Starting phenix.real_space_refine on Sun Dec 29 15:41:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ea4_27972/12_2024/8ea4_27972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ea4_27972/12_2024/8ea4_27972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ea4_27972/12_2024/8ea4_27972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ea4_27972/12_2024/8ea4_27972.map" model { file = "/net/cci-nas-00/data/ceres_data/8ea4_27972/12_2024/8ea4_27972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ea4_27972/12_2024/8ea4_27972.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 531 5.49 5 Mg 15 5.21 5 S 178 5.16 5 C 34722 2.51 5 N 10540 2.21 5 O 12063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 58049 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "K" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "L" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "M" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "O" Number of atoms: 4865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4865 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 582} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1306 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 13, 'TRANS': 150} Chain: "S" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "W" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4122 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 19, 'TRANS': 494} Chain: "X" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4068 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 19, 'TRANS': 487} Chain breaks: 1 Chain: "Y" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2453 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 11, 'TRANS': 292} Chain breaks: 3 Chain: "Z" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2426 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 289} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "x" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "y" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "z" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "1" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2010 Classifications: {'DNA': 98} Link IDs: {'rna3p': 97} Chain: "2" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "3" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 980 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "4" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 982 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "5" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "6" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 301 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "7" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 4896 Classifications: {'RNA': 230} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 23, 'rna3p_pur': 97, 'rna3p_pyr': 90} Link IDs: {'rna2p': 42, 'rna3p': 187} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.54, per 1000 atoms: 0.42 Number of scatterers: 58049 At special positions: 0 Unit cell: (142.978, 145.112, 316.899, 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 178 16.00 P 531 15.00 Mg 15 11.99 O 12063 8.00 N 10540 7.00 C 34722 6.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 51904 O5' DT 5 3 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.98 Conformation dependent library (CDL) restraints added in 4.7 seconds 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11018 Finding SS restraints... Secondary structure from input PDB file: 298 helices and 34 sheets defined 58.3% alpha, 9.9% beta 184 base pairs and 323 stacking pairs defined. Time for finding SS restraints: 16.32 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.797A pdb=" N LYS A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 53 removed outlier: 3.545A pdb=" N LYS A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.510A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 145 through 149 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 153 through 164 Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.013A pdb=" N ASP A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.728A pdb=" N ARG A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.851A pdb=" N GLU A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 Processing helix chain 'A' and resid 240 through 258 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.609A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 146 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.588A pdb=" N ILE B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 removed outlier: 4.086A pdb=" N ASP B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.993A pdb=" N GLU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 3.979A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 removed outlier: 3.654A pdb=" N ARG B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'C' and resid 20 through 29 removed outlier: 3.515A pdb=" N GLU C 24 " --> pdb=" O TRP C 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 53 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.875A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 173 through 181 removed outlier: 4.013A pdb=" N ASP C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.954A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.633A pdb=" N GLU C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 238 Processing helix chain 'C' and resid 240 through 258 removed outlier: 4.051A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'D' and resid 20 through 29 Processing helix chain 'D' and resid 36 through 53 Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 121 through 136 Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.937A pdb=" N ASP D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'D' and resid 200 through 215 removed outlier: 3.692A pdb=" N GLU D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 238 removed outlier: 4.357A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 257 removed outlier: 3.766A pdb=" N GLU D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 removed outlier: 3.793A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 30 removed outlier: 3.525A pdb=" N GLU E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 53 removed outlier: 3.833A pdb=" N GLY E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 75 Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 121 through 136 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 173 through 181 removed outlier: 4.076A pdb=" N ASP E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.959A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 215 removed outlier: 3.544A pdb=" N GLU E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 238 removed outlier: 3.803A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 259 Processing helix chain 'E' and resid 264 through 274 removed outlier: 4.139A pdb=" N GLU E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 29 Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.873A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 134 Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 173 through 181 removed outlier: 4.012A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.623A pdb=" N GLU F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.765A pdb=" N GLU F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 238 removed outlier: 4.357A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 258 removed outlier: 3.699A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 75 Processing helix chain 'G' and resid 101 through 113 removed outlier: 3.873A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 134 Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 173 through 181 removed outlier: 4.013A pdb=" N ASP G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 removed outlier: 3.622A pdb=" N GLU G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 215 removed outlier: 3.766A pdb=" N GLU G 209 " --> pdb=" O LYS G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 238 removed outlier: 4.357A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 removed outlier: 3.697A pdb=" N ARG G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 30 removed outlier: 3.687A pdb=" N GLY H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 53 removed outlier: 3.573A pdb=" N GLY H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 101 through 113 removed outlier: 3.506A pdb=" N LEU H 113 " --> pdb=" O ILE H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 