Starting phenix.real_space_refine (version: dev) on Thu Dec 22 09:28:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/12_2022/6m0r_30034_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/12_2022/6m0r_30034.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/12_2022/6m0r_30034_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/12_2022/6m0r_30034_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/12_2022/6m0r_30034_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/12_2022/6m0r_30034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/12_2022/6m0r_30034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/12_2022/6m0r_30034_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/12_2022/6m0r_30034_trim_updated.pdb" } resolution = 2.7 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= 0.001 sd= 0.010 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 125": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 352": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 799": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 46354 Number of models: 1 Model: "" Number of chains: 43 Chain: "D" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2340 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3012 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain: "N" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 830 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1159 Classifications: {'peptide': 71} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1044 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 5490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 5490 Classifications: {'peptide': 345} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 335} Chain: "A" Number of atoms: 12161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 12161 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 21, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 410 Unusual residues: {'PEE': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 100 Chain: "M" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "O" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "H" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "I" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "J" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "K" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 269 Unusual residues: {'EYR': 1, 'PEE': 5, 'PPV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 34 Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "L" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Time building chain proxies: 20.97, per 1000 atoms: 0.45 Number of scatterers: 46354 At special positions: 0 Unit cell: (135, 119.88, 126.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 135 16.00 P 32 15.00 O 4395 8.00 N 3574 7.00 C 15531 6.00 H 22687 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 38.84 Conformation dependent library (CDL) restraints added in 4.3 seconds 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 2 sheets defined 72.6% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'D' and resid 15 through 50 removed outlier: 3.868A pdb=" N PHE D 20 " --> pdb=" O PHE D 17 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 21 " --> pdb=" O PHE D 18 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 24 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA D 26 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL D 28 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU D 29 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS D 31 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 32 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 35 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 38 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 39 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 40 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 41 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 42 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA D 46 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 47 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE D 48 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR D 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 61 through 83 removed outlier: 3.830A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 127 removed outlier: 3.539A pdb=" N GLY D 102 " --> pdb=" O HIS D 98 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 105 " --> pdb=" O CYS D 101 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 153 removed outlier: 3.523A pdb=" N PHE D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 163 removed outlier: 3.689A pdb=" N SER D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 38 removed outlier: 3.610A pdb=" N TYR C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 27 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 56 through 89 removed outlier: 3.570A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 81 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 100 through 124 removed outlier: 3.761A pdb=" N PHE C 106 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS C 107 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 109 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 110 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE C 117 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C 118 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 121 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 122 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 123 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 176 removed outlier: 3.564A pdb=" N LEU C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 205 removed outlier: 3.913A pdb=" N VAL C 186 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 189 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C 190 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY C 191 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C 198 " --> pdb=" O GLY C 195 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 199 " --> pdb=" O LEU C 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 245 removed outlier: 3.516A pdb=" N VAL N 229 " --> pdb=" O MET N 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 24 removed