Starting phenix.real_space_refine on Sun Dec 29 06:57:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ea3_27971/12_2024/8ea3_27971.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ea3_27971/12_2024/8ea3_27971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ea3_27971/12_2024/8ea3_27971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ea3_27971/12_2024/8ea3_27971.map" model { file = "/net/cci-nas-00/data/ceres_data/8ea3_27971/12_2024/8ea3_27971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ea3_27971/12_2024/8ea3_27971.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.063 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 529 5.49 5 Mg 14 5.21 5 S 170 5.16 5 C 33408 2.51 5 N 10159 2.21 5 O 11675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 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: 55955 Number of models: 1 Model: "" Number of chains: 44 Chain: "1" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2031 Classifications: {'DNA': 99} Link IDs: {'rna3p': 98} Chain: "3" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1022 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 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': 24, 'rna3p_pur': 97, 'rna3p_pyr': 89} Link IDs: {'rna2p': 43, 'rna3p': 186} Chain breaks: 2 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: "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: 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: "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: "2" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 593 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "4" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 941 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} 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: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} 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: "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: 24.30, per 1000 atoms: 0.43 Number of scatterers: 55955 At special positions: 0 Unit cell: (144.045, 146.179, 314.765, 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 170 16.00 P 529 15.00 Mg 14 11.99 O 11675 8.00 N 10159 7.00 C 33408 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 54776 O5' DT 5 3 .*. O " rejected from bonding due to valence issues. Atom "ATOM 1473 O4' DC 1 42 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.97 Conformation dependent library (CDL) restraints added in 4.6 seconds 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10536 Finding SS restraints... Secondary structure from input PDB file: 282 helices and 33 sheets defined 58.0% alpha, 10.1% beta 181 base pairs and 326 stacking pairs defined. Time for finding SS restraints: 16.51 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.796A pdb=" N LYS A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.511A 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 removed outlier: 3.793A pdb=" N LEU A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.012A pdb=" N ASP A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.727A 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: 3.589A 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: 3.575A pdb=" N GLU B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 3.978A 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: 3.514A 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: 3.632A pdb=" N GLU C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.529A 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 259 removed outlier: 4.053A 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 removed outlier: 4.111A pdb=" N LEU D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) 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: 3.577A 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: 3.768A pdb=" N GLU D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 removed outlier: 3.792A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 30 removed outlier: 3.526A 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: 3.958A 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: 3.802A 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: 3.872A 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: 3.622A pdb=" N GLU F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.764A 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: 3.697A 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 30 removed outlier: 3.686A pdb=" N GLY G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 53 removed outlier: 3.572A pdb=" N GLY G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 75 Processing helix chain 'G' and resid 101 through 113 removed outlier: 3.505A pdb=" N LEU G 113 " --> pdb=" O ILE G 109 " (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 174 through 181 Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'G' and resid 201 through 215 Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.550A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 257 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 29 removed outlier: 3.599A pdb=" N LYS H 29 " --> pdb=" O ILE H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 52 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 101 through 113 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 164 Processing helix chain 'H' and resid 173 through 181 removed outlier: 3.991A pdb=" N ASP H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.883A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 215 removed outlier: 3.664A pdb=" N GLU H 209 " --> pdb=" O LYS H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 238 removed outlier: 3.707A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 258 removed outlier: 3.561A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 274 removed outlier: 3.893A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 30 removed outlier: 3.508A pdb=" N GLU I 24 " --> pdb=" O TRP I 20 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS I 29 " --> pdb=" O ILE I 25 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 53 removed outlier: 3.611A pdb=" N LYS I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 