" O3 NAG e 2 " pdb=" O7 NAG e 2 " model vdw 2.056 2.440 nonbonded pdb=" O3 NAG s 2 " pdb=" O7 NAG s 2 " model vdw 2.103 2.440 ... (remaining 199678 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' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'q' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'g' selection = chain 'h' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'b' selection = chain 'i' selection = chain 'p' } ncs_group { reference = chain 't' selection = chain 'u' selection = chain 'v' } 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=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.280 Check model and map are aligned: 0.360 Set scattering table: 0.250 Process input model: 68.190 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.550 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.008 0.208 26790 Z= 0.475 Angle : 1.373 36.033 36429 Z= 0.777 Chirality : 0.082 1.044 4503 Planarity : 0.018 0.446 4458 Dihedral : 14.778 107.660 11343 Min Nonbonded Distance : 1.242 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.82 % Allowed : 12.13 % Favored : 87.06 % Rotamer: Outliers : 2.62 % Allowed : 5.12 % Favored : 92.26 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 4.55 % Twisted General : 0.68 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.12), residues: 3183 helix: -2.59 (0.21), residues: 399 sheet: -2.26 (0.14), residues: 1014 loop : -3.75 (0.11), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP F 45 HIS 0.015 0.002 HIS N 35 PHE 0.030 0.003 PHE E 353 TYR 0.034 0.003 TYR U 92 ARG 0.008 0.001 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 872 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 MET cc_start: 0.6135 (mmt) cc_final: 0.5494 (mmp) REVERT: B 529 THR cc_start: 0.8325 (p) cc_final: 0.8081 (t) REVERT: B 530 MET cc_start: 0.7175 (mtp) cc_final: 0.6904 (mtp) REVERT: B 570 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8388 (p) REVERT: B 620 ASN cc_start: 0.7970 (t0) cc_final: 0.7648 (p0) REVERT: C 589 ASP cc_start: 0.9034 (m-30) cc_final: 0.8786 (m-30) REVERT: C 620 ASN cc_start: 0.7869 (t0) cc_final: 0.7508 (p0) REVERT: D 95 MET cc_start: 0.6817 (ttp) cc_final: 0.6527 (mtp) REVERT: D 107 ASP cc_start: 0.8209 (t70) cc_final: 0.7856 (t70) REVERT: D 166 ARG cc_start: 0.5234 (OUTLIER) cc_final: 0.4990 (ptm160) REVERT: D 423 ILE cc_start: 0.8604 (mt) cc_final: 0.7988 (mt) REVERT: D 475 MET cc_start: 0.7147 (mmt) cc_final: 0.6635 (tpp) REVERT: E 95 MET cc_start: 0.6901 (ttp) cc_final: 0.6686 (mtp) REVERT: E 194 ILE cc_start: 0.7688 (mp) cc_final: 0.6684 (mm) REVERT: E 353 PHE cc_start: 0.7835 (m-10) cc_final: 0.7503 (m-80) REVERT: E 475 MET cc_start: 0.7584 (mmt) cc_final: 0.7148 (mmm) REVERT: F 44 VAL cc_start: 0.8645 (t) cc_final: 0.7776 (t) REVERT: F 327 ARG cc_start: 0.7190 (mtt90) cc_final: 0.6594 (mtm180) REVERT: F 413 ASN cc_start: 0.5915 (OUTLIER) cc_final: 0.5496 (t0) REVERT: F 423 ILE cc_start: 0.8296 (mt) cc_final: 0.7681 (tt) REVERT: F 435 TYR cc_start: 0.5011 (m-80) cc_final: 0.4626 (m-10) REVERT: G 5 LEU cc_start: 0.8176 (mp) cc_final: 0.7907 (tt) REVERT: G 13 GLU cc_start: 0.7574 (tp30) cc_final: 0.7077 (tm-30) REVERT: H 5 LEU cc_start: 0.8023 (mp) cc_final: 0.7556 (tt) REVERT: H 79 SER cc_start: 0.8449 (m) cc_final: 0.7605 (p) REVERT: I 5 LEU cc_start: 0.7905 (mp) cc_final: 0.7593 (tt) REVERT: I 79 SER cc_start: 