outlier: 3.688A pdb=" N GLY M 9 " --> pdb=" O THR M 6 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE M 12 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL M 14 " --> pdb=" O PHE M 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 16 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET M 17 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER M 18 " --> pdb=" O SER M 15 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE M 21 " --> pdb=" O SER M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 55 removed outlier: 3.666A pdb=" N ILE M 38 " --> pdb=" O ARG M 34 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET M 47 " --> pdb=" O MET M 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR M 51 " --> pdb=" O MET M 47 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLN M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 43 removed outlier: 3.823A pdb=" N ILE E 15 " --> pdb=" O PHE E 12 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA E 18 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA E 20 " --> pdb=" O CYS E 17 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE E 23 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR E 24 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER E 25 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU E 26 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA E 29 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR E 30 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR E 32 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 33 " --> pdb=" O TYR E 30 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 34 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER E 35 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 38 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE E 39 " --> pdb=" O GLY E 36 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 41 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS E 43 " --> pdb=" O CYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 77 removed outlier: 3.904A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR E 76 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 119 removed outlier: 3.602A pdb=" N VAL E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 110 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 129 through 153 removed outlier: 4.346A pdb=" N LEU E 139 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 32 removed outlier: 4.776A pdb=" N CYS O 13 " --> pdb=" O LYS O 9 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE O 19 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL O 21 " --> pdb=" O SER O 17 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER O 25 " --> pdb=" O VAL O 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 39 No H-bonds generated for 'chain 'O' and resid 36 through 39' Processing helix chain 'O' and resid 48 through 74 removed outlier: 3.772A pdb=" N LEU O 57 " --> pdb=" O HIS O 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA O 58 " --> pdb=" O THR O 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE O 65 " --> pdb=" O VAL O 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 44 Proline residue: F 10 - end of helix removed outlier: 3.680A pdb=" N ILE F 15 " --> pdb=" O PHE F 12 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS F 17 " --> pdb=" O ALA F 14 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 18 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER F 19 " --> pdb=" O GLY F 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA F 20 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE F 22 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE F 23 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR F 24 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU F 26 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA F 28 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY F 31 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR F 32 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA F 33 " --> pdb=" O TYR F 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 34 " --> pdb=" O GLY F 31 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER F 35 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS F 40 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N CYS F 43 " --> pdb=" O CYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 52 through 77 removed outlier: 3.575A pdb=" N VAL F 55 " --> pdb=" O LYS F 52 " (cutoff:3.500A) Proline residue: F 56 - end of helix removed outlier: 3.504A pdb=" N ALA F 60 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY F 67 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 69 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL F 70 " --> pdb=" O GLY F 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 72 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL F 74 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR F 76 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 119 removed outlier: 3.613A pdb=" N GLN F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 116 " --> pdb=" O GLY F 112 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 153 removed outlier: 3.890A pdb=" N VAL F 127 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE F 130 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE F 134 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE F 135 " --> pdb=" O ILE F 132 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F 138 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU F 139 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY F 140 " --> pdb=" O GLU F 137 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY F 143 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL F 146 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 147 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU F 148 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 149 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN F 151 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 42 removed outlier: 4.213A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 52 No H-bonds generated for 'chain 'G' and resid 50 through 52' Processing helix chain 'G' and resid 55 through 77 removed outlier: 