75 Processing helix chain 'I' and resid 101 through 113 removed outlier: 3.602A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 136 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'I' and resid 150 through 151 No H-bonds generated for 'chain 'I' and resid 150 through 151' Processing helix chain 'I' and resid 152 through 164 removed outlier: 4.382A pdb=" N ASP I 156 " --> pdb=" O GLU I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 181 removed outlier: 4.070A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.555A pdb=" N GLU I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 215 Processing helix chain 'I' and resid 226 through 238 Processing helix chain 'I' and resid 240 through 258 removed outlier: 3.786A pdb=" N GLU I 246 " --> pdb=" O GLY I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 274 removed outlier: 3.758A pdb=" N GLU I 270 " --> pdb=" O ALA I 266 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU I 274 " --> pdb=" O GLU I 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 30 removed outlier: 3.630A pdb=" N GLU J 24 " --> pdb=" O TRP J 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE J 25 " --> pdb=" O LEU J 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 26 " --> pdb=" O GLN J 22 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 53 removed outlier: 3.693A pdb=" N GLY J 48 " --> pdb=" O ASP J 44 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 76 Processing helix chain 'J' and resid 101 through 113 removed outlier: 3.612A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU J 113 " --> pdb=" O ILE J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 136 removed outlier: 3.658A pdb=" N ASP J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 150 through 152 No H-bonds generated for 'chain 'J' and resid 150 through 152' Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 173 through 181 removed outlier: 4.005A pdb=" N ASP J 177 " --> pdb=" O THR J 173 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA J 178 " --> pdb=" O ASP J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.571A pdb=" N GLU J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 215 removed outlier: 3.501A pdb=" N LYS J 205 " --> pdb=" O GLY J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 238 removed outlier: 4.004A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 258 removed outlier: 3.590A pdb=" N ARG J 258 " --> pdb=" O ARG J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 273 Processing helix chain 'K' and resid 20 through 30 removed outlier: 3.699A pdb=" N GLU K 24 " --> pdb=" O TRP K 20 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA K 26 " --> pdb=" O GLN K 22 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 53 Processing helix chain 'K' and resid 65 through 75 Processing helix chain 'K' and resid 101 through 113 Processing helix chain 'K' and resid 121 through 134 Processing helix chain 'K' and resid 146 through 149 Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 173 through 181 removed outlier: 4.050A pdb=" N ASP K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 190 removed outlier: 3.553A pdb=" N GLU K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 215 Processing helix chain 'K' and resid 226 through 238 removed outlier: 3.695A pdb=" N ILE K 232 " --> pdb=" O GLU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 240 through 258 Processing helix chain 'K' and resid 264 through 275 removed outlier: 3.632A pdb=" N GLU K 274 " --> pdb=" O GLU K 270 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 30 removed outlier: 3.521A pdb=" N ALA L 26 " --> pdb=" O GLN L 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 53 removed outlier: 4.029A pdb=" N GLY L 48 " --> pdb=" O ASP L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 76 Processing helix chain 'L' and resid 101 through 113 Processing helix chain 'L' and resid 121 through 134 Processing helix chain 'L' and resid 145 through 149 Processing helix chain 'L' and resid 150 through 152 No H-bonds generated for 'chain 'L' and resid 150 through 152' Processing helix chain 'L' and resid 153 through 164 Processing helix chain 'L' and resid 173 through 181 removed outlier: 4.068A pdb=" N ASP L 177 " --> pdb=" O THR L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 removed outlier: 3.764A 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: 3.721A 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 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: 3.912A pdb=" N LEU O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 52 removed outlier: 3.510A 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: 3.906A 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: 4.271A 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 191 through 200 Processing helix chain 'O' and resid 210 through 233 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: 4.655A 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 removed outlier: 4.074A pdb=" N ALA O 417 " --> pdb=" O ASP O 413 " (cutoff:3.500A) 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: 4.172A pdb=" N ASN O 489 " --> pdb=" O TYR O 485 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.589A pdb=" N VAL Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 83 removed outlier: 3.653A 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: 3.527A pdb=" N GLU S 14 " --> pdb=" O LYS S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 46 removed outlier: 3.558A pdb=" N GLY S 41 " --> pdb=" O ASN S 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS S 42 " --> pdb=" O HIS S 38 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU S 45 " --> pdb=" O GLY S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 74 removed outlier: 3.685A pdb=" N GLY S 55 " --> pdb=" O HIS S 51 " (cutoff:3.500A) removed outlier: 3.521A 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 575 through 582 Processing helix chain 'x' and resid 575 through 582 Processing helix chain 'y' and resid 575 through 582 Processing helix chain 'z' and resid 575 through 582 removed outlier: 3.629A pdb=" N ARG z 579 " --> pdb=" O TYR z 575 " (cutoff:3.500A) 