Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 06:07:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/07_2023/6jx7_9891.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/07_2023/6jx7_9891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/07_2023/6jx7_9891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/07_2023/6jx7_9891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/07_2023/6jx7_9891.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/07_2023/6jx7_9891.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 sd= 0.895 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 156 5.16 5 C 20265 2.51 5 N 4938 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 268": "OE1" <-> "OE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1158": "OE1" <-> "OE2" Residue "A GLU 1161": "OE1" <-> "OE2" Residue "A GLU 1200": "OE1" <-> "OE2" Residue "A GLU 1204": "OE1" <-> "OE2" Residue "A PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1247": "OE1" <-> "OE2" Residue "A GLU 1316": "OE1" <-> "OE2" Residue "A GLU 1333": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 641": "OE1" <-> "OE2" Residue "B GLU 876": "OE1" <-> "OE2" Residue "B PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1158": "OE1" <-> "OE2" Residue "B GLU 1161": "OE1" <-> "OE2" Residue "B GLU 1200": "OE1" <-> "OE2" Residue "B GLU 1204": "OE1" <-> "OE2" Residue "B PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1247": "OE1" <-> "OE2" Residue "B GLU 1316": "OE1" <-> "OE2" Residue "B GLU 1333": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C GLU 876": "OE1" <-> "OE2" Residue "C PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1158": "OE1" <-> "OE2" Residue "C GLU 1161": "OE1" <-> "OE2" Residue "C GLU 1200": "OE1" <-> "OE2" Residue "C GLU 1204": "OE1" <-> "OE2" Residue "C PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1247": "OE1" <-> "OE2" Residue "C GLU 1316": "OE1" <-> "OE2" Residue "C GLU 1333": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 32115 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "B" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "C" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 chiralities: 7 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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 chiralities: 2 Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "S" 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 chiralities: 5 Chain: "T" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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 chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "k" 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 chiralities: 5 Chain: "l" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "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 chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 chiralities: 2 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "2" 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 chiralities: 5 Chain: "3" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 15.90, per 1000 atoms: 0.50 Number of scatterers: 32115 At special positions: 0 Unit cell: (180.96, 194.01, 180.09, 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 156 16.00 O 6756 8.00 N 4938 7.00 C 20265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 178 " distance=2.05 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 510 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 644 " distance=2.05 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 702 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 820 " - pdb=" SG CYS A 832 " distance=2.03 Simple disulfide: pdb=" SG CYS A 889 " - pdb=" SG CYS A 911 " distance=2.03 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS A1003 " - pdb=" SG CYS A1014 " distance=2.03 Simple disulfide: pdb=" SG CYS A1205 " - pdb=" SG CYS A1216 " distance=2.02 Simple disulfide: pdb=" SG CYS A1255 " - pdb=" SG CYS A1302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 178 " distance=2.05 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 510 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 644 " distance=2.05 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 702 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 820 " - pdb=" SG CYS B 832 " distance=2.03 Simple disulfide: pdb=" SG CYS B 889 " - pdb=" SG CYS B 911 " distance=2.03 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B1003 " - pdb=" SG CYS B1014 " distance=2.03 Simple disulfide: pdb=" SG CYS B1205 " - pdb=" SG CYS B1216 " distance=2.02 Simple disulfide: pdb=" SG CYS B1255 " - pdb=" SG CYS B1302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 178 " distance=2.05 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 510 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 644 " distance=2.05 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 702 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 820 " - pdb=" SG CYS C 832 " distance=2.03 Simple disulfide: pdb=" SG CYS C 889 " - pdb=" SG CYS C 911 " distance=2.03 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS C1003 " - pdb=" SG CYS C1014 " distance=2.03 Simple disulfide: pdb=" SG CYS C1205 " - pdb=" SG CYS C1216 " distance=2.02 Simple disulfide: pdb=" SG CYS C1255 " - pdb=" SG CYS C1302 " 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 3 4 " - " MAN 3 5 " " MAN I 4 " - " MAN I 5 " " MAN T 4 " - " MAN T 5 " " MAN a 4 " - " MAN a 5 " " MAN l 4 " - " MAN l 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA I 3 " - " MAN I 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA a 3 " - " MAN a 4 " " BMA k 3 " - " MAN k 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA 2 3 " - " MAN 2 5 " " BMA 3 3 " - " MAN 3 6 " " BMA I 3 " - " MAN I 6 " " MAN I 6 " - " MAN I 7 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 6 " " BMA a 3 " - " MAN a 6 " " MAN a 6 " - " MAN a 7 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 4 " " BMA k 3 " - " MAN k 5 " " BMA l 3 " - " MAN l 6 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 7 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG 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 d 2 " - " BMA d 3 " " 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 j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " 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 o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " 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 t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " BETA1-6 " NAG 1 1 " - " FUC 1 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 4 " " NAG j 1 " - " FUC j 4 " NAG-ASN " NAG 0 1 " - " ASN C 868 " " NAG 1 1 " - " ASN C 949 " " NAG 2 1 " - " ASN C1092 " " NAG 3 1 " - " ASN C1218 " " NAG 4 1 " - " ASN C1308 " " NAG A1508 " - " ASN A 260 " " NAG A1522 " - " ASN A 380 " " NAG A1523 " - " ASN A 464 " " NAG A1535 " - " ASN A 585 " " NAG A1536 " - " ASN A 590 " " NAG A1541 " - " ASN A 819 " " NAG A1568 " - " ASN A1257 " " NAG A1569 " - " ASN A1275 " " NAG A1572 " - " ASN A1325 " " NAG B1508 " - " ASN B 260 " " NAG B1522 " - " ASN B 380 " " NAG B1523 " - " ASN B 464 " " NAG B1535 " - " ASN B 585 " " NAG B1536 " - " ASN B 590 " " NAG B1541 " - " ASN B 819 " " NAG B1568 " - " ASN B1257 " " NAG B1569 " - " ASN B1275 " " NAG B1572 " - " ASN B1325 " " NAG C1509 " - " ASN C 260 " " NAG C1523 " - " ASN C 380 " " NAG C1524 " - " ASN C 464 " " NAG C1536 " - " ASN C 585 " " NAG C1537 " - " ASN C 590 " " NAG C1542 " - " ASN C 819 " " NAG C1569 " - " ASN C1257 " " NAG C1570 " - " ASN C1275 " " NAG C1573 " - " ASN C1325 " " NAG D 1 " - " ASN A 161 " " NAG E 1 " - " ASN A 246 " " NAG F 1 " - " ASN A 254 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 346 " " NAG I 1 " - " ASN A 357 " " NAG J 1 " - " ASN A 482 " " NAG K 1 " - " ASN A 491 " " NAG L 1 " - " ASN A 547 " " NAG M 1 " - " ASN A 774 " " NAG N 1 " - " ASN A 814 " " NAG O 1 " - " ASN A 841 " " NAG P 1 " - " ASN A 862 " " NAG Q 1 " - " ASN A 868 " " NAG R 1 " - " ASN A 949 " " NAG S 1 " - " ASN A1092 " " NAG T 1 " - " ASN A1218 " " NAG U 1 " - " ASN A1308 " " NAG V 1 " - " ASN B 161 " " NAG W 1 " - " ASN B 246 " " NAG X 1 " - " ASN B 254 " " NAG Y 1 " - " ASN B 331 " " NAG Z 1 " - " ASN B 346 " " NAG a 1 " - " ASN B 357 " " NAG b 1 " - " ASN B 482 " " NAG c 1 " - " ASN B 491 " " NAG d 1 " - " ASN B 547 " " NAG e 1 " - " ASN B 774 " " NAG f 1 " - " ASN B 814 " " NAG g 1 " - " ASN B 841 " " NAG h 1 " - " ASN B 862 " " NAG i 1 " - " ASN B 868 " " NAG j 1 " - " ASN B 949 " " NAG k 1 " - " ASN B1092 " " NAG l 1 " - " ASN B1218 " " NAG m 1 " - " ASN B1308 " " NAG n 1 " - " ASN C 161 " " NAG o 1 " - " ASN C 246 " " NAG p 1 " - " ASN C 254 " " NAG q 1 " - " ASN C 331 " " NAG r 1 " - " ASN C 346 " " NAG s 1 " - " ASN C 357 " " NAG t 1 " - " ASN C 482 " " NAG u 1 " - " ASN C 491 " " NAG v 1 " - " ASN C 547 " " NAG w 1 " - " ASN C 774 " " NAG x 1 " - " ASN C 814 " " NAG y 1 " - " ASN C 841 " " NAG z 1 " - " ASN C 862 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.72 Conformation dependent library (CDL) restraints added in 4.8 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7032 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 54 sheets defined 22.6% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 513 removed outlier: 3.556A pdb=" N ILE A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 574' Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR A 892 " --> pdb=" O ASP A 888 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 893 " --> pdb=" O CYS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN A 902 " --> pdb=" O ARG A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 902' Processing helix chain 'A' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN A 906 " --> pdb=" O LEU A 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 903 through 906' Processing helix chain 'A' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 915 " --> pdb=" O CYS A 911 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 970 removed outlier: 4.194A pdb=" N SER A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 969 " --> pdb=" O GLY A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 985 Processing helix chain 'A' and resid 1011 through 1019 removed outlier: 3.784A pdb=" N ASN A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY A1043 " --> pdb=" O SER A1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A1045 " --> pdb=" O ILE A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.873A pdb=" N ASN A1066 " --> pdb=" O GLN A1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A1080 " --> pdb=" O GLN A1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A1098 " --> pdb=" O THR A1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER A1116 " --> pdb=" O ASN A1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A1117 " --> pdb=" O SER A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU A1132 " --> pdb=" O GLN A1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1140 No H-bonds generated for 'chain 'A' and resid 1138 through 1140' Processing helix chain 'A' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA A1164 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A1168 " --> pdb=" O ALA A1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A1169 " --> pdb=" O GLN A1165 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A1187 " --> pdb=" O GLN A1183 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A1200 " --> pdb=" O GLN A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1294 No H-bonds generated for 'chain 'A' and resid 1292 through 1294' Processing helix chain 'A' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU A1316 " --> pdb=" O THR A1312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1317 " --> pdb=" O THR A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR A1327 " --> pdb=" O ASP A1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A1329 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A1330 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A1331 " --> pdb=" O THR A1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 removed outlier: 3.556A pdb=" N ILE B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU B 571 " --> pdb=" O GLY B 567 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 573 " --> pdb=" O PRO B 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 567 through 574' Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR B 892 " --> pdb=" O ASP B 888 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 893 " --> pdb=" O CYS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU B 901 " --> pdb=" O ASN B 897 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 902 " --> pdb=" O ARG B 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 897 through 902' Processing helix chain 'B' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN B 906 " --> pdb=" O LEU B 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 903 through 906' Processing helix chain 'B' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR B 913 " --> pdb=" O SER B 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 914 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 915 " --> pdb=" O CYS B 911 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 925 " --> pdb=" O GLY B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 970 removed outlier: 4.193A pdb=" N SER B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 969 " --> pdb=" O GLY B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 985 Processing helix chain 'B' and resid 1011 through 1019 removed outlier: 3.783A pdb=" N ASN B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY B1043 " --> pdb=" O SER B1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B1045 " --> pdb=" O ILE