3.841A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 67 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR G 76 " --> pdb=" O VAL G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 121 removed outlier: 3.553A pdb=" N GLN G 90 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 120 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 151 removed outlier: 3.822A pdb=" N VAL G 127 " --> pdb=" O ARG G 124 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET G 129 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE G 130 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU G 131 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE G 135 " --> pdb=" O ILE G 132 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL G 138 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY G 140 " --> pdb=" O GLU G 137 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 144 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 146 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU G 148 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN G 151 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 9 No H-bonds generated for 'chain 'H' and resid 7 through 9' Processing helix chain 'H' and resid 11 through 14 No H-bonds generated for 'chain 'H' and resid 11 through 14' Processing helix chain 'H' and resid 16 through 42 removed outlier: 3.646A pdb=" N ALA H 20 " --> pdb=" O GLY H 16 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY H 27 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 55 through 77 removed outlier: 3.565A pdb=" N ALA H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR H 66 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR H 76 " --> pdb=" O VAL H 72 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 119 removed outlier: 3.535A pdb=" N GLN H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE H 106 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL H 116 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ARG H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 137 removed outlier: 3.636A pdb=" N VAL H 127 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE H 130 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE H 132 " --> pdb=" O MET H 129 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE H 135 " --> pdb=" O ILE H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 153 removed outlier: 3.680A pdb=" N GLY H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 42 removed outlier: 3.542A pdb=" N PHE I 11 " --> pdb=" O TYR I 8 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA I 14 " --> pdb=" O PHE I 11 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE I 15 " --> pdb=" O PHE I 12 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA I 18 " --> pdb=" O ILE I 15 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER I 19 " --> pdb=" O GLY I 16 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA I 20 " --> pdb=" O CYS I 17 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE I 22 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE I 23 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR I 24 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU I 26 " --> pdb=" O PHE I 23 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA I 29 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY I 31 " --> pdb=" O ALA I 28 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR I 32 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS I 34 " --> pdb=" O GLY I 31 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER I 35 " --> pdb=" O THR I 32 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY I 36 " --> pdb=" O ALA I 33 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL I 37 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE I 39 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS I 40 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA I 41 " --> pdb=" O GLY I 38 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR I 42 " --> pdb=" O ILE I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 55 through 77 removed outlier: 3.589A pdb=" N ILE I 62 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER I 77 " --> pdb=" O LEU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 119 removed outlier: 3.792A pdb=" N GLN I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER I 119 " --> pdb=" O GLY I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 153 removed outlier: 3.628A pdb=" N VAL I 127 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE I 135 " --> pdb=" O ILE I 132 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL I 138 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR I 142 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU I 144 " --> pdb=" O LEU I 141 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL I 146 " --> pdb=" O GLY I 143 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU I 149 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN I 151 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 42 Proline residue: J 10 - end of helix removed outlier: 3.592A pdb=" N GLY J 13 " --> pdb=" O PRO J 10 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE J 15 " --> pdb=" O PHE J 12 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS J 17 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA J 18 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER J 19 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA J 20 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE J 22 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE J 23 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR J 24 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU J 26 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA J 28 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA J 29 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR J 30 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY J 31 " --> pdb=" O ALA J 28 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS J 34 " --> pdb=" O GLY J 31 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER J 35 " --> pdb=" O THR J 32 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL J 37 " --> pdb=" O LYS J 34 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE J 39 