Starting phenix.real_space_refine on Sun Feb 25 02:06:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/02_2024/6m0r_30034_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/02_2024/6m0r_30034.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/02_2024/6m0r_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_30034/02_2024/6m0r_30034_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/02_2024/6m0r_30034_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/02_2024/6m0r_30034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/02_2024/6m0r_30034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/02_2024/6m0r_30034_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0r_30034/02_2024/6m0r_30034_trim_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12 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: 20.21, per 1000 atoms: 0.44 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: 38.53 Conformation dependent library (CDL) restraints added in 5.0 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: 6.48 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: 16.57 Time building geometry restraints manager: 39.30 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=" 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=" C7 NAG P 2 " pdb=" N2 NAG P 2 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C7 NAG P 1 " pdb=" N2 NAG P 1 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C1 MAN P 4 " pdb=" O5 MAN P 4 " ideal model delta sigma weight residual 1.399 1.494 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 1.96e+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=" 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=" 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=" O3P PEE C 308 " pdb=" P PEE C 308 " pdb=" O4P PEE C 308 " ideal model delta sigma weight residual 92.91 105.03 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O3P PEE I 201 " pdb=" P PEE I 201 " pdb=" O4P PEE I 201 " ideal model delta sigma weight residual 92.91 104.84 -11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O3P PEE K 201 " pdb=" P PEE K 201 " pdb=" O4P PEE K 201 " ideal model delta sigma weight residual 92.91 104.79 -11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 83422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 21570 35.74 - 71.49: 659 71.49 - 107.23: 70 107.23 - 142.98: 108 142.98 - 178.72: 36 Dihedral angle restraints: 22443 sinusoidal: 12566 harmonic: 9877 Sorted by residual: dihedral pdb=" O2 PEE C 308 " pdb=" C1 PEE C 308 " pdb=" C2 PEE C 308 " pdb=" O3P PEE C 308 " ideal model delta sinusoidal sigma weight residual -59.96 118.76 -178.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PEE C 308 " pdb=" C1 PEE C 308 " pdb=" C2 PEE C 308 " pdb=" O3P PEE C 308 " ideal model delta sinusoidal sigma weight residual 62.73 -119.50 -177.77 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE J 202 " pdb=" C1 PEE J 202 " pdb=" C2 PEE J 202 " pdb=" O3P PEE J 202 " ideal model delta sinusoidal sigma weight residual -59.96 110.47 -170.43 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 22440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3097 0.070 - 0.139: 537 0.139 - 0.209: 66 0.209 - 0.278: 2 0.278 - 0.348: 1 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=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.35 2.00e-01 2.50e+01 3.02e+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 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: 0.410 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: 0.660 Extract box with map and model: 4.340 Check model and map are aligned: 0.670 Set scattering table: 0.410 Process input model: 141.310 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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= 0.704 Angle : 0.953 13.393 32153 Z= 0.452 Chirality : 0.054 0.348 3703 Planarity : 0.005 0.056 3865 Dihedral : 20.877 178.723 9104 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 647 HIS 0.015 0.002 HIS A 559 PHE 0.052 0.003 PHE B 192 TYR 0.030 0.003 TYR C 57 ARG 0.017 0.002 ARG A 799 *********************** 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 : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 