B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1067 removed outlier: 3.872A pdb=" N ASN B1066 " --> pdb=" O GLN B1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B1067 " --> pdb=" O ALA B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B1080 " --> pdb=" O GLN B1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B1098 " --> pdb=" O THR B1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B1099 " --> pdb=" O LEU B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER B1116 " --> pdb=" O ASN B1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B1117 " --> pdb=" O SER B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU B1132 " --> pdb=" O GLN B1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B1133 " --> pdb=" O GLY B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1140 No H-bonds generated for 'chain 'B' and resid 1138 through 1140' Processing helix chain 'B' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE B1153 " --> pdb=" O SER B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA B1164 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B1168 " --> pdb=" O ALA B1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B1169 " --> pdb=" O GLN B1165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B1183 " --> pdb=" O ALA B1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B1187 " --> pdb=" O GLN B1183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B1200 " --> pdb=" O GLN B1196 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1294 No H-bonds generated for 'chain 'B' and resid 1292 through 1294' Processing helix chain 'B' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN B1315 " --> pdb=" O HIS B1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B1316 " --> pdb=" O THR B1312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B1317 " --> pdb=" O THR B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR B1327 " --> pdb=" O ASP B1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B1329 " --> pdb=" O ASN B1325 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B1330 " --> pdb=" O LYS B1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B1331 " --> pdb=" O THR B1327 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 513 removed outlier: 3.555A pdb=" N ILE C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 566 Processing helix chain 'C' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 573 " --> pdb=" O PRO C 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 574' Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR C 892 " --> pdb=" O ASP C 888 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 893 " --> pdb=" O CYS C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU C 901 " --> pdb=" O ASN C 897 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 897 through 902' Processing helix chain 'C' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN C 906 " --> pdb=" O LEU C 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 903 through 906' Processing helix chain 'C' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR C 913 " --> pdb=" O SER C 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 914 " --> pdb=" O ALA C 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 915 " --> pdb=" O CYS C 911 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY C 921 " --> pdb=" O SER C 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 970 removed outlier: 4.194A pdb=" N SER C 968 " --> pdb=" O ASP C 964 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 969 " --> pdb=" O GLY C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 985 Processing helix chain 'C' and resid 1011 through 1019 removed outlier: 3.783A pdb=" N ASN C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY C1043 " --> pdb=" O SER C1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C1045 " --> pdb=" O ILE C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1067 removed outlier: 3.873A pdb=" N ASN C1066 " --> pdb=" O GLN C1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C1067 " --> pdb=" O ALA C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN C1079 " --> pdb=" O LEU C1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C1080 " --> pdb=" O GLN C1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C1098 " --> pdb=" O THR C1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C1099 " --> pdb=" O LEU C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER C1116 " --> pdb=" O ASN C1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C1117 " --> pdb=" O SER C1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU C1132 " --> pdb=" O GLN C1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER C1133 " --> pdb=" O GLY C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1140 No H-bonds generated for 'chain 'C' and resid 1138 through 1140' Processing helix chain 'C' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE C1153 " --> pdb=" O SER C1149 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA C1164 " --> pdb=" O VAL C1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN C1165 " --> pdb=" O GLU C1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C1168 " --> pdb=" O ALA C1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C1169 " --> pdb=" O GLN C1165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C1183 " --> pdb=" O ALA C1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C1187 " --> pdb=" O GLN C1183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C1200 " --> pdb=" O GLN C1196 " (cutoff:3.500A) Processing helix chain 'C' and resid 1292 through 1294 No H-bonds generated for 'chain 'C' and resid 1292 through 1294' Processing helix chain 'C' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN C1315 " --> pdb=" O HIS C1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C1316 " --> pdb=" O THR C1312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C1317 " --> pdb=" O THR C1313 " (cutoff:3.500A) Processing helix chain 'C' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR C1327 " --> pdb=" O ASP C1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C1329 " --> pdb=" O ASN C1325 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP C1330 " --> pdb=" O LYS C1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C1331 " --> pdb=" O THR C1327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA A 227 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A 107 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 124 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 151 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 180 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN A 199 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 324 removed outlier: 3.785A pdb=" N VAL A 312 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 482 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 320 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR A 480 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS A 322 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 478 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE A 447 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 324 removed outlier: 3.785A pdb=" N VAL A 312 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 482 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 320 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR A 480 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS A 322 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 478 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP A 485 " --> pdb=" O TYR A 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR A 500 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 487 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU A 498 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP A 489 " --> pdb=" O THR A 496 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA A 334 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 383 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 removed outlier: 5.796A pdb=" N TYR A 413 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 431 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N CYS A 415 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 427 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE A 770 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 809 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 771 " --> pdb=" O TYR A 807 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 807 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.503A pdb=" N GLY A 712 " --> pdb=" O TYR A 705 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU A 737 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 591 removed outlier: 3.553A pdb=" N HIS A 578 " --> pdb=" O HIS A 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 552 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 554 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU A 601 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 623 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 659 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 621 " --> pdb=" O VAL A 659 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU A 601 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 642 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 678 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 829 through 831 Processing sheet with id=AB4, first strand: chain 'A' and resid 843 through 844 removed outlier: 6.089A pdb=" N THR A 843 " --> pdb=" O VAL C 935 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 862 through 864 Processing sheet with id=AB6, first strand: chain 'A' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY A1232 " --> pdb=" O SER A1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER A1228 " --> pdb=" O GLY A1232 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A1234 " --> pdb=" O VAL A1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1226 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE A1236 " --> pdb=" O SER A1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A1224 " --> pdb=" O PHE A1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A1238 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AB8, first strand: chain 'A' and resid 934 through 935 Processing sheet with id=AB9, first strand: chain 'A' and resid 1296 through 1299 Processing sheet with id=AC1, first strand: chain 'A' and resid 1269 through 1273 Processing sheet with id=AC2, first strand: chain 'B' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA B 227 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 107 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 124 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 151 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 180 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN B 199 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL B 312 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN B 482 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 320 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 480 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS B 322 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 478 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 447 " --> pdb=" O TYR B 454 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL B 312 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN B 482 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 320 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 480 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS B 322 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 478 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP B 485 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR B 500 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET B 487 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU B 498 " --> pdb=" O MET B 487 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP B 489 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA B 334 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 383 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 386 through 387 removed outlier: 5.796A pdb=" N TYR B 413 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE B 431 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS B 415 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 427 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE B 770 " --> pdb=" O GLN B 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 809 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 771 " --> pdb=" O TYR B 807 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 807 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 534 through 537 removed outlier: 3.504A pdb=" N GLY B 712 " --> pdb=" O TYR B 705 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU B 737 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 588 through 591 removed outlier: 3.552A pdb=" N HIS B 578 " --> pdb=" O HIS B 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 552 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 554 " --> pdb=" O THR B 608 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU B 601 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 623 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 659 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 621 " --> pdb=" O VAL B 659 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU B 601 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 642 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 678 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 829 through 831 Processing sheet with id=AD5, first strand: chain 'B' and resid 862 through 864 Processing sheet with id=AD6, first strand: chain 'B' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY B1232 " --> pdb=" O SER B1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER B1228 " --> pdb=" O GLY B1232 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B1234 " --> pdb=" O VAL B1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B1226 " --> pdb=" O LEU B1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE B1236 " --> pdb=" O SER B1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B1224 " --> pdb=" O PHE B1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR B1238 " --> pdb=" O LEU B1222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 885 through 887 Processing sheet with id=AD8, first strand: chain 'B' and resid 934 through 935 Processing sheet with id=AD9, first strand: chain 'B' and resid 1296 through 1299 Processing sheet with id=AE1, first strand: chain 'B' and resid 1269 through 1273 Processing sheet with id=AE2, first strand: chain 'C' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA C 227 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 107 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 124 " --> pdb=" O SER C 228 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 151 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 180 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN C 199 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL C 312 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 482 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 320 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR C 480 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS C 322 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 478 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE C 447 " --> pdb=" O TYR C 454 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL C 312 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 482 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 320 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR C 480 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS C 322 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 478 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP C 485 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR C 500 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET C 487 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 498 " --> pdb=" O MET C 487 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP C 489 " --> pdb=" O THR C 496 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA C 334 " --> pdb=" O PHE C 465 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 383 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 386 through 387 removed outlier: 5.797A pdb=" N TYR C 413 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE C 431 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS C 415 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 427 " --> pdb=" O ALA C 417 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE C 770 " --> pdb=" O GLN C 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 809 " --> pdb=" O ALA C 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 771 " --> pdb=" O TYR C 807 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 807 " --> pdb=" O THR C 771 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 534 through 537 removed outlier: 3.503A pdb=" N GLY C 712 " --> pdb=" O TYR C 705 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU C 737 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 588 through 591 removed outlier: 3.553A pdb=" N HIS C 578 " --> pdb=" O HIS C 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 552 " --> pdb=" O LYS C 606 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 554 " --> pdb=" O THR C 608 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU C 601 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 623 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 659 " --> pdb=" O GLN C 621 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 621 " --> pdb=" O VAL C 659 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU C 601 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 642 " --> pdb=" O LYS C 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 678 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 829 through 831 Processing sheet with id=AF5, first strand: chain 'C' and resid 862 through 864 Processing sheet with id=AF6, first strand: chain 'C' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY C1232 " --> pdb=" O SER C1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER C1228 " --> pdb=" O GLY C1232 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C1234 " --> pdb=" O VAL C1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL C1226 " --> pdb=" O LEU C1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE C1236 " --> pdb=" O SER C1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER C1224 " --> pdb=" O PHE C1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C1238 " --> pdb=" O LEU C1222 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 885 through 887 Processing sheet with id=AF8, first strand: chain 'C' and resid 1296 through 1299 Processing sheet with id=AF9, first strand: chain 'C' and resid 1269 through 1273 875 hydrogen bonds defined for protein. 2427 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: 15.33 Time building geometry restraints manager: 17.52 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: 9685 1.34 - 1.47: 9241 1.47 - 1.60: 13642 1.60 - 1.73: 0 1.73 - 1.86: 222 Bond restraints: 32790 Sorted by residual: bond pdb=" C3 NAG 3 1 " pdb=" C4 NAG 3 1 " ideal model delta sigma weight residual 1.524 1.455 0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C3 NAG l 1 " pdb=" C4 NAG l 1 " ideal model delta sigma weight residual 1.524 1.456 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C3 NAG T 1 " pdb=" C4 NAG T 1 " ideal model delta sigma weight residual 1.524 1.456 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" N LYS B 85 " pdb=" CA LYS B 85 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.26e-02 6.30e+03 9.13e+00 bond pdb=" N TYR B 253 " pdb=" CA TYR B 253 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 9.08e+00 ... (remaining 32785 not shown) Histogram of bond angle deviations from ideal: 94.43 - 102.38: 126 102.38 - 110.32: 10180 110.32 - 118.27: 16119 118.27 - 126.21: 17855 126.21 - 134.16: 423 Bond angle restraints: 44703 Sorted by residual: angle pdb=" C GLN C 775 " pdb=" N THR C 776 " pdb=" CA THR C 776 " ideal model delta sigma weight residual 120.87 110.35 10.52 1.42e+00 4.96e-01 5.49e+01 angle pdb=" C GLN A 775 " pdb=" N THR A 776 " pdb=" CA THR A 776 " ideal model delta sigma weight residual 120.87 110.35 10.52 1.42e+00 4.96e-01 5.48e+01 angle pdb=" C GLN B 775 " pdb=" N THR B 776 " pdb=" CA THR B 776 " ideal model delta sigma weight residual 120.87 110.37 