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: 3.771A 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: 3.917A 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: 3.848A pdb=" N ALA X 42 " --> pdb=" O LEU X 38 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL X 44 " --> pdb=" O GLU X 40 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS X 45 " --> pdb=" O GLU X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 72 removed outlier: 4.177A 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: 4.032A 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: 4.021A 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 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: 3.821A 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 402 through 410 removed outlier: 3.527A pdb=" N ILE X 408 " --> pdb=" O ASP X 405 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 440 removed outlier: 3.848A 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: 3.785A 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: 3.606A 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: 3.513A 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: 4.439A pdb=" N GLY Y 438 " --> pdb=" O TYR Y 435 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA Y 440 " --> pdb=" O ALA Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 483 through 501 removed outlier: 3.918A 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: 5.175A 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: 3.788A pdb=" N ARG Y 513 " --> pdb=" O GLU Y 509 " (cutoff:3.500A) removed outlier: 3.606A 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 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.615A 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: 6.759A 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: 7.475A 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: 7.630A pdb=" N VAL C 171 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.664A 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: 8.405A pdb=" N GLY C 172 " --> pdb=" O CYS C 56 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL C 58 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.956A 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: 6.436A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.511A 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: 6.537A 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: 6.599A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS E 56 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLY E 172 " --> pdb=" O CYS E 56 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL E 58 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE E 196 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 6.917A 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: 6.677A 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: 8.330A pdb=" N GLY F 172 " --> pdb=" O CYS F 56 " (cutoff:3.500A) removed outlier: 6.228A 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: 6.777A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE G 196 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL G 59 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 80 through 82 removed outlier: 5.063A pdb=" N GLU H 82 " --> pdb=" O PRO H 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.488A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU I 141 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL I 171 " --> pdb=" O LEU I 141 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE I 143 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE I 196 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL I 59 " --> pdb=" O PHE I 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.696A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 6.644A 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: 6.458A pdb=" N VAL K 92 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASP K 144 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE K 94 " --> pdb=" O ASP K 144 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU K 141 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL K 171 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE K 143 " --> pdb=" O VAL K 171 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE K 196 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 6.919A 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: 6.663A pdb=" N VAL L 92 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU L 141 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL L 171 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE L 143 " --> pdb=" O VAL L 171 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG L 57 " --> pdb=" O LEU L 194 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE L 196 " --> pdb=" O ARG L 57 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL L 59 " --> pdb=" O PHE L 196 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 283 through 285 removed outlier: 6.844A pdb=" N LEU O 349 " --> pdb=" O ASP O 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP O 378 " --> pdb=" O LEU O 349 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN O 351 " --> pdb=" O CYS O 376 " (cutoff:3.500A) removed outlier: 4.832A 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=AC1, 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: 6.383A pdb=" N ASP O 465 " --> pdb=" O VAL O 471 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA O 473 " --> pdb=" O VAL O 463 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER O 445 " --> pdb=" O ALA O 540 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER O 542 " --> pdb=" O SER O 445 " (cutoff:3.500A) removed outlier: 7.071A 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: 6.619A 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: 3.518A pdb=" N VAL O 607 " --> pdb=" O GLY O 541 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY O 611 " --> pdb=" O LEU O 545 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 121 through 122 Processing sheet with id=AC3, first strand: chain 'W' and resid 33 through 35 removed outlier: 7.018A pdb=" N VAL Y 458 " --> pdb=" O LEU