VAL cc_start: 0.8003 (t) cc_final: 0.7783 (m) REVERT: I 111 VAL cc_start: 0.7804 (t) cc_final: 0.7566 (t) REVERT: B 223 ILE cc_start: 0.7757 (mt) cc_final: 0.7461 (mm) REVERT: B 262 PHE cc_start: 0.4926 (t80) cc_final: 0.4612 (t80) REVERT: A 132 GLU cc_start: 0.6392 (tt0) cc_final: 0.6149 (tt0) outliers start: 0 outliers final: 3 residues processed: 531 average time/residue: 2.1986 time to fit residues: 1397.5940 Evaluate side-chains 288 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 285 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain A residue 541 ILE 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: 2.9990 chunk 118 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 246 ASN M 29 ASN M 57 HIS I 82 GLN J 53 ASN 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: 0.7378 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23899 Z= 0.216 Angle : 0.647 6.465 32153 Z= 0.344 Chirality : 0.039 0.275 3703 Planarity : 0.005 0.060 3865 Dihedral : 22.978 178.541 4365 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.88 % Allowed : 9.44 % Favored : 88.68 % 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: -2.13 (0.14), residues: 2881 helix: -1.39 (0.10), residues: 2034 sheet: -0.88 (0.69), residues: 47 loop : -0.95 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 33 HIS 0.006 0.001 HIS A 559 PHE 0.036 0.002 PHE B 192 TYR 0.020 0.001 TYR F 85 ARG 0.004 0.001 ARG B 92 *********************** 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 381 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 337 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 PHE cc_start: 0.5880 (m-80) cc_final: 0.5397 (m-80) REVERT: C 20 PHE cc_start: 0.6652 (t80) cc_final: 0.6207 (m-80) REVERT: G 119 SER cc_start: 0.7900 (OUTLIER) cc_final: 0.7194 (m) REVERT: G 121 GLN cc_start: 0.6138 (mm-40) cc_final: 0.5778 (mm-40) REVERT: H 130 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6380 (mp) REVERT: L 90 GLN cc_start: 0.8657 (mt0) cc_final: 0.8421 (mt0) REVERT: L 155 THR cc_start: 0.7415 (OUTLIER) cc_final: 0.7190 (m) REVERT: B 164 ASN cc_start: 0.7229 (t0) cc_final: 0.7013 (t0) REVERT: B 262 PHE cc_start: 0.4602 (t80) cc_final: 0.4311 (t80) REVERT: A 806 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7676 (mtm) outliers start: 44 outliers final: 22 residues processed: 362 average time/residue: 2.1595 time to fit residues: 943.3478 Evaluate side-chains 299 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 273 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 818 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 ASN N 246 ASN J 53 ASN B 10 ASN B 32 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN A 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 23899 Z= 0.390 Angle : 0.723 12.664 32153 Z= 0.378 Chirality : 0.044 0.281 3703 Planarity : 0.005 0.061 3865 Dihedral : 21.452 177.465 4361 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.90 % Allowed : 10.25 % Favored : 86.85 % 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: -2.06 (0.14), residues: 2881 helix: -1.26 (0.10), residues: 2063 sheet: -0.80 (0.83), residues: 31 loop : -1.14 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 77 HIS 0.037 0.002 HIS A 523 PHE 0.044 0.002 PHE C 80 TYR 0.018 0.002 TYR B 188 ARG 0.008 0.001 ARG L 117 *********************** 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 408 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 340 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 MET cc_start: 0.7832 (mtt) cc_final: 0.7524 (mtt) REVERT: M 44 MET cc_start: 0.8514 (mtm) cc_final: 0.8173 (mtt) REVERT: E 3 GLU cc_start: 0.7534 (pm20) cc_final: 0.6640 (pt0) REVERT: G 121 GLN cc_start: 0.6702 (mm110) cc_final: 0.6249 (mm110) REVERT: J 46 ARG cc_start: 0.7248 (mtt90) cc_final: 0.6781 (mmm160) REVERT: J 59 MET cc_start: 0.8395 (mtt) cc_final: 0.8190 (mtt) REVERT: K 51 PHE cc_start: 0.8192 (m-80) cc_final: 0.7636 (m-80) REVERT: L 3 GLU cc_start: 0.6838 (tt0) cc_final: 0.6624 (tt0) REVERT: L 155 THR cc_start: 0.7488 (m) cc_final: 0.7257 (p) REVERT: L 157 ASP cc_start: 0.5821 (m-30) cc_final: 0.5501 (m-30) REVERT: B 125 GLN cc_start: 0.8460 (mt0) cc_final: 