145 through 149 Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 153 through 162 Processing helix chain 'H' and resid 174 through 181 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'H' and resid 201 through 215 Processing helix chain 'H' and resid 226 through 238 removed outlier: 3.549A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 257 Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'I' and resid 20 through 29 removed outlier: 3.598A pdb=" N LYS I 29 " --> pdb=" O ILE I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 53 Processing helix chain 'I' and resid 65 through 75 Processing helix chain 'I' and resid 101 through 113 Processing helix chain 'I' and resid 121 through 134 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 173 through 181 removed outlier: 3.989A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.883A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 215 removed outlier: 3.664A pdb=" N GLU I 209 " --> pdb=" O LYS I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 238 removed outlier: 3.707A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 258 removed outlier: 3.562A pdb=" N ARG I 258 " --> pdb=" O ARG I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 274 removed outlier: 3.894A pdb=" N GLU I 274 " --> pdb=" O GLU I 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 30 removed outlier: 3.508A pdb=" N GLU J 24 " --> pdb=" O TRP J 20 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 53 removed outlier: 3.523A pdb=" N LYS J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 75 Processing helix chain 'J' and resid 101 through 113 removed outlier: 3.602A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 136 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 150 through 151 No H-bonds generated for 'chain 'J' and resid 150 through 151' Processing helix chain 'J' and resid 152 through 164 removed outlier: 4.384A pdb=" N ASP J 156 " --> pdb=" O GLU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 181 removed outlier: 4.070A pdb=" N ASP J 177 " --> pdb=" O THR J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.553A pdb=" N GLU J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 215 Processing helix chain 'J' and resid 226 through 238 Processing helix chain 'J' and resid 240 through 258 removed outlier: 3.787A pdb=" N GLU J 246 " --> pdb=" O GLY J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 274 removed outlier: 3.758A pdb=" N GLU J 270 " --> pdb=" O ALA J 266 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 30 removed outlier: 3.631A pdb=" N GLU K 24 " --> pdb=" O TRP K 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA K 26 " --> pdb=" O GLN K 22 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 53 removed outlier: 3.692A pdb=" N GLY K 48 " --> pdb=" O ASP K 44 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS K 51 " --> pdb=" O ASP K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 76 Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.611A pdb=" N PHE K 106 " --> pdb=" O PRO K 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 113 " --> pdb=" O ILE K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 136 removed outlier: 3.656A pdb=" N ASP K 127 " --> pdb=" O SER K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 149 Processing helix chain 'K' and resid 150 through 152 No H-bonds generated for 'chain 'K' and resid 150 through 152' Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 173 through 181 removed outlier: 4.004A pdb=" N ASP K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA K 178 " --> pdb=" O ASP K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 190 removed outlier: 3.571A pdb=" N GLU K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 215 removed outlier: 3.500A pdb=" N LYS K 205 " --> pdb=" O GLY K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 238 removed outlier: 4.003A pdb=" N ILE K 232 " --> pdb=" O GLU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 240 through 258 removed outlier: 3.590A pdb=" N ARG K 258 " --> pdb=" O ARG K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 273 Processing helix chain 'L' and resid 20 through 30 removed outlier: 3.699A pdb=" N GLU L 24 " --> pdb=" O TRP L 20 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA L 26 " --> pdb=" O GLN L 22 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU L 28 " --> pdb=" O GLU L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 53 Processing helix chain 'L' and resid 65 through 75 Processing helix chain 'L' and resid 101 through 113 removed outlier: 3.767A pdb=" N LEU L 113 " --> pdb=" O ILE L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 134 Processing helix chain 'L' and resid 146 through 149 Processing helix chain 'L' and resid 150 through 151 No H-bonds generated for 'chain 'L' and resid 150 through 151' Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.289A pdb=" N ASP L 156 " --> pdb=" O GLU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 181 removed outlier: 4.051A pdb=" N ASP L 177 " --> pdb=" O THR L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 removed outlier: 3.553A pdb=" N GLU L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 215 Processing helix chain 'L' and resid 226 through 238 removed outlier: 3.696A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 258 Processing helix chain 'L' and resid 264 through 275 removed outlier: 3.631A pdb=" N GLU L 274 " --> pdb=" O GLU L 270 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 30 removed outlier: 3.522A pdb=" N ALA M 26 " --> pdb=" O GLN M 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG M 27 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 53 removed outlier: 4.026A pdb=" N GLY M 48 " --> pdb=" O ASP M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 76 Processing helix chain 'M' and resid 101 through 113 Processing helix chain 'M' and resid 121 through 134 Processing helix chain 'M' and resid 145 through 149 Processing helix chain 'M' and resid 150 through 152 No H-bonds generated for 'chain 'M' and resid 150 through 152' Processing helix chain 'M' and resid 153 through 164 Processing helix chain 'M' and resid 173 through 181 removed outlier: 4.067A pdb=" N ASP M 177 " --> pdb=" O THR M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 190 removed outlier: 3.763A pdb=" N ARG M 189 " --> pdb=" O GLN M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 215 Processing helix chain 'M' and resid 226 through 238 removed outlier: 3.721A pdb=" N ILE M 232 " --> pdb=" O GLU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 258 Processing helix chain 'M' and resid 264 through 273 Processing helix chain 'O' and resid 13 through 40 removed outlier: 3.885A pdb=" N THR O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Proline residue: O 30 - end of helix removed outlier: 3.515A pdb=" N LEU O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 52 removed outlier: 3.509A pdb=" N TRP O 48 " --> pdb=" O ASP O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 64 Processing helix chain 'O' and resid 65 through 67 No H-bonds generated for 'chain 'O' and resid 65 through 67' Processing helix chain 'O' and resid 76 through 115 removed outlier: 3.905A pdb=" N ALA O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG O 100 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP O 111 " --> pdb=" O GLY O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 126 Processing helix chain 'O' and resid 128 through 144 Processing helix chain 'O' and resid 174 through 184 Processing helix chain 'O' and resid 190 through 200 removed outlier: 3.897A pdb=" N ILE O 194 " --> pdb=" O SER O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 232 Processing helix chain 'O' and resid 244 through 257 Processing helix chain 'O' and resid 261 through 273 Processing helix chain 'O' and resid 287 through 289 No H-bonds generated for 'chain 'O' and resid 287 through 289' Processing helix chain 'O' and resid 318 through 337 removed outlier: 4.656A pdb=" N HIS O 323 " --> pdb=" O ASN O 319 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP O 324 " --> pdb=" O ARG O 320 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE O 325 " --> pdb=" O GLN O 321 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU O 329 " --> pdb=" O PHE O 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 343 through 347 Processing helix chain 'O' and resid 364 through 369 Processing helix chain 'O' and resid 380 