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS J 40 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA J 41 " --> pdb=" O GLY J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 53 removed outlier: 4.822A pdb=" N PHE J 51 " --> pdb=" O ASP J 48 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS J 52 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 63 removed outlier: 3.518A pdb=" N ALA J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 75 removed outlier: 3.875A pdb=" N VAL J 70 " --> pdb=" O TYR J 66 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 101 removed outlier: 3.672A pdb=" N GLN J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 121 removed outlier: 3.608A pdb=" N ILE J 110 " --> pdb=" O PHE J 106 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 154 removed outlier: 4.425A pdb=" N VAL J 127 " --> pdb=" O ARG J 124 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE J 130 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU J 131 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE J 134 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE J 135 " --> pdb=" O ILE J 132 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU J 137 " --> pdb=" O ILE J 134 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL J 138 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU J 139 " --> pdb=" O ALA J 136 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY J 140 " --> pdb=" O GLU J 137 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR J 142 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY J 143 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL J 146 " --> pdb=" O GLY J 143 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU J 149 " --> pdb=" O VAL J 146 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU J 150 " --> pdb=" O ALA J 147 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN J 151 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA J 154 " --> pdb=" O ASN J 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 42 removed outlier: 3.507A pdb=" N PHE K 12 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA K 14 " --> pdb=" O PHE K 11 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE K 15 " --> pdb=" O PHE K 12 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER K 19 " --> pdb=" O GLY K 16 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA K 20 " --> pdb=" O CYS K 17 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE K 22 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE K 23 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR K 24 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU K 26 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY K 27 " --> pdb=" O THR K 24 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA K 28 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 29 " --> pdb=" O LEU K 26 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR K 30 " --> pdb=" O GLY K 27 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY K 31 " --> pdb=" O ALA K 28 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA K 33 " --> pdb=" O TYR K 30 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS K 34 " --> pdb=" O GLY K 31 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER K 35 " --> pdb=" O THR K 32 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY K 36 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL K 37 " --> pdb=" O LYS K 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY K 38 " --> pdb=" O SER K 35 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE K 39 " --> pdb=" O GLY K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 52 removed outlier: 5.080A pdb=" N PHE K 51 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS K 52 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 77 removed outlier: 3.543A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR K 66 " --> pdb=" O ILE K 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY K 67 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER K 77 " --> pdb=" O LEU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 120 removed outlier: 3.519A pdb=" N ALA K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 153 removed outlier: 3.927A pdb=" N VAL K 127 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE K 130 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE K 135 " --> pdb=" O ILE K 132 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA K 136 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL K 138 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR K 142 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL K 146 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU K 149 " --> pdb=" O VAL K 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN K 151 " --> pdb=" O LEU K 148 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER K 152 " --> pdb=" O LEU K 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 42 removed outlier: 3.819A pdb=" N ALA L 14 " --> pdb=" O PHE L 11 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE L 15 " --> pdb=" O PHE L 12 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS L 17 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA L 18 " --> pdb=" O ILE L 15 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 20 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE L 22 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE L 23 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR L 24 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER L 25 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU L 26 " --> pdb=" O PHE L 23 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY L 27 " --> pdb=" O THR L 24 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY L 31 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA L 33 " --> pdb=" O TYR L 30 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS L 34 " --> pdb=" O GLY L 31 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER L 35 " --> pdb=" O THR L 32 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE L 39 " --> pdb=" O GLY L 36 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR L 42 " --> pdb=" O ILE L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 55 through 77 removed outlier: 3.580A pdb=" N GLY L 61 