0.8247 (mt0) REVERT: B 140 SER cc_start: 0.7227 (OUTLIER) cc_final: 0.6921 (m) REVERT: B 262 PHE cc_start: 0.6085 (t80) cc_final: 0.5873 (t80) REVERT: B 303 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: A 112 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7478 (ptp-110) REVERT: A 124 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6660 (mpt) REVERT: A 250 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.6659 (mtp85) REVERT: A 565 MET cc_start: 0.7104 (tpt) cc_final: 0.6894 (tmm) REVERT: A 789 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8409 (mm-30) outliers start: 68 outliers final: 22 residues processed: 380 average time/residue: 2.4978 time to fit residues: 1116.3403 Evaluate side-chains 297 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 269 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 818 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 I 53 ASN J 121 GLN B 340 ASN A 442 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.6594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23899 Z= 0.186 Angle : 0.529 6.032 32153 Z= 0.278 Chirality : 0.036 0.205 3703 Planarity : 0.004 0.090 3865 Dihedral : 19.750 178.276 4359 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.96 % Allowed : 12.77 % Favored : 85.27 % 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: -1.23 (0.15), residues: 2881 helix: -0.64 (0.11), residues: 2051 sheet: -0.68 (0.80), residues: 31 loop : -0.82 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 204 HIS 0.006 0.001 HIS A 559 PHE 0.021 0.001 PHE B 192 TYR 0.013 0.001 TYR F 85 ARG 0.009 0.000 ARG M 68 *********************** 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 340 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 294 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 PHE cc_start: 0.6877 (m-80) cc_final: 0.6496 (m-80) REVERT: C 20 PHE cc_start: 0.6855 (t80) cc_final: 0.6534 (t80) REVERT: C 133 MET cc_start: 0.8642 (tpp) cc_final: 0.7992 (tpp) REVERT: C 205 MET cc_start: 0.8235 (mtt) cc_final: 0.7988 (mtt) REVERT: E 3 GLU cc_start: 0.7632 (pm20) cc_final: 0.6799 (pt0) REVERT: E 42 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8482 (t) REVERT: G 59 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6763 (mpt) REVERT: G 121 GLN cc_start: 0.6670 (mm110) cc_final: 0.6260 (mm110) REVERT: I 51 PHE cc_start: 0.8507 (m-10) cc_final: 0.8268 (m-10) REVERT: J 46 ARG cc_start: 0.7358 (mtt90) cc_final: 0.6870 (mmm160) REVERT: J 59 MET cc_start: 0.8413 (mtt) cc_final: 0.8187 (mtt) REVERT: K 51 PHE cc_start: 0.8086 (m-80) cc_final: 0.7527 (m-80) REVERT: L 155 THR cc_start: 0.7492 (m) cc_final: 0.7264 (p) REVERT: B 93 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8745 (tttt) REVERT: B 206 GLU cc_start: 0.8078 (tp30) cc_final: 0.7852 (pt0) REVERT: B 262 PHE cc_start: 0.6319 (t80) cc_final: 0.6084 (t80) REVERT: B 303 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7456 (mm-40) REVERT: A 112 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7491 (ptp-110) REVERT: A 116 TYR cc_start: 0.7282 (t80) cc_final: 0.6918 (t80) REVERT: A 124 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6388 (mpt) REVERT: A 250 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6725 (mtp85) REVERT: A 548 MET cc_start: 0.8829 (mtm) cc_final: 0.8602 (mtm) REVERT: A 565 MET cc_start: 0.7221 (tpt) cc_final: 0.7019 (mmm) outliers start: 46 outliers final: 26 residues processed: 325 average time/residue: 2.3699 time to fit residues: 916.3062 Evaluate side-chains 292 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 260 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 230 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 781 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 243 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 ASN J 121 GLN B 45 GLN B 164 ASN B 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23899 Z= 0.264 Angle : 0.557 5.904 32153 Z= 0.291 Chirality : 0.037 0.148 3703 Planarity : 0.004 0.075 3865 Dihedral : 19.032 163.589 4359 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.35 % Allowed : 12.85 % Favored : 84.80 % 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: -0.47 (0.11), residues: 2058 sheet: -0.62 (0.76), residues: 37 loop : -0.80 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 751 HIS 0.005 0.001 HIS A 559 PHE 0.031 0.002 PHE C 80 TYR 0.013 0.001 TYR I 85 ARG 0.008 0.001 ARG M 68 *********************** 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 339 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 284 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 PHE cc_start: 0.7130 (m-80) cc_final: 0.6796 (m-80) REVERT: C 20 PHE cc_start: 0.6936 (t80) cc_final: 0.6580 (t80) REVERT: C 133 MET cc_start: 0.8611 (tpp) cc_final: 0.7985 (tpp) REVERT: M 70 GLU cc_start: 0.6681 (tm-30) cc_final: 0.6436 (mm-30) REVERT: E 3 GLU cc_start: 0.7761 (pm20) cc_final: 0.7042 (pt0) REVERT: O 19 PHE cc_start: 0.6792 (m-10) cc_final: 0.5737 (m-80) REVERT: G 121 GLN cc_start: 0.6660 (mm110) cc_final: 0.6228 (mm110) REVERT: H 76 TYR cc_start: 0.8615 (m-10) cc_final: 0.8376 (m-10) REVERT: H 106 PHE cc_start: 0.8800 (m-10) cc_final: 0.8483 (m-80) REVERT: K 51 PHE cc_start: 0.8150 (m-80) cc_final: 0.7537 (m-80) REVERT: B 31 ILE cc_start: 0.8575 (mt) cc_final: 0.8342 (mm) REVERT: B 140 SER cc_start: 0.7482 (OUTLIER) cc_final: 0.7168 (p) REVERT: B 262 PHE cc_start: 0.7065 (t80) cc_final: 0.6812 (t80) REVERT: B 303 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7426 (mm-40) REVERT: A 112 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7511 (ptp-110) REVERT: A 116 TYR cc_start: 0.7429 (t80) cc_final: 0.7016 (t80) REVERT: A 122 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7761 (tt) REVERT: A 250 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7039 (mtp85) REVERT: A 639 LEU cc_start: 0.7633 (tt) cc_final: 0.7011 (mp) outliers start: 55 outliers final: 23 residues processed: 321 average time/residue: 2.3180 time to fit residues: 905.4299 Evaluate side-chains 288 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 260 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 781 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 225 optimal weight: 0.3980 chunk 125 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 ASN B 244 ASN A 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.7797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23899 Z= 0.272 Angle : 0.564 6.546 32153 Z= 0.295 Chirality : 0.038 0.148 3703 Planarity : 0.004 0.103 3865 Dihedral : 18.634 153.916 4359 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.56 % Allowed : 12.98 % Favored : 84.46 % 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: -1.01 (0.15), residues: 2881 helix: -0.45 (0.11), residues: 2049 sheet: -0.69 (0.76), residues: 37 loop : -0.82 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 310 HIS 0.005 0.001 HIS A 796 PHE 0.029 0.002 PHE C 80 TYR 0.013 0.001 TYR B 71 ARG 0.012 0.001 ARG M 68 *********************** 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 346 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 286 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 PHE cc_start: 0.7195 (m-80) cc_final: 0.6903 (m-80) REVERT: C 20 PHE cc_start: 0.6941 (t80) cc_final: 0.6632 (t80) REVERT: C 133 MET cc_start: 0.8641 (tpp) cc_final: 0.7996 (tpp) REVERT: M 70 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6401 (mm-30) REVERT: E 3 GLU cc_start: 0.7828 (pm20) cc_final: 0.7241 (pt0) REVERT: O 19 PHE cc_start: 0.7215 (m-10) cc_final: 0.6150 (m-80) REVERT: G 76 TYR cc_start: 0.8556 (m-10) cc_final: 0.8296 (m-10) REVERT: G 121 GLN cc_start: 0.6784 (mm110) cc_final: 0.6350 (mm-40) REVERT: H 106 PHE cc_start: 0.8758 (m-10) cc_final: 0.8423 (m-10) REVERT: I 51 PHE cc_start: 0.8691 (m-10) cc_final: 0.8479 (m-10) REVERT: J 51 PHE cc_start: 0.8095 (m-10) cc_final: 0.7819 (m-10) REVERT: K 51 PHE cc_start: 0.8171 (m-80) cc_final: 0.7675 (m-80) REVERT: K 133 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8387 (mp) REVERT: B 286 ASP cc_start: 0.8054 (m-30) cc_final: 0.7725 (m-30) REVERT: B 303 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7493 (mm-40) REVERT: A 116 TYR cc_start: 0.7431 (t80) cc_final: 0.7031 (t80) REVERT: A 122 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7896 (tt) REVERT: A 129 ASP cc_start: 0.7504 (m-30) cc_final: 0.6847 (t70) REVERT: A 250 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7177 (mtp85) REVERT: A 502 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6852 (mmmm) REVERT: A 565 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7434 (tmm) REVERT: A 639 LEU cc_start: 0.7710 (tt) cc_final: 0.7098 (mp) outliers start: 60 outliers final: 33 residues processed: 327 average time/residue: 2.1403 time to fit residues: 844.8935 Evaluate side-chains 297 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 258 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 230 SER Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 781 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.8079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23899 Z= 0.310 Angle : 0.578 6.441 32153 Z= 0.302 Chirality : 0.038 0.161 3703 Planarity : 0.004 0.050 3865 Dihedral : 18.387 148.860 4359 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.60 % Allowed : 13.62 % Favored : 83.77 % 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: -1.01 (0.15), residues: 2881 helix: -0.45 (0.11), residues: 2054 sheet: -0.60 (0.78), residues: 39 loop : -0.84 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 751 HIS 0.005 0.001 HIS A 796 PHE 0.032 0.002 PHE C 80 TYR 0.013 0.001 TYR G 85 ARG 0.009 0.001 ARG M 68 *********************** 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 334 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 273 time to evaluate : 3.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7597 (tm-30) REVERT: C 20 PHE cc_start: 0.6971 (t80) cc_final: 0.6699 (t80) REVERT: C 133 MET cc_start: 0.8622 (tpp) cc_final: 0.7973 (tpp) REVERT: C 189 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7732 (mp) REVERT: M 70 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6431 (mm-30) REVERT: E 3 GLU cc_start: 0.7861 (pm20) cc_final: 0.7351 (pt0) REVERT: O 19 PHE cc_start: 0.7309 (m-10) cc_final: 0.6448 (m-80) REVERT: G 76 TYR cc_start: 0.8551 (m-10) cc_final: 0.8308 (m-10) REVERT: H 51 PHE cc_start: 0.7492 (m-10) cc_final: 0.7290 (m-10) REVERT: H 76 TYR cc_start: 0.8702 (m-10) cc_final: 0.8500 (m-10) REVERT: K 51 PHE cc_start: 0.8205 (m-80) cc_final: 0.7682 (m-80) REVERT: K 133 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8405 (mp) REVERT: L 157 ASP cc_start: 0.6229 (m-30) cc_final: 0.5935 (m-30) REVERT: B 164 ASN cc_start: 0.7642 (t160) cc_final: 0.7263 (t0) REVERT: B 286 ASP cc_start: 0.8140 (m-30) cc_final: 0.7809 (m-30) REVERT: B 303 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7420 (mm-40) REVERT: A 116 TYR cc_start: 0.7495 (t80) cc_final: 0.7162 (t80) REVERT: A 122 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7940 (tt) REVERT: A 129 ASP cc_start: 0.7594 (m-30) cc_final: 0.7097 (t70) REVERT: A 250 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7373 (mtp85) REVERT: A 502 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6847 (mmmm) REVERT: A 639 LEU cc_start: 0.7781 (tt) cc_final: 0.7171 (mp) outliers start: 61 outliers final: 32 residues processed: 310 average time/residue: 2.2016 time to fit residues: 830.9202 Evaluate side-chains 298 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 260 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 230 SER Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 781 THR 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: 0.9990 chunk 161 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.8221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23899 Z= 0.187 Angle : 0.502 6.462 32153 Z= 0.263 Chirality : 0.035 0.142 3703 Planarity : 0.004 0.113 3865 Dihedral : 17.438 146.515 4359 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.45 % Allowed : 15.37 % Favored : 83.18 % 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: -0.65 (0.15), residues: 2881 helix: -0.17 (0.11), residues: 2047 sheet: -0.46 (0.78), residues: 39 loop : -0.75 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 33 HIS 0.003 0.001 HIS A 559 PHE 0.019 0.001 PHE C 80 TYR 0.012 0.001 TYR G 85 ARG 0.018 0.000 ARG M 68 *********************** 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 302 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 268 