10.50 1.42e+00 4.96e-01 5.47e+01 angle pdb=" C ASN A 774 " pdb=" CA ASN A 774 " pdb=" CB ASN A 774 " ideal model delta sigma weight residual 110.42 95.72 14.70 1.99e+00 2.53e-01 5.45e+01 angle pdb=" C ASN B 774 " pdb=" CA ASN B 774 " pdb=" CB ASN B 774 " ideal model delta sigma weight residual 110.42 95.73 14.69 1.99e+00 2.53e-01 5.45e+01 ... (remaining 44698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 15720 17.75 - 35.51: 1596 35.51 - 53.26: 207 53.26 - 71.01: 63 71.01 - 88.77: 27 Dihedral angle restraints: 17613 sinusoidal: 6654 harmonic: 10959 Sorted by residual: dihedral pdb=" C ASN A 774 " pdb=" N ASN A 774 " pdb=" CA ASN A 774 " pdb=" CB ASN A 774 " ideal model delta harmonic sigma weight residual -122.60 -99.83 -22.77 0 2.50e+00 1.60e-01 8.30e+01 dihedral pdb=" C ASN C 774 " pdb=" N ASN C 774 " pdb=" CA ASN C 774 " pdb=" CB ASN C 774 " ideal model delta harmonic sigma weight residual -122.60 -99.84 -22.76 0 2.50e+00 1.60e-01 8.29e+01 dihedral pdb=" C ASN B 774 " pdb=" N ASN B 774 " pdb=" CA ASN B 774 " pdb=" CB ASN B 774 " ideal model delta harmonic sigma weight residual -122.60 -99.84 -22.76 0 2.50e+00 1.60e-01 8.29e+01 ... (remaining 17610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 5703 0.310 - 0.619: 56 0.619 - 0.929: 13 0.929 - 1.239: 3 1.239 - 1.548: 3 Chirality restraints: 5778 Sorted by residual: chirality pdb=" C1 MAN T 6 " pdb=" O6 BMA T 3 " pdb=" C2 MAN T 6 " pdb=" O5 MAN T 6 " both_signs ideal model delta sigma weight residual False 2.40 0.85 1.55 2.00e-02 2.50e+03 5.99e+03 chirality pdb=" C1 MAN l 6 " pdb=" O6 BMA l 3 " pdb=" C2 MAN l 6 " pdb=" O5 MAN l 6 " both_signs ideal model delta sigma weight residual False 2.40 0.85 1.55 2.00e-02 2.50e+03 5.99e+03 chirality pdb=" C1 MAN 3 6 " pdb=" O6 BMA 3 3 " pdb=" C2 MAN 3 6 " pdb=" O5 MAN 3 6 " both_signs ideal model delta sigma weight residual False 2.40 0.86 1.54 2.00e-02 2.50e+03 5.95e+03 ... (remaining 5775 not shown) Planarity restraints: 5457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG M 2 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG e 2 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG e 2 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG e 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG e 2 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG w 2 " 0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG w 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG w 2 " 0.161 2.00e-02 2.50e+03 pdb=" N2 NAG w 2 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG w 2 " 0.104 2.00e-02 2.50e+03 ... (remaining 5454 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 847 2.65 - 3.21: 29237 3.21 - 3.78: 49006 3.78 - 4.34: 62037 4.34 - 4.90: 100985 Nonbonded interactions: 242112 Sorted by model distance: nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.092 2.440 nonbonded pdb=" O3 NAG w 1 " pdb=" O7 NAG w 1 " model vdw 2.092 2.440 nonbonded pdb=" O3 NAG e 1 " pdb=" O7 NAG e 1 " model vdw 2.092 2.440 nonbonded pdb=" OD1 ASN B 254 " pdb=" OG1 THR B 256 " model vdw 2.172 2.440 nonbonded pdb=" OD1 ASN C 254 " pdb=" OG1 THR C 256 " model vdw 2.173 2.440 ... (remaining 242107 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 '0' selection = chain '4' selection = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = (chain '1' and resid 1 through 3) selection = (chain 'J' and resid 1 through 3) selection = (chain 'L' and resid 1 through 3) selection = (chain 'O' and resid 1 through 3) selection = (chain 'P' and resid 1 through 3) selection = (chain 'R' and resid 1 through 3) selection = (chain 'b' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) selection = (chain 'g' and resid 1 through 3) selection = (chain 'h' and resid 1 through 3) selection = (chain 'j' and resid 1 through 3) selection = (chain 't' and resid 1 through 3) selection = (chain 'v' and resid 1 through 3) selection = (chain 'y' and resid 1 through 3) selection = (chain 'z' and resid 1 through 3) } ncs_group { reference = chain '2' selection = chain 'S' selection = chain 'k' } ncs_group { reference = chain '3' selection = chain 'I' selection = chain 'T' selection = chain 'a' selection = chain 'l' selection = chain 's' } ncs_group { reference = (chain 'A' and (resid 62 through 1337 or resid 1522 through 1523 or resid 1536 t \ hrough 1572)) selection = (chain 'B' and (resid 62 through 1337 or resid 1522 through 1523 or resid 1536 t \ hrough 1572)) selection = (chain 'C' and (resid 62 through 1337 or resid 1509 through 1523 or resid 1536 t \ hrough 1570)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'o' selection = chain 'q' selection = chain 'r' } 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: 11.020 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: 0.030 Extract box with map and model: 22.360 Check model and map are aligned: 0.550 Set scattering table: 0.270 Process input model: 88.040 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 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 : 0.010 0.072 32790 Z= 0.607 Angle : 1.263 16.774 44703 Z= 0.604 Chirality : 0.098 1.548 5778 Planarity : 0.020 0.299 5376 Dihedral : 14.573 88.768 10455 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.32 % Favored : 87.36 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.20 (0.10), residues: 3717 helix: -3.94 (0.08), residues: 729 sheet: -2.68 (0.16), residues: 906 loop : -3.75 (0.10), residues: 2082 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 782 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 807 average time/residue: 0.4207 time to fit residues: 550.8216 Evaluate side-chains 523 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 514 time to evaluate : 3.766 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 9 average time/residue: 0.2818 time to fit residues: 9.7799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.6980 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 96 optimal weight: 0.0970 chunk 190 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 337 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 92 GLN A 93 ASN A 95 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 220 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 411 ASN A 418 ASN ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN A 660 HIS A 667 GLN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN A 763 ASN A 899 HIS A 906 GLN A1066 ASN A1122 GLN A1126 ASN B 83 ASN B 92 GLN B 93 ASN B 95 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN B 220 ASN B 372 GLN B 411 ASN B 418 ASN B 450 ASN B 458 GLN B 551 HIS ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN B 660 HIS B 667 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 ASN B 899 HIS B1066 ASN B1122 GLN B1126 ASN C 77 ASN C 83 ASN C 92 GLN C 93 ASN C 95 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 177 GLN C 220 ASN C 372 GLN C 411 ASN C 418 ASN ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN C 660 HIS C 667 GLN ** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 758 GLN C 763 ASN C 986 ASN C1066 ASN C1122 GLN C1126 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 32790 Z= 0.198 Angle : 0.815 10.351 44703 Z= 0.385 Chirality : 0.051 0.422 5778 Planarity : 0.004 0.056 5376 Dihedral : 6.796 36.646 4014 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.57 % Favored : 88.35 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.33 % 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: -3.97 (0.12), residues: 3717 helix: -1.30 (0.16), residues: 759 sheet: -2.33 (0.16), residues: 864 loop : -3.42 (0.11), residues: 2094 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 646 time to evaluate : 3.