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 63 " --> pdb=" O MET L 59 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY L 67 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR L 76 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER L 77 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 119 removed outlier: 3.596A pdb=" N PHE L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE L 89 " --> pdb=" O TYR L 85 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY L 94 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA L 103 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 137 removed outlier: 3.820A pdb=" N PHE L 126 " --> pdb=" O PRO L 123 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL L 127 " --> pdb=" O ARG L 124 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY L 128 " --> pdb=" O LEU L 125 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU L 131 " --> pdb=" O GLY L 128 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU L 133 " --> pdb=" O ILE L 130 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE L 135 " --> pdb=" O ILE L 132 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA L 136 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU L 137 " --> pdb=" O ILE L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 153 removed outlier: 3.717A pdb=" N VAL L 146 " --> pdb=" O TYR L 142 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG L 153 " --> pdb=" O LEU L 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 22 removed outlier: 3.604A pdb=" N ASP B 9 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN B 10 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY B 11 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N PHE B 12 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 13 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 14 " --> pdb=" O GLY B 11 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 18 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 22 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 34 removed outlier: 3.670A pdb=" N LEU B 33 " --> pdb=" O GLN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 48 removed outlier: 3.701A pdb=" N LEU B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 86 removed outlier: 3.510A pdb=" N LYS B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 115 removed outlier: 3.748A pdb=" N PHE B 94 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 95 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 97 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 98 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY B 101 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET B 103 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 105 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 108 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 110 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE B 111 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 4.534A pdb=" N ARG B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 159 through 165 removed outlier: 3.682A pdb=" N PHE B 162 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS B 163 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN B 164 " --> pdb=" O TYR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 198 removed outlier: 3.592A pdb=" N ILE B 179 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 229 removed outlier: 3.544A pdb=" N THR B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.963A pdb=" N ASP B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 removed outlier: 3.695A pdb=" N HIS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.800A pdb=" N ALA B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 299 removed outlier: 3.638A pdb=" N GLU B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.723A pdb=" N ALA B 311 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP B 312 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 314 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 317 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B 324 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 329 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN B 332 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.875A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 removed outlier: 3.810A pdb=" N ARG A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 146 removed outlier: 3.631A pdb=" N ARG A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 193 through 206 removed outlier: 3.501A pdb=" N VAL A 196 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 197 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR A 198 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 199 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 201 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 202 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 203 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 206 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.764A pdb=" N LYS A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 304 removed outlier: 3.834A pdb=" N THR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 325 removed outlier: 4.094A pdb=" N GLU A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 347 through 360 removed outlier: 3.525A pdb=" N ALA A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.698A pdb=" N ILE A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 422 removed outlier: 4.174A pdb=" N THR A 414 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N PHE A 415 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 3.633A pdb=" N PHE A 419 " --> pdb=" O PRO A 416 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 421 " --> pdb=" O MET A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.514A pdb=" N LEU A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.574A pdb=" N LYS A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 460 Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.605A pdb=" N SER A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 528 through 562 removed outlier: 3.691A pdb=" N SER A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 551 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 554 " --> pdb=" O TYR A 550 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 