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 PHE cc_start: 0.6967 (t80) cc_final: 0.6701 (t80) REVERT: C 133 MET cc_start: 0.8596 (tpp) cc_final: 0.7915 (tpp) REVERT: C 189 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7719 (mp) REVERT: M 70 GLU cc_start: 0.6718 (tm-30) cc_final: 0.6409 (mm-30) REVERT: E 3 GLU cc_start: 0.7834 (pm20) cc_final: 0.7374 (pt0) REVERT: O 19 PHE cc_start: 0.7477 (m-10) cc_final: 0.6764 (m-80) REVERT: H 76 TYR cc_start: 0.8686 (m-10) cc_final: 0.8474 (m-10) REVERT: I 51 PHE cc_start: 0.8753 (m-10) cc_final: 0.8549 (m-10) REVERT: K 51 PHE cc_start: 0.8289 (m-80) cc_final: 0.7740 (m-80) REVERT: L 157 ASP cc_start: 0.6003 (m-30) cc_final: 0.5757 (m-30) REVERT: B 286 ASP cc_start: 0.8087 (m-30) cc_final: 0.7811 (m-30) REVERT: B 303 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7252 (mm-40) REVERT: A 116 TYR cc_start: 0.7498 (t80) cc_final: 0.7164 (t80) REVERT: A 124 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6633 (mpp) REVERT: A 129 ASP cc_start: 0.7580 (m-30) cc_final: 0.7143 (t70) REVERT: A 250 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7347 (mtp85) REVERT: A 502 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6763 (mmmm) REVERT: A 639 LEU cc_start: 0.7660 (tt) cc_final: 0.7085 (mp) REVERT: A 825 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6563 (tttt) outliers start: 34 outliers final: 22 residues processed: 291 average time/residue: 2.0869 time to fit residues: 736.5057 Evaluate side-chains 285 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 257 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 230 SER Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 825 LYS 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: 3.9990 chunk 236 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 151 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 251 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 A 23 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.8328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23899 Z= 0.293 Angle : 0.557 6.423 32153 Z= 0.291 Chirality : 0.038 0.149 3703 Planarity : 0.004 0.082 3865 Dihedral : 17.586 146.969 4359 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.09 % Allowed : 14.90 % Favored : 83.01 % 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: -0.83 (0.15), residues: 2881 helix: -0.30 (0.11), residues: 2056 sheet: -0.48 (0.79), residues: 39 loop : -0.83 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 751 HIS 0.005 0.001 HIS A 796 PHE 0.032 0.002 PHE C 80 TYR 0.013 0.001 TYR G 85 ARG 0.011 0.001 ARG M 68 *********************** 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 307 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 258 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 GLU cc_start: 0.7288 (tt0) cc_final: 0.6988 (pm20) REVERT: C 20 PHE cc_start: 0.6979 (t80) cc_final: 0.6683 (t80) REVERT: C 133 MET cc_start: 0.8590 (tpp) cc_final: 0.7908 (tpp) REVERT: C 189 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7766 (mp) REVERT: M 70 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6481 (mm-30) REVERT: E 3 GLU cc_start: 0.7834 (pm20) cc_final: 0.7452 (pt0) REVERT: O 19 PHE cc_start: 0.7663 (m-10) cc_final: 0.7124 (m-80) REVERT: G 46 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7657 (mtp180) REVERT: H 76 TYR cc_start: 0.8699 (m-10) cc_final: 0.8496 (m-10) REVERT: K 51 PHE cc_start: 0.8324 (m-80) cc_final: 0.7794 (m-80) REVERT: K 54 ILE cc_start: 0.8325 (mm) cc_final: 0.7983 (tp) REVERT: K 133 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8408 (mp) REVERT: B 164 ASN cc_start: 0.7611 (t160) cc_final: 0.7224 (t0) REVERT: B 286 ASP cc_start: 0.8159 (m-30) cc_final: 0.7807 (m-30) REVERT: B 303 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7387 (mm-40) REVERT: A 116 TYR cc_start: 0.7526 (t80) cc_final: 0.7194 (t80) REVERT: A 129 ASP cc_start: 0.7686 (m-30) cc_final: 0.7180 (t70) REVERT: A 250 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7419 (mtp85) REVERT: A 502 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6765 (mmmm) REVERT: A 639 LEU cc_start: 0.7748 (tt) cc_final: 0.7158 (mp) REVERT: A 825 