through 382 No H-bonds generated for 'chain 'O' and resid 380 through 382' Processing helix chain 'O' and resid 383 through 406 removed outlier: 3.670A pdb=" N ILE O 389 " --> pdb=" O GLU O 385 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 429 Processing helix chain 'O' and resid 476 through 481 Processing helix chain 'O' and resid 482 through 484 No H-bonds generated for 'chain 'O' and resid 482 through 484' Processing helix chain 'O' and resid 485 through 508 removed outlier: 4.171A pdb=" N ASN O 489 " --> pdb=" O TYR O 485 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN O 508 " --> pdb=" O LYS O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 516 through 538 Processing helix chain 'O' and resid 550 through 564 Processing helix chain 'O' and resid 570 through 576 Processing helix chain 'O' and resid 578 through 588 Processing helix chain 'O' and resid 589 through 605 Processing helix chain 'O' and resid 618 through 633 Processing helix chain 'Q' and resid 21 through 33 Processing helix chain 'Q' and resid 36 through 44 Processing helix chain 'Q' and resid 46 through 48 No H-bonds generated for 'chain 'Q' and resid 46 through 48' Processing helix chain 'Q' and resid 49 through 54 Processing helix chain 'Q' and resid 63 through 75 removed outlier: 3.607A pdb=" N VAL Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 83 removed outlier: 3.651A pdb=" N GLN Q 83 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 106 removed outlier: 3.856A pdb=" N ALA Q 105 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 116 Processing helix chain 'Q' and resid 142 through 146 Processing helix chain 'Q' and resid 157 through 161 Processing helix chain 'S' and resid 4 through 16 removed outlier: 3.528A pdb=" N GLU S 14 " --> pdb=" O LYS S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 44 removed outlier: 4.085A pdb=" N GLY S 41 " --> pdb=" O ASN S 37 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS S 42 " --> pdb=" O HIS S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 74 removed outlier: 3.670A pdb=" N ARG S 53 " --> pdb=" O ASP S 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG S 54 " --> pdb=" O HIS S 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY S 55 " --> pdb=" O HIS S 51 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG S 72 " --> pdb=" O ASP S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 86 Processing helix chain 'W' and resid 39 through 52 Processing helix chain 'W' and resid 57 through 73 Processing helix chain 'W' and resid 75 through 89 Processing helix chain 'W' and resid 90 through 94 Processing helix chain 'W' and resid 108 through 123 Processing helix chain 'W' and resid 130 through 146 Processing helix chain 'W' and resid 152 through 160 Processing helix chain 'W' and resid 160 through 171 removed outlier: 4.049A pdb=" N GLN W 167 " --> pdb=" O ILE W 163 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN W 168 " --> pdb=" O LEU W 164 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS W 169 " --> pdb=" O GLU W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 248 through 261 Processing helix chain 'W' and resid 266 through 270 Processing helix chain 'W' and resid 294 through 305 Processing helix chain 'W' and resid 313 through 316 Processing helix chain 'W' and resid 317 through 331 Proline residue: W 323 - end of helix Processing helix chain 'W' and resid 332 through 335 Processing helix chain 'W' and resid 342 through 346 Processing helix chain 'W' and resid 357 through 372 Processing helix chain 'W' and resid 373 through 376 Processing helix chain 'W' and resid 385 through 394 Processing helix chain 'W' and resid 402 through 410 removed outlier: 3.918A pdb=" N ILE W 408 " --> pdb=" O ASP W 405 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 423 removed outlier: 3.821A pdb=" N CYS W 423 " --> pdb=" O ARG W 420 " (cutoff:3.500A) Processing helix chain 'W' and resid 435 through 440 Processing helix chain 'W' and resid 483 through 498 Processing helix chain 'W' and resid 502 through 520 removed outlier: 3.572A pdb=" N LYS W 520 " --> pdb=" O LEU W 516 " (cutoff:3.500A) Processing helix chain 'W' and resid 525 through 541 Processing helix chain 'X' and resid 38 through 51 removed outlier: 3.850A pdb=" N ALA X 42 " --> pdb=" O LEU X 38 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL X 44 " --> pdb=" O GLU X 40 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS X 45 " --> pdb=" O GLU X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 72 removed outlier: 4.178A pdb=" N GLY X 62 " --> pdb=" O ARG X 58 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN X 63 " --> pdb=" O THR X 59 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU X 70 " --> pdb=" O ARG X 66 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS X 71 " --> pdb=" O GLU X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 90 Processing helix chain 'X' and resid 91 through 95 Processing helix chain 'X' and resid 108 through 122 Processing helix chain 'X' and resid 130 through 145 Processing helix chain 'X' and resid 152 through 161 Processing helix chain 'X' and resid 161 through 173 removed outlier: 4.020A pdb=" N GLN X 167 " --> pdb=" O ILE X 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 248 through 261 Processing helix chain 'X' and resid 266 through 270 Processing helix chain 'X' and resid 294 through 305 Processing helix chain 'X' and resid 313 through 316 Processing helix chain 'X' and resid 317 through 331 Proline residue: X 323 - end of helix Processing helix chain 'X' and resid 332 through 335 Processing helix chain 'X' and resid 357 through 372 removed outlier: 3.823A pdb=" N ARG X 367 " --> pdb=" O GLN X 363 " (cutoff:3.500A) Processing helix chain 'X' and resid 373 through 376 Processing helix chain 'X' and resid 385 through 394 Processing helix chain 'X' and resid 404 through 410 Processing helix chain 'X' and resid 435 through 440 removed outlier: 3.849A pdb=" N ALA X 440 " --> pdb=" O ALA X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 483 through 498 Processing helix chain 'X' and resid 502 through 516 removed outlier: 3.747A pdb=" N ASP X 512 " --> pdb=" O GLN X 508 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ARG X 513 " --> pdb=" O GLU X 509 " (cutoff:3.500A) Processing helix chain 'X' and resid 525 through 542 removed outlier: 3.605A pdb=" N SER X 542 " --> pdb=" O ALA X 538 " (cutoff:3.500A) Processing helix chain 'Y' and resid 251 through 261 Processing helix chain 'Y' and resid 266 through 270 removed outlier: 3.514A pdb=" N TYR Y 269 " --> pdb=" O GLY Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 296 through 305 Processing helix chain 'Y' and resid 323 through 331 Processing helix chain 'Y' and resid 332 through 335 Processing helix chain 'Y' and resid 357 through 372 Processing helix chain 'Y' and resid 378 through 382 Processing helix chain 'Y' and resid 385 through 393 Processing helix chain 'Y' and resid 402 through 410 removed outlier: 4.342A pdb=" N ILE Y 408 " --> pdb=" O ASP Y 405 " (cutoff:3.500A) Processing helix chain 'Y' and resid 435 through 440 removed outlier: 4.438A pdb=" N GLY Y 438 " --> pdb=" O TYR Y 435 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA Y 440 " --> pdb=" O ALA Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 483 through 501 removed outlier: 3.919A pdb=" N ILE Y 501 " --> pdb=" O ALA Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 505 through 518 removed outlier: 3.641A pdb=" N VAL Y 510 " --> pdb=" O LEU Y 506 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL Y 511 " --> pdb=" O LEU Y 507 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP Y 512 " --> pdb=" O GLN Y 508 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG Y 513 " --> pdb=" O GLU Y 509 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA Y 518 " --> pdb=" O ASP Y 514 " (cutoff:3.500A) Processing helix chain 'Z' and resid 248 through 261 Processing helix chain 'Z' and resid 266 through 270 Processing helix chain 'Z' and resid 296 through 305 Processing helix chain 'Z' and resid 323 through 331 Processing helix chain 'Z' and resid 332 through 335 Processing helix chain 'Z' and resid 357 through 372 Processing helix chain 'Z' and resid 373 through 376 Processing helix chain 'Z' and resid 385 through 393 Processing helix chain 'Z' and resid 402 through 410 removed outlier: 4.564A pdb=" N ILE Z 408 " --> pdb=" O ASP Z 405 " (cutoff:3.500A) Processing helix chain 'Z' and resid 436 through 440 Processing