583 removed outlier: 5.080A pdb=" N ILE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Proline residue: A 574 - end of helix removed outlier: 3.502A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.541A pdb=" N VAL A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 595 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 601 No H-bonds generated for 'chain 'A' and resid 598 through 601' Processing helix chain 'A' and resid 608 through 617 removed outlier: 3.647A pdb=" N MET A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 658 removed outlier: 4.012A pdb=" N PHE A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 3.530A pdb=" N VAL A 651 " --> pdb=" O TRP A 647 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Proline residue: A 653 - end of helix Processing helix chain 'A' and resid 707 through 760 removed outlier: 3.633A pdb=" N HIS A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 718 " --> pdb=" O HIS A 714 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 719 " --> pdb=" O GLN A 715 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 730 " --> pdb=" O CYS A 726 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 733 " --> pdb=" O HIS A 729 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU A 734 " --> pdb=" O THR A 730 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE A 757 " --> pdb=" O MET A 753 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 784 removed outlier: 3.803A pdb=" N ALA A 775 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 802 removed outlier: 3.573A pdb=" N HIS A 801 " --> pdb=" O SER A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 808 No H-bonds generated for 'chain 'A' and resid 806 through 808' Processing sheet with id= A, first strand: chain 'A' and resid 335 through 342 removed outlier: 4.084A pdb=" N LEU A 16 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 186 through 192 1196 hydrogen bonds defined for protein. 2745 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: 17.04 Time building geometry restraints manager: 40.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 22621 1.03 - 1.23: 166 1.23 - 1.42: 9355 1.42 - 1.62: 14237 1.62 - 1.82: 207 Bond restraints: 46586 Sorted by residual: bond pdb=" C7 NAG P 2 " pdb=" N2 NAG P 2 " ideal model delta sigma weight residual 1.337 1.474 -0.137 1.10e-02 8.26e+03 1.56e+02 bond pdb=" C7 NAG P 1 " pdb=" N2 NAG P 1 " ideal model delta sigma weight residual 1.337 1.458 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" O32 PPV A 906 " pdb=" P2 PPV A 906 " ideal model delta sigma weight residual 1.510 1.667 -0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C2 NAG P 2 " pdb=" N2 NAG P 2 " ideal model delta sigma weight residual 1.454 1.513 -0.059 1.00e-02 1.00e+04 3.50e+01 bond pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " ideal model delta sigma weight residual 1.454 1.499 -0.045 1.00e-02 1.00e+04 2.06e+01 ... (remaining 46581 not shown) Histogram of bond angle deviations from ideal: 97.64 - 104.95: 347 104.95 - 112.26: 52729 112.26 - 119.56: 12605 119.56 - 126.87: 17550 126.87 - 134.18: 196 Bond angle restraints: 83427 Sorted by residual: angle pdb=" C2 NAG P 2 " pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 109.64 113.68 -4.04 5.38e-01 3.45e+00 5.65e+01 angle pdb=" O3P PEE A 905 " pdb=" P PEE A 905 " pdb=" O4P PEE A 905 " ideal model delta sigma weight residual 92.91 106.30 -13.39 3.00e+00 1.11e-01 1.99e+01 angle pdb=" C1 NAG P 2 " pdb=" C2 NAG P 2 " pdb=" C3 NAG P 2 " ideal model delta sigma weight residual 110.19 114.14 -3.95 9.25e-01 1.17e+00 1.83e+01 angle pdb=" O3P PEE A 902 " pdb=" P PEE A 902 " pdb=" O4P PEE A 902 " ideal model delta sigma weight residual 92.91 105.24 -12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C8 NAG P 2 " pdb=" C7 NAG P 2 " pdb=" N2 NAG P 2 " ideal model delta sigma weight residual 116.06 120.10 -4.04 9.90e-01 1.02e+00 1.67e+01 ... (remaining 83422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 18536 32.94 - 65.88: 179 65.88 - 98.82: 37 98.82 - 131.75: 34 131.75 - 164.69: 24 Dihedral angle restraints: 18810 sinusoidal: 8933 harmonic: 9877 Sorted by residual: dihedral pdb=" C12 PEE H 201 " pdb=" C10 PEE H 201 " pdb=" C11 PEE H 201 " pdb=" O4 PEE H 201 " ideal model delta sinusoidal sigma weight residual 340.53 175.84 164.69 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C32 PEE A 905 " pdb=" C30 PEE A 905 " pdb=" C31 PEE A 905 " pdb=" O3 PEE A 905 " ideal model delta sinusoidal sigma weight residual 161.16 -2.13 163.29 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C12 PEE E 202 " pdb=" C10 PEE E 202 " pdb=" C11 PEE E 202 " pdb=" O4 PEE E 202 " ideal model delta sinusoidal sigma weight residual -19.47 -176.33 156.86 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 18807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2265 0.045 - 0.089: 1116 0.089 - 0.134: 242 0.134 - 0.178: 65 0.178 - 0.223: 15 Chirality restraints: 3703 Sorted by residual: chirality pdb=" C1 MAN P 5 " pdb=" O6 BMA P 3 " pdb=" C2 MAN P 5 " pdb=" O5 MAN P 5 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.47e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 7.56e+00 chirality pdb=" C1 MAN P 4 " pdb=" O3 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 2.37 0.03 2.00e-02 2.50e+03 2.60e+00 ... (remaining 3700 not shown) Planarity restraints: 6678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 192 " -0.022 2.00e-02 2.50e+03 1.85e-02 1.02e+01 pdb=" CG PHE B 192 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE B 192 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE B 192 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 192 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 192 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 192 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE B 192 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE B 192 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 192 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 192 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE B 192 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 647 " 0.014 2.00e-02 2.50e+03 1.41e-02 7.99e+00 pdb=" CG TRP A 647 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 647 