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6612 (tttt) outliers start: 49 outliers final: 28 residues processed: 288 average time/residue: 2.2058 time to fit residues: 773.5015 Evaluate side-chains 286 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 252 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 230 SER Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 825 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 1.9990 chunk 266 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 279 optimal weight: 0.5980 chunk 257 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.8368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23899 Z= 0.167 Angle : 0.488 5.923 32153 Z= 0.256 Chirality : 0.035 0.144 3703 Planarity : 0.004 0.095 3865 Dihedral : 16.750 148.526 4359 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.24 % Allowed : 15.84 % Favored : 82.92 % 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: -0.45 (0.15), residues: 2881 helix: -0.01 (0.11), residues: 2047 sheet: -0.63 (0.74), residues: 44 loop : -0.67 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 33 HIS 0.003 0.001 HIS A 559 PHE 0.018 0.001 PHE C 80 TYR 0.012 0.001 TYR G 85 ARG 0.013 0.000 ARG M 68 ********************** 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 293 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 264 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 PHE cc_start: 0.7108 (t80) cc_final: 0.6816 (t80) REVERT: C 133 MET cc_start: 0.8578 (tpp) cc_final: 0.7890 (tpp) REVERT: M 70 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6463 (mm-30) REVERT: E 3 GLU cc_start: 0.7808 (pm20) cc_final: 0.7459 (pt0) REVERT: E 156 GLN cc_start: 0.7884 (mt0) cc_final: 0.7629 (tp40) REVERT: O 19 PHE cc_start: 0.7614 (m-10) cc_final: 0.7105 (m-80) REVERT: G 46 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.7662 (mtp180) REVERT: G 121 GLN cc_start: 0.6741 (mm110) cc_final: 0.6300 (mm110) REVERT: H 76 TYR cc_start: 0.8660 (m-10) cc_final: 0.8448 (m-10) REVERT: J 51 PHE cc_start: 0.8177 (m-10) cc_final: 0.7962 (m-10) REVERT: K 51 PHE cc_start: 0.8316 (m-80) cc_final: 0.7785 (m-80) REVERT: K 54 ILE cc_start: 0.8359 (mm) cc_final: 0.8014 (tp) REVERT: B 164 ASN cc_start: 0.7557 (t160) cc_final: 0.7171 (t0) REVERT: B 286 ASP cc_start: 0.8098 (m-30) cc_final: 0.7754 (m-30) REVERT: B 303 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7197 (mm-40) REVERT: A 116 TYR cc_start: 0.7483 (t80) cc_final: 0.7168 (t80) REVERT: A 129 ASP cc_start: 0.7614 (m-30) cc_final: 0.7344 (t70) REVERT: A 250 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7388 (mtp85) REVERT: A 502 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6710 (mmmm) REVERT: A 639 LEU cc_start: 0.7631 (tt) cc_final: 0.7086 (mp) REVERT: A 825 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6589 (tttt) outliers start: 29 outliers final: 22 residues processed: 288 average time/residue: 2.2099 time to fit residues: 765.7329 Evaluate side-chains 286 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 260 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 230 SER Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 825 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 53 ASN I 53 ASN K 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106496 restraints weight = 77165.520| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.48 r_work: 0.3161 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.8464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23899 Z= 0.321 Angle : 0.573 7.189 32153 Z= 0.299 Chirality : 0.038 0.151 3703 Planarity : 0.004 0.081 3865 Dihedral : 17.223 158.033 4359 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.71 % Allowed : 15.58 % Favored : 82.71 % 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: -0.81 (0.15), residues: 2881 helix: -0.27 (0.11), residues: 2056 sheet: -0.81 (0.74), residues: 44 loop : -0.85 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 751 HIS 0.006 0.001 HIS A 796 PHE 0.036 0.002 PHE C 80 TYR 0.013 0.001 TYR G 85 ARG 0.012 0.001 ARG M 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14671.96 seconds wall clock time: 259 minutes 1.38 seconds (15541.38 seconds total)