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 56 residues processed: 717 average time/residue: 0.4104 time to fit residues: 498.0835 Evaluate side-chains 594 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 538 time to evaluate : 4.529 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 3 residues processed: 56 average time/residue: 0.3745 time to fit residues: 43.8070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 281 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 338 optimal weight: 0.8980 chunk 365 optimal weight: 0.8980 chunk 301 optimal weight: 5.9990 chunk 335 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN A 916 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 GLN B 906 GLN ** B1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1227 ASN B1315 GLN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN C 515 HIS C 583 GLN ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 906 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 32790 Z= 0.193 Angle : 0.718 9.551 44703 Z= 0.346 Chirality : 0.049 0.393 5778 Planarity : 0.004 0.045 5376 Dihedral : 6.361 32.494 4014 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.78 % Favored : 88.14 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.17 % 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: -3.45 (0.12), residues: 3717 helix: -0.28 (0.18), residues: 762 sheet: -2.07 (0.16), residues: 912 loop : -3.33 (0.11), residues: 2043 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 572 time to evaluate : 3.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 60 residues processed: 635 average time/residue: 0.3758 time to fit residues: 403.7770 Evaluate side-chains 588 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 528 time to evaluate : 3.224 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 60 outliers final: 1 residues processed: 60 average time/residue: 0.2717 time to fit residues: 35.4901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 7.9990 chunk 254 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 339 optimal weight: 8.9990 chunk 359 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 321 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 109 HIS ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 HIS ** A1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN ** B1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 ASN C1112 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 32790 Z= 0.294 Angle : 0.739 9.656 44703 Z= 0.359 Chirality : 0.049 0.328 5778 Planarity : 0.004 0.044 5376 Dihedral : 6.255 33.202 4014 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -3.18 (0.13), residues: 3717 helix: 0.20 (0.19), residues: 756 sheet: -2.06 (0.16), residues: 921 loop : -3.18 (0.12), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 571 time to evaluate : 3.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 56 residues processed: 643 average time/residue: 0.3957 time to fit residues: 425.6534 Evaluate side-chains 577 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 521 time to evaluate : 3.431 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.2852 time to fit residues: 34.8126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 322 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS A 515 HIS ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 ASN A1112 ASN A1269 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 ASN ** B1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 GLN ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 ASN C1078 ASN C1269 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 32790 Z= 0.325 Angle : 0.745 9.613 44703 Z= 0.363 Chirality : 0.049 0.343 5778 Planarity : 0.004 0.043 5376 Dihedral : 6.238 30.895 4014 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.62 % Favored : 87.30 % Rotamer Outliers : 3.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.05 (0.13), residues: 3717 helix: 0.44 (0.19), residues: 756 sheet: -2.08 (0.17), residues: 903 loop : -3.09 (0.12), residues: 2058 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 546 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 64 residues processed: 610 average time/residue: 0.3804 time to fit residues: 393.1232 Evaluate side-chains 580 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 516 time to evaluate : 3.533 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.2933 time to fit residues: 40.2675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.8980 chunk 323 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 211 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 359 optimal weight: 0.5980 chunk 298 optimal weight: 7.9990 chunk 166 optimal weight: 0.0020 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 0.0010 chunk 188 optimal weight: 0.7980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1155 ASN ** B1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1269 HIS C 92 GLN ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 906 GLN C 986 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 32790 Z= 0.150 Angle : 0.669 9.634 44703 Z= 0.325 Chirality : 0.047 0.332 5778 Planarity : 0.003 0.040 5376 Dihedral : 5.916 29.908 4014 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.13), residues: 3717 helix: 0.76 (0.19), residues: 780 sheet: -1.78 (0.18), residues: 825 loop : -2.93 (0.12), residues: 2112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 588 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 20 residues processed: 601 average time/residue: 0.4087 time to fit residues: 410.7143 Evaluate side-chains 543 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 523 time to evaluate : 3.454 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2848 time to fit residues: 15.5652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 262 optimal weight: 5.9990 chunk 203 optimal weight: 0.2980 chunk 302 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 358 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** A1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1227 ASN B1269 HIS