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 647 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 647 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 647 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 647 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 647 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 647 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 647 " 0.018 2.00e-02 2.50e+03 pdb=" HD1 TRP A 647 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP A 647 " 0.006 2.00e-02 2.50e+03 pdb=" HE3 TRP A 647 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 647 " -0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 647 " 0.013 2.00e-02 2.50e+03 pdb=" HH2 TRP A 647 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 21 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A 22 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.031 5.00e-02 4.00e+02 ... (remaining 6675 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3697 2.23 - 2.82: 99105 2.82 - 3.42: 113018 3.42 - 4.01: 161074 4.01 - 4.60: 259014 Nonbonded interactions: 635908 Sorted by model distance: nonbonded pdb=" O ASN B 283 " pdb=" HD1 HIS B 287 " model vdw 1.639 1.850 nonbonded pdb=" OE1 GLN B 318 " pdb="HH21 ARG B 321 " model vdw 1.648 1.850 nonbonded pdb="HH11 ARG L 117 " pdb=" OE1 GLN B 86 " model vdw 1.653 1.850 nonbonded pdb=" HZ3 LYS B 186 " pdb=" O LEU B 242 " model vdw 1.711 1.850 nonbonded pdb="HH22 ARG A 799 " pdb=" O HOH A1003 " model vdw 1.712 1.850 ... (remaining 635903 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 'E' and resid 1 through 159) selection = (chain 'F' and resid 1 through 159) selection = (chain 'G' and resid 1 through 159) selection = (chain 'H' and resid 1 through 159) selection = (chain 'I' and resid 1 through 159) selection = (chain 'J' and resid 1 through 159) selection = (chain 'K' and resid 1 through 159) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 S 135 5.16 5 C 15531 2.51 5 N 3574 2.21 5 O 4395 1.98 5 H 22687 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.360 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: 0.720 Extract box with map and model: 6.100 Check model and map are aligned: 0.730 Convert atoms to be neutral: 0.390 Process input model: 140.450 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 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 : 0.011 0.157 23899 Z= 0.702 Angle : 0.951 13.393 32153 Z= 0.460 Chirality : 0.054 0.223 3703 Planarity : 0.005 0.056 3865 Dihedral : 14.854 164.693 8740 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.12), residues: 2881 helix: -3.21 (0.07), residues: 2040 sheet: -0.55 (0.93), residues: 31 loop : -1.50 (0.21), residues: 810 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 531 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 3 residues processed: 531 average time/residue: 1.9563 time to fit residues: 1264.4885 Evaluate side-chains 285 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 282 time to evaluate : 3.666 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.6301 time to fit residues: 7.0961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 246 ASN M 57 HIS I 82 GLN J 53 ASN J 121 GLN L 82 GLN B 7 ASN A 123 GLN A 374 ASN A 614 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 23899 Z= 0.213 Angle : 0.621 6.097 32153 Z= 0.336 Chirality : 0.038 0.147 3703 Planarity : 0.005 0.064 3865 Dihedral : 15.778 155.705 3995 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -2.15 (0.14), residues: 2881 helix: -1.40 (0.10), residues: 2036 sheet: -0.67 (0.72), residues: 45 loop : -0.99 (0.22), residues: 800 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 335 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 19 residues processed: 358 average time/residue: 1.9276 time to fit residues: 851.1282 Evaluate side-chains 296 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 277 time to evaluate : 3.480 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 5 average time/residue: 0.8600 time to fit residues: 10.5725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 246 ASN J 53 ASN B 10 ASN B 32 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 271 ASN A 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.123 23899 Z= 0.436 Angle : 0.744 9.068 32153 Z= 0.394 Chirality : 0.046 0.451 3703 Planarity : 0.005 0.056 3865 Dihedral : 14.614 153.927 3995 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -2.07 (0.14), residues: 2881 helix: -1.25 (0.10), residues: 2062 sheet: -1.40 (0.69), residues: 41 loop : -1.16 (0.21), residues: 778 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 343 time to evaluate : 3.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 25 residues processed: 384 average time/residue: 2.2430 time to fit residues: 1030.9460 Evaluate side-chains 295 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 270 time to evaluate : 4.084 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 14 residues processed: 11 average time/residue: 0.9377 time to fit residues: 19.2311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN B 340 ASN A 442 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23899 Z= 0.166 Angle : 0.511 6.591 32153 Z= 0.270 Chirality : 0.035 0.144 3703 Planarity : 0.004 0.092 3865 Dihedral : 13.016 155.388 3995 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.14 (0.15), residues: 2881 helix: -0.57 (0.11), residues: 2050 sheet: -0.98 (0.70), residues: 41 loop : -0.79 (0.22), residues: 790 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 283 time to evaluate : 3.