0.8525 (m) cc_final: 0.7936 (p) REVERT: J 72 GLU cc_start: 0.7286 (tt0) cc_final: 0.6918 (tt0) REVERT: J 81 MET cc_start: 0.7666 (tmm) cc_final: 0.7426 (tmm) REVERT: J 95 TYR cc_start: 0.7907 (m-80) cc_final: 0.7241 (m-80) REVERT: K 50 ILE cc_start: 0.6959 (mt) cc_final: 0.6171 (mm) REVERT: L 33 SER cc_start: 0.5840 (m) cc_final: 0.5383 (t) REVERT: L 76 THR cc_start: 0.8018 (p) cc_final: 0.7140 (p) REVERT: L 81 MET cc_start: 0.7761 (tmm) cc_final: 0.7396 (tmm) REVERT: L 88 SER cc_start: 0.6997 (m) cc_final: 0.6588 (t) REVERT: M 50 ILE cc_start: 0.6989 (mt) cc_final: 0.6259 (mm) REVERT: M 51 PHE cc_start: 0.7169 (p90) cc_final: 0.6838 (p90) REVERT: N 33 SER cc_start: 0.6182 (m) cc_final: 0.5490 (t) REVERT: N 55 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7535 (mm-30) REVERT: N 67 ARG cc_start: 0.3838 (ptt180) cc_final: 0.3232 (ptt-90) REVERT: N 76 THR cc_start: 0.8059 (p) cc_final: 0.7677 (p) REVERT: N 88 SER cc_start: 0.6534 (m) cc_final: 0.5965 (t) REVERT: N 90 ASP cc_start: 0.5509 (m-30) cc_final: 0.5243 (m-30) REVERT: N 95 TYR cc_start: 0.7772 (m-80) cc_final: 0.7476 (m-80) REVERT: O 49 LEU cc_start: 0.6222 (tp) cc_final: 0.5971 (tp) REVERT: O 93 TRP cc_start: 0.7789 (t-100) cc_final: 0.7583 (t-100) REVERT: P 111 LEU cc_start: 0.8619 (mm) cc_final: 0.8244 (mt) REVERT: P 122 TRP cc_start: 0.8704 (m100) cc_final: 0.8492 (m100) REVERT: Q 33 TRP cc_start: 0.8872 (m100) cc_final: 0.7871 (m100) REVERT: Q 78 ASN cc_start: 0.8822 (t0) cc_final: 0.8433 (t0) REVERT: R 90 THR cc_start: 0.8559 (p) cc_final: 0.8242 (p) REVERT: R 105 TYR cc_start: 0.8199 (t80) cc_final: 0.7834 (t80) REVERT: R 111 LEU cc_start: 0.8927 (mm) cc_final: 0.8400 (mt) REVERT: S 2 ILE cc_start: 0.8918 (mt) cc_final: 0.8262 (pt) REVERT: S 78 ASN cc_start: 0.8171 (t0) cc_final: 0.7215 (t0) REVERT: T 63 PHE cc_start: 0.7810 (t80) cc_final: 0.7514 (t80) REVERT: T 67 VAL cc_start: 0.8624 (t) cc_final: 0.8091 (m) REVERT: T 105 TYR cc_start: 0.8214 (t80) cc_final: 0.7947 (t80) REVERT: T 111 LEU cc_start: 0.8925 (mm) cc_final: 0.8361 (mt) REVERT: T 122 TRP cc_start: 0.8700 (m100) cc_final: 0.8093 (m100) REVERT: U 2 ILE cc_start: 0.8741 (mt) cc_final: 0.8125 (pt) REVERT: U 33 TRP cc_start: 0.9140 (m100) cc_final: 0.8861 (m100) REVERT: U 70 THR cc_start: 0.7227 (p) cc_final: 0.6906 (p) REVERT: U 78 ASN cc_start: 0.8513 (t0) cc_final: 0.7543 (t0) outliers start: 69 outliers final: 18 residues processed: 910 average time/residue: 0.3914 time to fit residues: 546.3311 Evaluate side-chains 491 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 470 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 185 optimal weight: 0.2980 chunk 288 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN A 630 GLN A 641 HIS B 630 GLN B 641 HIS C 630 GLN C 641 HIS D 229 ASN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 229 ASN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 229 ASN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN I 73 ASN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN K 7 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN M 7 GLN M 40 GLN ** N 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN O 7 GLN ** O 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN U 38 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26790 Z= 0.254 Angle : 0.860 12.551 36429 Z= 0.435 Chirality : 0.053 0.472 4503 Planarity : 0.007 0.093 4458 Dihedral : 13.210 81.651 5931 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.74 % Favored : 88.72 % Rotamer: Outliers : 0.19 % Allowed : 3.38 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.12), residues: 3183 helix: -1.42 (0.24), residues: 387 sheet: -2.04 (0.15), residues: 1029 loop : -3.55 (0.11), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 45 HIS 0.005 0.001 HIS E 105 PHE 0.036 0.002 PHE P 63 TYR 0.031 0.002 TYR N 114 ARG 0.008 0.001 ARG F 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 624 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 GLN cc_start: 0.8401 (pm20) cc_final: 0.7965 (pm20) REVERT: A 629 MET cc_start: 0.6612 (mmt) cc_final: 0.6287 (mmp) REVERT: B 620 ASN cc_start: 0.7919 (t0) cc_final: 0.7537 (p0) REVERT: C 565 MET cc_start: 0.5326 (mmm) cc_final: 0.5108 (mmp) REVERT: C 589 ASP cc_start: 0.9069 (m-30) cc_final: 0.8475 (m-30) REVERT: C 620 ASN cc_start: 0.7920 (t0) cc_final: 0.7451 (p0) REVERT: C 629 MET cc_start: 0.6860 (mmt) cc_final: 0.6169 (mmp) REVERT: D 95 MET cc_start: 0.6971 (ttp) cc_final: 0.6507 (mtp) REVERT: D 423 ILE cc_start: 0.8551 (mt) cc_final: 0.7781 (mt) REVERT: D 477 ASP cc_start: 0.7092 (t0) cc_final: 0.6875 (t0) REVERT: E 95 MET cc_start: 0.7252 (ttp) cc_final: 0.6506 (mtp) REVERT: E 104 MET cc_start: 0.8386 (tpp) cc_final: 0.7837 (tpp) REVERT: F 104 MET cc_start: 0.7612 (ttt) cc_final: 0.7411 (ttt) REVERT: F 327 ARG cc_start: 0.6782 (mtt90) cc_final: 0.6399 (mtm180) REVERT: F 435 TYR cc_start: 0.5257 (m-80) cc_final: 0.4983 (m-10) REVERT: G 5 LEU cc_start: 0.8274 (mp) cc_final: 0.7928 (tt) REVERT: G 13 GLU cc_start: 0.7397 (tp30) cc_final: 0.6805 (tm-30) REVERT: G 58 ARG cc_start: 0.7147 (ptm-80) cc_final: 0.6834 (mtp-110) REVERT: H 5 LEU cc_start: 0.7961 (mp) cc_final: 0.7539 (tt) REVERT: H 78 ASP cc_start: 0.7943 (m-30) cc_final: 0.7672 (m-30) REVERT: H 79 SER cc_start: 0.8428 (m) cc_final: 0.7698 (p) REVERT: I 5 LEU cc_start: 0.7891 (mp) cc_final: 0.7560 (tt) REVERT: I 79 SER cc_start: 0.8552 (m) cc_final: 0.7928 (p) REVERT: J 10 GLU cc_start: 0.7528 (tp30) cc_final: 0.6902 (tp30) REVERT: J 76 THR cc_start: 0.8004 (p) cc_final: 0.7768 (p) REVERT: J 95 TYR cc_start: 0.7730 (m-80) cc_final: 0.7234 (m-80) REVERT: K 48 LEU cc_start: 0.6581 (pp) cc_final: 0.6223 (pp) REVERT: K 108 LYS cc_start: 0.8752 (ptmt) cc_final: 0.8132 (tppt) REVERT: L 24 VAL cc_start: 0.8306 (t) cc_final: 0.8063 (t) REVERT: L 46 GLU cc_start: 0.8815 (tp30) cc_final: 0.8536 (tp30) REVERT: L 55 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6941 (mm-30) REVERT: L 88 SER cc_start: 0.6798 (m) cc_final: 0.6402 (t) REVERT: L 112 LEU cc_start: 0.8169 (mt) cc_final: 0.7969 (mp) REVERT: M 93 TRP cc_start: 0.7778 (t-100) cc_final: 0.7395 (t-100) REVERT: M 101 GLN cc_start: 0.8831 (tt0) cc_final: 0.8584 (tt0) REVERT: N 70 MET cc_start: 0.7004 (mtp) cc_final: 0.6644 (mtt) REVERT: N 90 ASP cc_start: 0.5513 (m-30) cc_final: 0.5195 (m-30) REVERT: O 93 TRP cc_start: 0.7889 (t-100) cc_final: 0.7677 (t-100) REVERT: P 126 THR cc_start: 0.6720 (p) cc_final: 0.6486 (p) REVERT: Q 2 ILE cc_start: 0.8810 (mt) cc_final: 0.8557 (mt) REVERT: Q 78 ASN cc_start: 0.8887 (t0) cc_final: 0.8019 (t0) REVERT: R 10 GLU cc_start: 0.6742 (mp0) cc_final: 0.6533 (mp0) REVERT: R 105 TYR cc_start: 0.8016 (t80) cc_final: 0.7502 (t80) REVERT: S 9 SER cc_start: 0.7585 (m) cc_final: 0.7245 (t) REVERT: S 27 GLN cc_start: 0.7717 (mp10) cc_final: 0.7395 (mp10) REVERT: S 38 GLN cc_start: 0.8415 (tm130) cc_final: 0.8031 (tm-30) REVERT: S 40 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7775 (ttm170) REVERT: S 78 ASN cc_start: 0.8359 (t0) cc_final: 0.7343 (t0) REVERT: S 101 GLN cc_start: 0.7310 (mt0) cc_final: 0.6817 (mp10) REVERT: T 67 VAL cc_start: 0.8201 (t) cc_final: 0.7989 (m) REVERT: T 105 TYR cc_start: 0.8052 (t80) cc_final: 0.7705 (t80) REVERT: T 111 LEU cc_start: 0.9047 (mm) cc_final: 0.8469 (mt) REVERT: T 122 TRP cc_start: 0.8742 (m100) cc_final: 0.8024 (m100) REVERT: U 23 CYS cc_start: 0.2496 (p) cc_final: 0.2100 (p) REVERT: U 27 GLN cc_start: 0.7635 (mp10) cc_final: 0.7402 (mp10) REVERT: U 38 GLN cc_start: 0.8253 (tm130) cc_final: 0.8021 (tm-30) REVERT: U 78 ASN cc_start: 0.8727 (t0) cc_final: 0.8279 (t0) REVERT: U 101 GLN cc_start: 0.6958 (mt0) cc_final: 0.6707 (mp10) outliers start: 5 outliers final: 0 residues processed: 628 average time/residue: 0.3941 time to fit residues: 392.4080 Evaluate side-chains 409 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.915 > 50: distance: 36 - 134: 37.042 distance: 65 - 72: 21.846 distance: 72 - 73: 12.906 distance: 73 - 74: 5.007 distance: 73 - 76: 34.799 distance: 74 - 75: 41.007 distance: 74 - 83: 44.041 distance: 76 - 77: 45.503 distance: 77 - 78: 20.567 distance: 78 - 79: 7.423 distance: 79 - 80: 17.727 distance: 80 - 81: 11.561 distance: 80 - 82: 9.488 distance: 83 - 84: 53.780 distance: 83 - 89: 5.819 distance: 84 - 85: 62.082 distance: 84 - 87: 40.051 distance: 85 - 86: 44.770 distance: 85 - 90: 16.794 distance: 87 - 88: 26.898 distance: 88 - 89: 49.492 distance: 90 - 91: 29.153 distance: 91 - 92: 22.619 distance: 92 - 93: 8.825 distance: 92 - 94: 21.810 distance: 94 - 95: 48.924 distance: 95 - 96: 63.234 distance: 95 - 98: 9.038 distance: 96 - 97: 55.989 distance: 96 - 103: 31.416 distance: 98 - 99: 48.544 distance: 99 - 100: 27.318 distance: 100 - 101: 5.800 distance: 101 - 102: 18.347 distance: 103 - 104: 12.712 distance: 104 - 105: 35.888 distance: 104 - 107: 46.291 distance: 105 - 106: 35.236 distance: 105 - 108: 29.235 distance: 108 - 109: 14.611 distance: 108 - 114: 18.446 distance: 109 - 110: 41.522 distance: 109 - 112: 40.480 distance: 110 - 111: 15.321 distance: 110 - 115: 55.839 distance: 112 - 113: 26.212 distance: 113 - 114: 22.961 distance: 115 - 116: 42.663 distance: 116 - 117: 43.386 distance: 116 - 119: 54.456 distance: 117 - 118: 32.084 distance: 117 - 126: 10.961 distance: 119 - 120: 42.698 distance: 120 - 121: 27.311 distance: 121 - 122: 19.377 distance: 122 - 123: 9.339 distance: 123 - 124: 30.822 distance: 123 - 125: 33.266 distance: 126 - 127: 42.191 distance: 127 - 128: 25.942 distance: 127 - 130: 31.257 distance: 128 - 129: 52.276 distance: 128 - 134: 43.701 distance: 130 - 131: 43.982 distance: 131 - 132: 42.870 distance: 131 - 133: 56.578 distance: 134 - 135: 46.482 distance: 135 - 136: 45.830 distance: 135 - 138: 22.168 distance: 136 - 137: 50.148 distance: 136 - 142: 39.339 distance: 138 - 139: 33.685 distance: 139 - 140: 18.628 distance: 139 - 141: 26.006 distance: 142 - 143: 19.004 distance: 143 - 144: 28.105 distance: 143 - 146: 40.866 distance: 144 - 145: 21.894 distance: 144 - 150: 29.613 distance: 146 - 147: 60.788 distance: 146 - 148: 38.805 distance: 147 - 149: 19.867