helix chain 'Z' and resid 483 through 502 Processing helix chain 'Z' and resid 504 through 524 removed outlier: 3.638A pdb=" N LYS Z 524 " --> pdb=" O LYS Z 520 " (cutoff:3.500A) Processing helix chain 'w' and resid 575 through 582 Processing helix chain 'x' and resid 575 through 582 removed outlier: 3.615A pdb=" N ARG x 579 " --> pdb=" O TYR x 575 " (cutoff:3.500A) Processing helix chain 'y' and resid 575 through 582 Processing helix chain 'z' and resid 575 through 582 removed outlier: 3.627A pdb=" N ARG z 579 " --> pdb=" O TYR z 575 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA2, first strand: chain 'B' and resid 32 through 33 removed outlier: 3.693A pdb=" N ILE B 33 " --> pdb=" O TRP z 573 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP z 573 " --> pdb=" O ILE B 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.617A pdb=" N VAL B 92 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASP B 144 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE B 94 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 141 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL B 171 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B 143 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.665A pdb=" N VAL C 92 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU C 141 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL C 171 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 143 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS C 56 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N GLY C 172 " --> pdb=" O CYS C 56 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 58 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C 59 " --> pdb=" O PHE C 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.435A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU D 141 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL D 171 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 143 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.600A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS E 56 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLY E 172 " --> pdb=" O CYS E 56 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL E 58 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE E 196 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL E 59 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.676A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS F 56 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N GLY F 172 " --> pdb=" O CYS F 56 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL F 58 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.677A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS G 56 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N GLY G 172 " --> pdb=" O CYS G 56 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL G 58 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.777A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE H 196 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL H 59 " --> pdb=" O PHE H 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.377A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU I 141 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL I 171 " --> pdb=" O LEU I 141 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE I 143 " --> pdb=" O VAL I 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 80 through 82 removed outlier: 5.409A pdb=" N GLU I 82 " --> pdb=" O PRO I 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.639A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU J 141 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL J 171 " --> pdb=" O LEU J 141 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE J 143 " --> pdb=" O VAL J 171 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 59 " --> pdb=" O PHE J 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.696A pdb=" N VAL K 92 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE K 196 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL K 59 " --> pdb=" O PHE K 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 91 through 94 removed outlier: 6.457A pdb=" N VAL L 92 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASP L 144 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE L 94 " --> pdb=" O ASP L 144 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU L 141 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL L 171 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE L 143 " --> pdb=" O VAL L 171 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG L 57 " --> pdb=" O LEU L 194 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE L 196 " --> pdb=" O ARG L 57 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL L 59 " --> pdb=" O PHE L 196 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 91 through 94 removed outlier: 6.664A pdb=" N VAL M 92 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU M 141 " --> pdb=" O VAL M 169 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL M 171 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE M 143 " --> pdb=" O VAL M 171 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG M 57 " --> pdb=" O LEU M 194 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N PHE M 196 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL M 59 " --> pdb=" O PHE M 196 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 283 through 285 removed outlier: 6.843A pdb=" N LEU O 349 " --> pdb=" O ASP O 378 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP O 378 " --> pdb=" O LEU O 349 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN O 351 " --> pdb=" O CYS O 376 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU O 371 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU O 301 " --> pdb=" O VAL O 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 470 through 475 removed outlier: 5.464A pdb=" N VAL O 471 " --> pdb=" O ASP O 465 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP O 465 " --> pdb=" O VAL O 471 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA O 473 " --> pdb=" O VAL O 463 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER O 445 " --> pdb=" O ALA O 540 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER O 542 " --> pdb=" O SER O 445 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE O 447 " --> pdb=" O SER O 542 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL O 544 " --> pdb=" O ILE O 447 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL O 449 " --> pdb=" O VAL O 544 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N VAL O 451 " --> pdb=" O PRO O 546 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL O 607 " --> pdb=" O GLY O 541 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY O 611 " --> pdb=" O LEU O 545 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 121 through 122 Processing sheet with id=AC4, first strand: chain 'W' and resid 32 through 34 removed outlier: 4.153A pdb=" N ASN W 32 " --> pdb=" O PHE Y 468 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL Y 458 " --> pdb=" O LEU Y 469 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG Y 471 " --> pdb=" O ILE Y 456 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE Y 456 " --> pdb=" O ARG Y 471 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N HIS Y 473 " --> pdb=" O THR Y 454 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR Y 454 " --> pdb=" O HIS Y 473 " (cutoff:3.500A) removed outlier: 11.958A pdb=" N GLN Y 475 " --> pdb=" O ASP Y 452 " (cutoff:3.500A) removed outlier: 15.760A pdb=" N ASP Y 452 " --> pdb=" O GLN Y 475 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR Y 455 " --> pdb=" O ASP Y 449 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP Y 449 " --> pdb=" O THR Y 455 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLN Y 461 " --> pdb=" O THR Y 443 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR Y 443 " --> pdb=" O GLN Y 461 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU Y 446 " --> pdb=" O SER Y 414 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N SER Y 414 " --> pdb=" O LEU Y 446 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE Y 448 " --> pdb=" O LYS Y 412 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LYS Y 412 " --> pdb=" O PHE Y 448 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 32 through 34 removed outlier: 4.153A pdb=" N ASN W 32 " --> pdb=" O PHE Y 468 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N MET Y 430 " --> pdb=" O GLN Y 