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 312 average time/residue: 2.1295 time to fit residues: 806.6668 Evaluate side-chains 280 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 256 time to evaluate : 3.698 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 1.2229 time to fit residues: 10.9685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN B 45 GLN A 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 23899 Z= 0.403 Angle : 0.688 7.975 32153 Z= 0.361 Chirality : 0.043 0.193 3703 Planarity : 0.005 0.085 3865 Dihedral : 13.982 165.838 3995 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.56 (0.15), residues: 2881 helix: -0.87 (0.11), residues: 2056 sheet: -0.75 (0.74), residues: 37 loop : -1.00 (0.21), residues: 788 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 355 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 294 time to evaluate : 4.218 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 335 average time/residue: 2.0451 time to fit residues: 834.3642 Evaluate side-chains 289 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 258 time to evaluate : 3.865 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 21 residues processed: 10 average time/residue: 0.9904 time to fit residues: 18.2873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 142 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN K 121 GLN B 164 ASN A 23 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.7754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 23899 Z= 0.212 Angle : 0.525 5.223 32153 Z= 0.278 Chirality : 0.036 0.143 3703 Planarity : 0.004 0.041 3865 Dihedral : 12.953 170.177 3995 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.05 (0.15), residues: 2881 helix: -0.47 (0.11), residues: 2051 sheet: -0.63 (0.71), residues: 37 loop : -0.90 (0.21), residues: 793 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 273 time to evaluate : 4.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 29 residues processed: 310 average time/residue: 2.0443 time to fit residues: 779.4162 Evaluate side-chains 282 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 253 time to evaluate : 3.736 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 5 average time/residue: 1.0966 time to fit residues: 12.2625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN G 53 ASN B 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.8012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 23899 Z= 0.290 Angle : 0.558 6.069 32153 Z= 0.294 Chirality : 0.038 0.153 3703 Planarity : 0.004 0.117 3865 Dihedral : 12.772 176.364 3995 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.02 (0.15), residues: 2881 helix: -0.44 (0.11), residues: 2064 sheet: -0.61 (0.73), residues: 37 loop : -0.91 (0.21), residues: 780 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 266 time to evaluate : 3.873 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 30 residues processed: 301 average time/residue: 2.0276 time to fit residues: 746.4066 Evaluate side-chains 286 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 256 time to evaluate : 3.680 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 1.1710 time to fit residues: 7.7105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 53 ASN A 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.8213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 23899 Z= 0.270 Angle : 0.544 5.918 32153 Z= 0.287 Chirality : 0.037 0.146 3703 Planarity : 0.004 0.040 3865 Dihedral : 12.517 176.717 3995 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.95 (0.15), residues: 2881 helix: -0.38 (0.11), residues: 2065 sheet: -0.61 (0.74), residues: 37 loop : -0.89 (0.21), residues: 779 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 260 time to evaluate : 3.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 37 residues processed: 295 average time/residue: 1.9790 time to fit residues: 721.8173 Evaluate side-chains 287 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 250 time to evaluate : 3.682 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 30 residues processed: 7 average time/residue: 1.0222 time to fit residues: 14.6443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 53 ASN K 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.8344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 23899 Z= 0.282 Angle : 0.547 5.520 32153 Z= 0.288 Chirality : 0.037 0.151 3703 Planarity : 0.004 0.041 3865 Dihedral : 12.314 174.042 3995 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.91 (0.15), residues: 2881 helix: -0.34 (0.11), residues: 2055 sheet: -0.63 (0.75), residues: 39 loop : -0.89 (0.21), residues: 787 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 257 time to evaluate : 4.166 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 32 residues processed: 293 average time/residue: 1.8901 time to fit residues: 684.4055 Evaluate side-chains 281 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 249 time to evaluate : 3.738 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 27 residues processed: 5 average time/residue: 0.8159 time to fit residues: 10.6474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 279 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 53 ASN A 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.8400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 23899 Z= 0.152 Angle : 0.478 5.864 32153 Z= 0.253 Chirality : 0.035 0.142 3703 Planarity : 0.003 0.039 3865 Dihedral : 11.366 174.140 3995 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.44 (0.15), residues: 2881 helix: 0.00 (0.11), residues: 2053 sheet: -0.62 (0.73), residues: 44 loop : -0.69 (0.21), residues: 784 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 261 time to evaluate : 4.103 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 28 residues processed: 289 average time/residue: 2.0156 time to fit residues: 719.6774 Evaluate side-chains 276 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 248 time to evaluate : 3.846 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 1.9556 time to fit residues: 6.9334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 4.9990 chunk 237 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105793 restraints weight = 77148.897| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.43 r_work: 0.3168 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.8480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 23899 Z= 0.289 Angle : 0.549 5.603 32153 Z= 0.288 Chirality : 0.037 0.148 3703 Planarity : 0.004 0.040 3865 Dihedral : 11.756 167.360 3995 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.66 (0.15), residues: 2881 helix: -0.16 (0.11), residues: 2054 sheet: -0.64 (0.76), residues: 44 loop : -0.79 (0.21), residues: 783 =============================================================================== Job complete usr+sys time: 14033.01 seconds wall clock time: 245 minutes 9.25 seconds (14709.25 seconds total)