C 621 GLN ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 32790 Z= 0.169 Angle : 0.655 9.609 44703 Z= 0.318 Chirality : 0.047 0.330 5778 Planarity : 0.003 0.042 5376 Dihedral : 5.737 29.551 4014 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.14), residues: 3717 helix: 0.97 (0.20), residues: 774 sheet: -1.67 (0.18), residues: 822 loop : -2.83 (0.12), residues: 2121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 539 time to evaluate : 3.434 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 outliers start: 44 outliers final: 23 residues processed: 564 average time/residue: 0.4006 time to fit residues: 382.7581 Evaluate side-chains 545 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 522 time to evaluate : 3.490 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3086 time to fit residues: 17.9317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 244 optimal weight: 0.0670 chunk 177 optimal weight: 0.3980 chunk 33 optimal weight: 8.9990 chunk 281 optimal weight: 6.9990 overall best weight: 1.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN A 623 GLN ** A1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 ASN B1298 GLN B1315 GLN ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 32790 Z= 0.192 Angle : 0.668 10.051 44703 Z= 0.325 Chirality : 0.047 0.324 5778 Planarity : 0.003 0.041 5376 Dihedral : 5.722 29.124 4014 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.14), residues: 3717 helix: 1.06 (0.20), residues: 768 sheet: -1.60 (0.18), residues: 816 loop : -2.77 (0.12), residues: 2133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 542 time to evaluate : 3.434 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 outliers start: 49 outliers final: 29 residues processed: 568 average time/residue: 0.3922 time to fit residues: 375.9745 Evaluate side-chains 548 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 519 time to evaluate : 3.275 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3189 time to fit residues: 23.0594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.6980 chunk 343 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 262 optimal weight: 0.0020 chunk 102 optimal weight: 5.9990 chunk 301 optimal weight: 0.2980 chunk 316 optimal weight: 0.7980 chunk 332 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 GLN ** A1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 GLN B1187 GLN B1269 HIS C 621 GLN ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 32790 Z= 0.157 Angle : 0.660 11.825 44703 Z= 0.322 Chirality : 0.046 0.319 5778 Planarity : 0.003 0.040 5376 Dihedral : 5.618 28.618 4014 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3717 helix: 1.21 (0.20), residues: 750 sheet: -1.60 (0.18), residues: 849 loop : -2.68 (0.13), residues: 2118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 549 time to evaluate : 3.546 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 outliers start: 30 outliers final: 22 residues processed: 567 average time/residue: 0.3999 time to fit residues: 380.5695 Evaluate side-chains 544 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 522 time to evaluate : 3.493 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3284 time to fit residues: 18.2428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.1980 chunk 353 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 370 optimal weight: 0.0370 chunk 341 optimal weight: 2.9990 chunk 295 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN ** A1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 32790 Z= 0.222 Angle : 0.695 12.966 44703 Z= 0.341 Chirality : 0.047 0.318 5778 Planarity : 0.003 0.039 5376 Dihedral : 5.669 28.326 4014 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.86 % Favored : 88.11 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.14), residues: 3717 helix: 1.09 (0.20), residues: 768 sheet: -1.70 (0.17), residues: 891 loop : -2.71 (0.13), residues: 2058 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 526 time to evaluate : 3.678 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 outliers start: 21 outliers final: 15 residues processed: 533 average time/residue: 0.3931 time to fit residues: 355.0863 Evaluate side-chains 528 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 513 time to evaluate : 3.547 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2872 time to fit residues: 12.8858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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: 59.8899 > 50: distance: 32 - 54: 20.815 distance: 36 - 63: 18.819 distance: 42 - 72: 25.095 distance: 50 - 54: 20.338 distance: 54 - 55: 15.656 distance: 55 - 56: 12.585 distance: 55 - 58: 23.123 distance: 56 - 57: 21.833 distance: 56 - 63: 27.147 distance: 58 - 59: 21.134 distance: 59 - 60: 16.733 distance: 60 - 61: 20.728 distance: 60 - 62: 14.192 distance: 63 - 64: 11.650 distance: 64 - 65: 9.984 distance: 64 - 67: 12.967 distance: 65 - 66: 34.437 distance: 65 - 72: 9.038 distance: 67 - 68: 32.081 distance: 68 - 69: 14.065 distance: 69 - 70: 32.689 distance: 69 - 71: 39.833 distance: 72 - 73: 18.779 distance: 73 - 74: 9.570 distance: 73 - 76: 8.751 distance: 74 - 75: 30.955 distance: 74 - 80: 11.839 distance: 76 - 77: 16.418 distance: 77 - 78: 15.229 distance: 77 - 79: 12.077 distance: 80 - 81: 8.921 distance: 81 - 82: 21.404 distance: 81 - 84: 10.930 distance: 82 - 83: 13.255 distance: 82 - 89: 13.114 distance: 84 - 85: 4.104 distance: 85 - 86: 7.221 distance: 86 - 87: 14.461 distance: 87 - 88: 18.255 distance: 89 - 90: 27.647 distance: 90 - 91: 23.176 distance: 90 - 93: 25.920 distance: 91 - 92: 20.713 distance: 91 - 99: 7.198 distance: 93 - 94: 9.522 distance: 94 - 95: 8.079 distance: 94 - 96: 8.523 distance: 95 - 97: 8.056 distance: 96 - 98: 11.131 distance: 97 - 98: 7.739 distance: 99 - 100: 15.212 distance: 100 - 101: 34.631 distance: 100 - 103: 27.000 distance: 101 - 102: 40.306 distance: 101 - 108: 52.074 distance: 103 - 104: 19.980 distance: 104 - 105: 29.053 distance: 105 - 106: 29.472 distance: 105 - 107: 34.595 distance: 108 - 109: 50.995 distance: 109 - 110: 6.093 distance: 109 - 112: 21.745 distance: 110 - 111: 11.563 distance: 110 - 116: 30.139 distance: 112 - 113: 21.939 distance: 113 - 114: 25.520 distance: 113 - 115: 35.563 distance: 116 - 117: 32.432 distance: 116 - 122: 20.151 distance: 117 - 118: 34.258 distance: 117 - 120: 20.030 distance: 118 - 119: 17.112 distance: 118 - 123: 35.042 distance: 120 - 121: 24.160 distance: 121 - 122: 11.049 distance: 123 - 124: 13.355 distance: 124 - 125: 18.327 distance: 124 - 127: 11.543 distance: 125 - 126: 15.826 distance: 125 - 131: 12.510 distance: 127 - 128: 6.925 distance: 128 - 129: 9.666 distance: 128 - 130: 11.437 distance: 131 - 132: 18.632 distance: 131 - 163: 19.941 distance: 132 - 133: 16.481 distance: 133 - 134: 22.331 distance: 133 - 135: 13.882 distance: 134 - 160: 34.164