475 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 184 through 186 Processing sheet with id=AC7, first strand: chain 'W' and resid 237 through 243 removed outlier: 6.283A pdb=" N ILE W 237 " --> pdb=" O ASP W 231 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP W 231 " --> pdb=" O ILE W 237 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP W 205 " --> pdb=" O THR W 228 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP W 202 " --> pdb=" O TYR W 285 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'W' and resid 411 through 417 removed outlier: 5.494A pdb=" N LYS W 412 " --> pdb=" O PHE W 448 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE W 448 " --> pdb=" O LYS W 412 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER W 414 " --> pdb=" O LEU W 446 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU W 446 " --> pdb=" O SER W 414 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR W 443 " --> pdb=" O GLN W 461 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLN W 461 " --> pdb=" O THR W 443 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE W 456 " --> pdb=" O ARG W 471 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG W 471 " --> pdb=" O ILE W 456 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL W 458 " --> pdb=" O LEU W 469 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG W 432 " --> pdb=" O HIS W 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 33 through 35 removed outlier: 6.872A pdb=" N VAL Z 458 " --> pdb=" O LEU Z 469 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG Z 471 " --> pdb=" O ILE Z 456 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE Z 456 " --> pdb=" O ARG Z 471 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N HIS Z 473 " --> pdb=" O THR Z 454 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N THR Z 454 " --> pdb=" O HIS Z 473 " (cutoff:3.500A) removed outlier: 11.801A pdb=" N GLN Z 475 " --> pdb=" O ASP Z 452 " (cutoff:3.500A) removed outlier: 15.460A pdb=" N ASP Z 452 " --> pdb=" O GLN Z 475 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR Z 455 " --> pdb=" O ASP Z 449 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASP Z 449 " --> pdb=" O THR Z 455 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLN Z 461 " --> pdb=" O THR Z 443 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR Z 443 " --> pdb=" O GLN Z 461 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU Z 446 " --> pdb=" O SER Z 414 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER Z 414 " --> pdb=" O LEU Z 446 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE Z 448 " --> pdb=" O LYS Z 412 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS Z 412 " --> pdb=" O PHE Z 448 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 33 through 35 removed outlier: 4.674A pdb=" N MET Z 430 " --> pdb=" O GLN Z 475 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 184 through 186 Processing sheet with id=AD3, first strand: chain 'X' and resid 237 through 243 removed outlier: 6.402A pdb=" N ILE X 237 " --> pdb=" O ASP X 231 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP X 231 " --> pdb=" O ILE X 237 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR X 228 " --> pdb=" O ASP X 205 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP X 205 " --> pdb=" O THR X 228 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP X 202 " --> pdb=" O TYR X 285 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE X 284 " --> pdb=" O HIS X 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 411 through 417 removed outlier: 4.268A pdb=" N ARG X 415 " --> pdb=" O VAL X 444 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL X 444 " --> pdb=" O ARG X 415 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR X 443 " --> pdb=" O GLN X 461 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLN X 461 " --> pdb=" O THR X 443 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP X 449 " --> pdb=" O THR X 455 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR X 455 " --> pdb=" O ASP X 449 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR X 454 " --> pdb=" O HIS X 473 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS X 473 " --> pdb=" O THR X 454 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE X 456 " --> pdb=" O ARG X 471 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG X 471 " --> pdb=" O ILE X 456 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL X 458 " --> pdb=" O LEU X 469 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 237 through 243 removed outlier: 6.150A pdb=" N ILE Y 237 " --> pdb=" O ASP Y 231 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP Y 231 " --> pdb=" O ILE Y 237 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY Y 239 " --> pdb=" O VAL Y 229 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TRP Y 202 " --> pdb=" O TYR Y 285 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE Y 284 " --> pdb=" O HIS Y 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 213 through 214 removed outlier: 3.972A pdb=" N LEU Y 213 " --> pdb=" O LEU Y 221 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 236 through 243 removed outlier: 7.025A pdb=" N VAL Z 229 " --> pdb=" O MET Z 238 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE Z 240 " --> pdb=" O THR Z 227 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR Z 227 " --> pdb=" O ILE Z 240 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU Z 242 " --> pdb=" O TRP Z 225 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP Z 225 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) 2384 hydrogen bonds defined for protein. 6801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 445 hydrogen bonds 862 hydrogen bond angles 0 basepair planarities 184 basepair parallelities 323 stacking parallelities Total time for adding SS restraints: 25.47 Time building geometry restraints manager: 13.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 8502 1.29 - 1.42: 17420 1.42 - 1.56: 32832 1.56 - 1.69: 1051 1.69 - 1.83: 262 Bond restraints: 60067 Sorted by residual: bond pdb=" C VAL B 186 " pdb=" O VAL B 186 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.10e-02 8.26e+03 5.59e+01 bond pdb=" C GLU B 184 " pdb=" O GLU B 184 " ideal model delta sigma weight residual 1.236 1.151 0.085 1.18e-02 7.18e+03 5.22e+01 bond pdb=" C GLN F 38 " pdb=" O GLN F 38 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.19e-02 7.06e+03 5.20e+01 bond pdb=" C GLN A 38 " pdb=" O GLN A 38 " ideal model delta sigma weight residual 1.237 1.152 0.085 1.19e-02 7.06e+03 5.06e+01 bond pdb=" C GLN G 38 " pdb=" O GLN G 38 " ideal model delta sigma weight residual 1.237 1.152 0.085 1.19e-02 7.06e+03 5.05e+01 ... (remaining 60062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.23: 82669 5.23 - 10.47: 620 10.47 - 15.70: 6 15.70 - 20.94: 0 20.94 - 26.17: 1 Bond angle restraints: 83296 Sorted by residual: angle pdb=" C GLN X 425 " pdb=" CA GLN X 425 " pdb=" CB GLN X 425 " ideal model delta sigma weight residual 109.37 135.54 -26.17 1.83e+00 2.99e-01 2.05e+02 angle pdb=" C ARG Y 223 " pdb=" N PRO Y 224 " pdb=" CA PRO Y 224 " ideal model delta sigma weight residual 120.14 130.19 -10.05 1.06e+00 8.90e-01 8.98e+01 angle pdb=" C3' G 7 230 " pdb=" O3' G 7 230 " pdb=" P G 7 231 " ideal model delta sigma weight residual 120.20 107.09 13.11 1.50e+00 4.44e-01 7.64e+01 angle pdb=" N VAL L 208 " pdb=" CA VAL L 208 " pdb=" C VAL L 208 " ideal model delta sigma weight residual 110.42 102.49 7.93 9.60e-01 1.09e+00 6.82e+01 angle pdb=" N VAL L 215 " pdb=" CA VAL L 215 " pdb=" C VAL L 215 " ideal model delta sigma weight residual 111.56 118.66 -7.10 8.60e-01 1.35e+00 6.82e+01 ... (remaining 83291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 34410 35.55 - 71.10: 2075 71.10 - 106.65: 157 106.65 - 142.20: 7 142.20 - 177.75: 9 Dihedral angle restraints: 36658 sinusoidal: 19619 harmonic: 17039 Sorted by residual: dihedral pdb=" O4' U 7 49 " pdb=" C2' U 7 49 " pdb=" C1' U 7 49 " pdb=" C3' U 7 49 " ideal model delta sinusoidal sigma weight residual -35.00 33.91 -68.91 1 8.00e+00 1.56e-02 9.60e+01 dihedral pdb=" CD ARG W 367 " pdb=" NE ARG W 367 " pdb=" CZ ARG W 367 " pdb=" NH1 ARG W 367 " ideal model delta sinusoidal sigma weight residual 0.00 89.14 -89.14 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" C4' U 7 49 " pdb=" C3' U 7 49 " pdb=" C2' U 7 49 " pdb=" C1' U 7 49 " ideal model delta sinusoidal sigma weight residual -35.00 29.37 -64.37 1 8.00e+00 1.56e-02 8.51e+01 ... (remaining 36655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 9271 0.215 - 0.431: 200 0.431 - 0.646: 1 0.646 - 0.861: 1 0.861 - 1.077: 1 Chirality restraints: 9474 Sorted by residual: chirality pdb=" CA GLU L 24 " pdb=" N GLU L 24 " pdb=" C GLU L 24 " pdb=" CB GLU L 24 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA GLN L 22 " pdb=" N GLN L 22 " pdb=" C GLN L 22 " pdb=" CB GLN L 22 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA LEU W 477 " pdb=" N LEU W 477 " pdb=" C LEU W 477 " pdb=" CB LEU W 477 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 9471 not shown) Planarity restraints: 8821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 7 174 " 0.359 2.00e-02 2.50e+03 1.44e-01 6.26e+02 pdb=" N9 G 7 174 " -0.063 2.00e-02 2.50e+03 pdb=" C8 G 7 174 " -0.084 2.00e-02 2.50e+03 pdb=" N7 G 7 174 " -0.117 2.00e-02 2.50e+03 pdb=" C5 G 7 174 " -0.089 2.00e-02 2.50e+03 pdb=" C6 G 7 174 " 0.045 2.00e-02 2.50e+03 pdb=" O6 G 7 174 " 0.194 2.00e-02 2.50e+03 pdb=" N1 G 7 174 " 0.099 2.00e-02 2.50e+03 pdb=" C2 G 7 174 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G 7 174 " -0.081 2.00e-02 2.50e+03 pdb=" N3 G 7 174 " -0.116 2.00e-02 2.50e+03 pdb=" C4 G 7 174 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA 1 62 " 0.323 2.00e-02 2.50e+03 1.41e-01 5.46e+02 pdb=" N9 DA 1 62 " -0.033 2.00e-02 2.50e+03 pdb=" C8 DA 1 62 " -0.087 2.00e-02 2.50e+03 pdb=" N7 DA 1 62 " -0.108 2.00e-02 2.50e+03 pdb=" C5 DA 1 62 " -0.087 2.00e-02 2.50e+03 pdb=" C6 DA 1 62 " 0.036 2.00e-02 2.50e+03 pdb=" N6 DA 1 62 " 0.197 2.00e-02 2.50e+03 pdb=" N1 DA 1 62 " 0.083 2.00e-02 2.50e+03 pdb=" C2 DA 1 62 " -0.056 2.00e-02 2.50e+03 pdb=" N3 DA 1 62 " -0.138 2.00e-02 2.50e+03 pdb=" C4 DA 1 62 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 3 -1 " 0.139 2.00e-02 2.50e+03 1.15e-01 3.29e+02 pdb=" N1 DT 3 -1 " 0.058 2.00e-02 2.50e+03 pdb=" C2 DT 3 -1 " -0.012 2.00e-02 2.50e+03 pdb=" O2 DT 3 -1 " -0.250 2.00e-02 2.50e+03 pdb=" N3 DT 3 -1 " 0.115 2.00e-02 2.50e+03 pdb=" C4 DT 3 -1 " 0.077 2.00e-02 2.50e+03 pdb=" O4 DT 3 -1 " 0.068 2.00e-02 2.50e+03 pdb=" C5 DT 3 -1 " -0.019 2.00e-02 2.50e+03 pdb=" C7 DT 3 -1 " -0.147 2.00e-02 2.50e+03 pdb=" C6 DT 3 -1 " -0.028 2.00e-02 2.50e+03 ... (remaining 8818 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 53 1.88 - 2.64: 1055 2.64 - 3.39: 74882 3.39 - 4.15: 149067 4.15 - 4.90: 246709 Nonbonded interactions: 471766 Sorted by model distance: nonbonded pdb=" NH1 ARG O 300 " pdb=" N2 G 7 86 " model vdw 1.131 3.200 nonbonded pdb=" NE2 HIS O 503 " pdb=" OP1 U 7 242 " model vdw 1.373 3.120 nonbonded pdb=" OE1 GLN X 330 " pdb=" OH TYR X 368 " model vdw 1.421 3.040 nonbonded pdb=" OG1 THR G 67 " pdb="MG MG G 301 " model vdw 1.432 2.170 nonbonded pdb=" OG1 THR F 67 " pdb="MG MG F 301 " model vdw 1.432 2.170 ... (remaining 471761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '2' and (resid 1 through 11 or resid 13 through 18 or resid 20 through 25 \ or resid 27)) selection = (chain '5' and (resid 1 through 11 or resid 13 through 18 or resid 20 through 25 \ or resid 27)) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = (chain 'W' and (resid 29 through 516 or resid 524 through 542 or resid 600)) selection = chain 'X' } ncs_group { reference = (chain 'Y' and (resid 196 through 287 or resid 295 through 340 or resid 354 thro \ ugh 525 or (resid 526 and (name N or name CA or name C or name O or name CB )) o \ r resid 527)) selection = chain 'Z' } ncs_group { reference = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } 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: 13.770 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: 0.060 Extract box with map and model: 1.710 Check model and map are aligned: 0.330 Set scattering table: 0.410 Process input model: 113.460 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.360 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: 0.020 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 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 : 0.013 0.087 60067 Z= 0.847 Angle : 1.628 26.173 83296 Z= 1.135 Chirality : 0.084 1.077 9474 Planarity : 0.020 0.494 8821 Dihedral : 18.837 177.746 25640 Min Nonbonded Distance : 1.131 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 0.21 % Allowed : 1.39 % Favored : 98.40 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.10), residues: 5809 helix: -1.21 (0.08), residues: 3036 sheet: 0.30 (0.20), residues: 584 loop : -0.01 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.216 0.023 TRP H 20 HIS 0.019 0.002 HIS X 258 PHE 0.088 0.010 PHE O 45 TYR 0.146 0.018 TYR I 112 ARG 0.020 0.001 ARG Z 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 879 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: I 159 ASP cc_start: 0.5668 (t70) cc_final: 0.5199 (t0) REVERT: Y 381 MET cc_start: -0.2101 (mtt) cc_final: -0.3841 (ttm) REVERT: Z 238 MET cc_start: 0.1992 (mmp) cc_final: 0.1211 (tpt) outliers start: 11 outliers final: 7 residues processed: 884 average time/residue: 1.6602 time to fit residues: 1797.9877 Evaluate side-chains 312 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 305 time to evaluate : 4.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain Y residue 463 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 522 optimal weight: 5.9990 chunk 469 optimal weight: 8.9990 chunk 260 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 316 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 485 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 295 optimal weight: 7.9990 chunk 361 optimal weight: 6.9990 chunk 562 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN E 22 GLN E 97 HIS E 213 GLN F 213 GLN F 269 GLN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 269 GLN ** O 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 323 HIS ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 370 HIS ** O 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 603 GLN ** S 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 HIS Y 299 GLN Z 295 ASN Z 464 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 60067 Z= 0.295 Angle : 0.740 13.440 83296 Z= 0.388 Chirality : 0.042 0.200 9474 Planarity : 0.005 0.073 8821 Dihedral : 20.927 173.918 13511 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.97 % Allowed : 9.88 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.11), residues: 5809 helix: 0.84 (0.09), residues: 3089 sheet: 0.39 (0.20), residues: 640 loop : 0.35 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP y 573 HIS 0.012 0.002 HIS I 97 PHE 0.031 0.002 PHE Q 158 TYR 0.028 0.002 TYR A 112 ARG 0.015 0.001 ARG X 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 335 time to evaluate : 4.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 159 ASP cc_start: 0.6069 (m-30) cc_final: 0.5652 (m-30) REVERT: Y 381 MET cc_start: -0.1800 (mtt) cc_final: -0.3950 (ttm) outliers start: 101 outliers final: 28 residues processed: 417 average time/residue: 1.4990 time to fit residues: 786.6856 Evaluate side-chains 257 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain O residue 213 LYS Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain W residue 506 LEU Chi-restraints excluded: chain X residue 225 TRP Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Z residue 306 PHE Chi-restraints excluded: chain y residue 572 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 312 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 467 optimal weight: 9.9990 chunk 382 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 563 optimal weight: 6.9990 chunk 608 optimal weight: 20.0000 chunk 501 optimal weight: 5.9990 chunk 558 optimal weight: 5.9990 chunk 191 optimal weight: 0.5980 chunk 451 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN D 213 GLN ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS M 37 GLN O 321 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 HIS ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 295 ASN Y 299 GLN Z 464 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 60067 Z= 0.204 Angle : 0.611 11.303 83296 Z= 0.323 Chirality : 0.038 0.177 9474 Planarity : 0.004 0.053 8821 Dihedral : 20.834 178.977 13495 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.50 % Allowed : 11.35 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.34 (0.11), residues: 5809 helix: 1.33 (0.09), residues: 3086 sheet: 0.71 (0.20), residues: 628 loop : 0.48 (0.14), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP y 573 HIS 0.007 0.001 HIS I 97 PHE 0.048 0.001 PHE Z 306 TYR 0.020 0.001 TYR A 112 ARG 0.009 0.000 ARG Y 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 275 time to evaluate : 4.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 229 MET cc_start: 0.5825 (mmm) cc_final: 0.5548 (mmp) REVERT: Y 381 MET cc_start: -0.1702 (mtt) cc_final: -0.3852 (ttm) REVERT: Z 238 MET cc_start: 0.1683 (mmt) cc_final: 0.1341 (tpt) outliers start: 77 outliers final: 36 residues processed: 342 average time/residue: 1.3680 time to fit residues: 599.5162 Evaluate side-chains 252 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 5.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain W residue 506 LEU Chi-restraints excluded: chain X residue 225 TRP Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain y residue 572 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 556 optimal weight: 0.9980 chunk 423 optimal weight: 4.9990 chunk 292 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 268 optimal weight: 0.7980 chunk 378 optimal weight: 4.9990 chunk 565 optimal weight: 8.9990 chunk 598 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 535 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN G 213 GLN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 97 HIS ** M 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 500 HIS O 521 GLN Q 24 HIS ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 413 GLN ** Z 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 60067 Z= 0.301 Angle : 0.651 14.593 83296 Z= 0.340 Chirality : 0.040 0.500 9474 Planarity : 0.004 0.049 8821 Dihedral : 20.935 177.503 13495 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.07 % Allowed : 10.98 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.41 (0.11), residues: 5809 helix: 1.48 (0.09), residues: 3073 sheet: 0.28 (0.22), residues: 567 loop : 0.51 (0.14), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP y 573 HIS 0.010 0.001 HIS I 97 PHE 0.038 0.002 PHE Q 158 TYR 0.021 0.002 TYR w 582 ARG 0.011 0.001 ARG X 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 247 time to evaluate : 4.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7254 (ttp80) REVERT: G 38 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: L 196 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6643 (m-10) REVERT: Y 381 MET cc_start: -0.1726 (mtt) cc_final: -0.3383 (ttm) REVERT: Z 238 MET cc_start: 0.1788 (mmt) cc_final: 0.1557 (mmt) outliers start: 106 outliers final: 39 residues processed: 337 average time/residue: 1.4021 time to fit residues: 604.8997 Evaluate side-chains 250 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 4.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 225 LYS Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain X residue 225 TRP Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 296 HIS Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain y residue 572 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 498 optimal weight: 10.0000 chunk 339 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 445 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 510 optimal weight: 0.9980 chunk 413 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 537 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 GLN I 38 GLN I 97 HIS K 37 GLN K 97 HIS ** M 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 496 GLN ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 425 GLN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 60067 Z= 0.188 Angle : 0.583 11.723 83296 Z= 0.305 Chirality : 0.037 0.289 9474 Planarity : 0.004 0.050 8821 Dihedral : 20.923 176.886 13495 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.52 % Allowed : 11.99 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.11), residues: 5809 helix: 1.69 (0.09), residues: 3079 sheet: 0.23 (0.21), residues: 578 loop : 0.60 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP y 573 HIS 0.007 0.001 HIS K 97 PHE 0.035 0.001 PHE A 190 TYR 0.020 0.001 TYR w 582 ARG 0.011 0.000 ARG M 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 247 time to evaluate : 4.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 ILE cc_start: 0.8439 (pp) cc_final: 0.8214 (pt) REVERT: L 196 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.6592 (m-10) REVERT: Y 381 MET cc_start: -0.1826 (mtt) cc_final: -0.3483 (ttm) REVERT: Z 238 MET cc_start: 0.1672 (mmt) cc_final: 0.1457 (mmt) outliers start: 78 outliers final: 37 residues processed: 311 average time/residue: 1.3666 time to fit residues: 547.7558 Evaluate side-chains 237 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain X residue 225 TRP Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain Y residue 296 HIS Chi-restraints excluded: chain Y residue 426 PHE Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain y residue 572 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 201 optimal weight: 7.9990 chunk 538 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 351 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 598 optimal weight: 10.9990 chunk 497 optimal weight: 30.0000 chunk 277 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 198 optimal weight: 0.6980 chunk 314 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 77 HIS K 97 HIS ** M 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 522 HIS ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 60067 Z= 0.248 Angle : 0.615 16.511 83296 Z= 0.318 Chirality : 0.038 0.275 9474 Planarity : 0.004 0.077 8821 Dihedral : 20.973 176.755 13495 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.60 % Allowed : 12.83 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.66 (0.11), residues: 5809 helix: 1.73 (0.09), residues: 3076 sheet: 0.20 (0.21), residues: 578 loop : 0.60 (0.14), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP y 573 HIS 0.007 0.001 HIS K 97 PHE 0.035 0.001 PHE A 190 TYR 0.015 0.001 TYR W 61 ARG 0.016 0.000 ARG M 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 205 time to evaluate : 4.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 ILE cc_start: 0.8460 (pp) cc_final: 0.8255 (pt) REVERT: L 196 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6508 (m-10) outliers start: 82 outliers final: 44 residues processed: 274 average time/residue: 1.3167 time to fit residues: 468.0002 Evaluate side-chains 236 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain X residue 225 TRP Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 272 HIS Chi-restraints excluded: chain Y residue 296 HIS Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain y residue 572 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 577 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 341 optimal weight: 6.9990 chunk 437 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 504 optimal weight: 9.9990 chunk 334 optimal weight: 10.0000 chunk 596 optimal weight: 10.0000 chunk 373 optimal weight: 6.9990 chunk 363 optimal weight: 20.0000 chunk 275 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN C 213 GLN F 77 HIS ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 HIS ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 367 ASN O 484 ASN ** O 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN ** Q 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 167 GLN ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 428 ASN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 60067 Z= 0.558 Angle : 0.832 13.434 83296 Z= 0.426 Chirality : 0.044 0.227 9474 Planarity : 0.006 0.088 8821 Dihedral : 21.405 179.736 13495 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.01 % Allowed : 13.17 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.11), residues: 5809 helix: 1.06 (0.09), residues: 3078 sheet: 0.01 (0.20), residues: 670 loop : 0.20 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 225 HIS 0.012 0.002 HIS K 97 PHE 0.053 0.003 PHE A 190 TYR 0.030 0.002 TYR G 240 ARG 0.015 0.001 ARG z 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 192 time to evaluate : 4.690 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: A 170 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8385 (mp) REVERT: L 196 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6593 (m-10) REVERT: Y 381 MET cc_start: -0.1751 (mtt) cc_final: -0.3562 (ttm) outliers start: 103 outliers final: 50 residues processed: 279 average time/residue: 1.3126 time to fit residues: 477.5899 Evaluate side-chains 226 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 4.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 225 LYS Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain O residue 213 LYS Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain X residue 225 TRP Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 272 HIS Chi-restraints excluded: chain Y residue 296 HIS Chi-restraints excluded: chain Y residue 355 ARG Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain Z residue 324 PHE Chi-restraints excluded: chain w residue 578 LEU Chi-restraints excluded: chain y residue 572 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 369 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 356 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 379 optimal weight: 7.9990 chunk 406 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 468 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 HIS K 38 GLN ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN Q 83 GLN W 206 HIS W 375 GLN ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 428 ASN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 60067 Z= 0.179 Angle : 0.625 15.181 83296 Z= 0.324 Chirality : 0.038 0.205 9474 Planarity : 0.004 0.059 8821 Dihedral : 21.298 176.710 13495 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.45 % Allowed : 14.20 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.49 (0.11), residues: 5809 helix: 1.61 (0.09), residues: 3077 sheet: 0.22 (0.22), residues: 544 loop : 0.46 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP y 573 HIS 0.011 0.001 HIS D 193 PHE 0.028 0.001 PHE A 190 TYR 0.022 0.001 TYR A 112 ARG 0.015 0.001 ARG z 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 212 time to evaluate : 4.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 196 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.6573 (m-10) REVERT: Y 381 MET cc_start: -0.1934 (mtt) cc_final: -0.3246 (ttm) REVERT: Z 381 MET cc_start: -0.0351 (mtp) cc_final: -0.1178 (mtt) REVERT: w 580 GLU cc_start: 0.5855 (pp20) cc_final: 0.5161 (pp20) outliers start: 74 outliers final: 41 residues processed: 278 average time/residue: 1.4233 time to fit residues: 505.9800 Evaluate side-chains 227 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 4.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 269 GLN Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain X residue 225 TRP Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain X residue 513 ARG Chi-restraints excluded: chain Y residue 272 HIS Chi-restraints excluded: chain Y residue 296 HIS Chi-restraints excluded: chain Y residue 355 ARG Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain y residue 572 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 542 optimal weight: 20.0000 chunk 571 optimal weight: 9.9990 chunk 521 optimal weight: 8.9990 chunk 555 optimal weight: 7.9990 chunk 334 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 436 optimal weight: 6.9990 chunk 170 optimal weight: 0.3980 chunk 502 optimal weight: 10.0000 chunk 525 optimal weight: 0.1980 chunk 554 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN I 22 GLN K 38 GLN K 97 HIS ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 206 HIS ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 464 ASN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 60067 Z= 0.374 Angle : 0.718 15.612 83296 Z= 0.368 Chirality : 0.041 0.226 9474 Planarity : 0.005 0.051 8821 Dihedral : 21.419 177.719 13495 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.19 % Allowed : 14.87 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.21 (0.11), residues: 5809 helix: 1.41 (0.09), residues: 3071 sheet: 0.05 (0.19), residues: 678 loop : 0.33 (0.15), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP y 573 HIS 0.008 0.001 HIS K 97 PHE 0.042 0.002 PHE A 190 TYR 0.021 0.002 TYR A 112 ARG 0.012 0.001 ARG z 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 4.657 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: L 196 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6589 (m-10) REVERT: Y 381 MET cc_start: -0.1868 (mtt) cc_final: -0.3687 (ttm) REVERT: Z 238 MET cc_start: 0.2145 (tpp) cc_final: 0.1690 (tpt) REVERT: w 575 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.5637 (t80) REVERT: w 582 TYR cc_start: 0.5390 (t80) cc_final: 0.5103 (t80) outliers start: 61 outliers final: 39 residues processed: 244 average time/residue: 1.3657 time to fit residues: 429.5073 Evaluate side-chains 219 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain X residue 225 TRP Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain X residue 513 ARG Chi-restraints excluded: chain Y residue 272 HIS Chi-restraints excluded: chain Y residue 296 HIS Chi-restraints excluded: chain Y residue 426 PHE Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain w residue 575 TYR Chi-restraints excluded: chain y residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 365 optimal weight: 5.9990 chunk 587 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 408 optimal weight: 8.9990 chunk 616 optimal weight: 10.0000 chunk 567 optimal weight: 0.0570 chunk 491 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 379 optimal weight: 2.9990 chunk 301 optimal weight: 5.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 213 GLN K 97 HIS ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 206 HIS ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 428 ASN Y 464 ASN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 60067 Z= 0.307 Angle : 0.698 15.701 83296 Z= 0.359 Chirality : 0.040 0.244 9474 Planarity : 0.004 0.076 8821 Dihedral : 21.447 177.345 13495 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.02 % Allowed : 15.20 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.25 (0.11), residues: 5809 helix: 1.46 (0.09), residues: 3070 sheet: 0.03 (0.20), residues: 678 loop : 0.32 (0.15), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP y 573 HIS 0.011 0.001 HIS K 97 PHE 0.058 0.002 PHE Y 426 TYR 0.019 0.002 TYR A 112 ARG 0.019 0.001 ARG z 579 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 4.608 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: L 196 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6480 (m-10) REVERT: Y 381 MET cc_start: -0.1866 (mtt) cc_final: -0.3714 (ttm) REVERT: Z 238 MET cc_start: 0.2105 (tpp) cc_final: 0.1177 (tpt) REVERT: Z 430 MET cc_start: 0.5430 (tpp) cc_final: 0.5115 (tpt) REVERT: w 575 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.5673 (t80) REVERT: w 580 GLU cc_start: 0.5872 (pp20) cc_final: 0.5000 (pp20) outliers start: 52 outliers final: 37 residues processed: 231 average time/residue: 1.3628 time to fit residues: 407.6468 Evaluate side-chains 216 residues out of total 5121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 4.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain W residue 506 LEU Chi-restraints excluded: chain X residue 225 TRP Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain X residue 513 ARG Chi-restraints excluded: chain Y residue 272 HIS Chi-restraints excluded: chain Y residue 296 HIS Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain w residue 575 TYR Chi-restraints excluded: chain y residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 390 optimal weight: 0.0670 chunk 523 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 452 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 491 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 505 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN K 97 HIS ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 206 HIS ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 428 ASN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.062762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.042628 restraints weight = 325825.859| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.37 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 60067 Z= 0.180 Angle : 0.656 13.943 83296 Z= 0.338 Chirality : 0.039 0.253 9474 Planarity : 0.004 0.065 8821 Dihedral : 21.284 175.285 13495 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.84 % Allowed : 15.37 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.58 (0.11), residues: 5809 helix: 1.77 (0.09), residues: 3058 sheet: 0.15 (0.22), residues: 543 loop : 0.39 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP y 573 HIS 0.007 0.001 HIS K 97 PHE 0.020 0.001 PHE Z 332 TYR 0.019 0.001 TYR M 75 ARG 0.012 0.000 ARG O 587 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12198.53 seconds wall clock time: 215 minutes 26.97 seconds (12926.97 seconds total)