Y 469 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ARG Y 471 " --> pdb=" O ILE Y 456 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE Y 456 " --> pdb=" O ARG Y 471 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N HIS Y 473 " --> pdb=" O THR Y 454 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR Y 454 " --> pdb=" O HIS Y 473 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N GLN Y 475 " --> pdb=" O ASP Y 452 " (cutoff:3.500A) removed outlier: 15.759A 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: 5.313A pdb=" N ASP Y 449 " --> pdb=" O THR Y 455 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN Y 461 " --> pdb=" O THR Y 443 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR Y 443 " --> pdb=" O GLN Y 461 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU Y 446 " --> pdb=" O SER Y 414 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N SER Y 414 " --> pdb=" O LEU Y 446 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE Y 448 " --> pdb=" O LYS Y 412 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS Y 412 " --> pdb=" O PHE Y 448 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 33 through 35 removed outlier: 4.757A pdb=" N MET Y 430 " --> pdb=" O GLN Y 475 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 184 through 186 Processing sheet with id=AC6, 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: 3.581A pdb=" N ASP W 205 " --> pdb=" O THR W 228 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP W 202 " --> pdb=" O TYR W 285 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE W 284 " --> pdb=" O HIS W 309 " (cutoff:3.500A) Processing sheet with id=AC7, 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: 6.983A 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: 8.293A pdb=" N THR W 443 " --> pdb=" O GLN W 461 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLN W 461 " --> pdb=" O THR W 443 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE W 456 " --> pdb=" O ARG W 471 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG W 471 " --> pdb=" O ILE W 456 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL W 458 " --> pdb=" O LEU W 469 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG W 432 " --> pdb=" O HIS W 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 33 through 35 removed outlier: 6.870A 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: 8.023A 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: 15.459A pdb=" N ASP Z 452 " --> pdb=" O GLN Z 475 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR Z 455 " --> pdb=" O ASP Z 449 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP Z 449 " --> pdb=" O THR Z 455 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLN Z 461 " --> pdb=" O THR Z 443 " (cutoff:3.500A) removed outlier: 8.452A 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=AC9, 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=AD1, first strand: chain 'X' and resid 184 through 186 Processing sheet with id=AD2, first strand: chain 'X' and resid 237 through 243 removed outlier: 6.389A pdb=" N ILE X 237 " --> pdb=" O ASP X 231 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP X 231 " --> pdb=" O ILE X 237 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR X 228 " --> pdb=" O ASP X 205 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP X 205 " --> pdb=" O THR X 228 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP X 202 " --> pdb=" O TYR X 285 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 411 through 417 removed outlier: 4.419A pdb=" N ARG X 415 " --> pdb=" O VAL X 444 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL X 444 " --> pdb=" O ARG X 415 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR X 443 " --> pdb=" O GLN X 461 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLN X 461 " --> pdb=" O THR X 443 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP X 449 " --> pdb=" O THR X 455 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR X 455 " --> pdb=" O ASP X 449 " (cutoff:3.500A) removed outlier: 8.293A 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: 5.577A pdb=" N ILE X 456 " --> pdb=" O ARG X 471 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG X 471 " --> pdb=" O ILE X 456 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL X 458 " --> pdb=" O LEU X 469 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 237 through 243 removed outlier: 6.149A pdb=" N ILE Y 237 " --> pdb=" O ASP Y 231 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP Y 231 " --> pdb=" O ILE Y 237 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY Y 239 " --> pdb=" O VAL Y 229 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TRP Y 202 " --> pdb=" O TYR Y 285 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE Y 284 " --> pdb=" O HIS Y 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 213 through 214 removed outlier: 3.973A pdb=" N LEU Y 213 " --> pdb=" O LEU Y 221 " (cutoff:3.500A) Processing sheet with id=AD6, 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: 4.564A pdb=" N ILE Z 240 " --> pdb=" O THR Z 227 " (cutoff:3.500A) removed outlier: 6.719A 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: 6.757A pdb=" N TRP Z 225 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) 2283 hydrogen bonds defined for protein. 6501 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 434 hydrogen bonds 840 hydrogen bond angles 0 basepair planarities 181 basepair parallelities 326 stacking parallelities Total time for adding SS restraints: 20.89 Time building geometry restraints manager: 12.98 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: 8148 1.29 - 1.42: 16959 1.42 - 1.56: 31542 1.56 - 1.69: 1043 1.69 - 1.83: 250 Bond restraints: 57942 Sorted by residual: bond pdb=" C ASN Z 463 " pdb=" N ASN Z 464 " ideal model delta sigma weight residual 1.332 1.220 0.112 1.40e-02 5.10e+03 6.44e+01 bond pdb=" C VAL B 186 " pdb=" O VAL B 186 " ideal model delta sigma weight residual 1.236 1.154 0.083 1.10e-02 8.26e+03 5.63e+01 bond pdb=" C ARG X 355 " pdb=" N LEU X 356 " ideal model delta sigma weight residual 1.330 1.228 0.103 1.38e-02 5.25e+03 5.52e+01 bond pdb=" C GLN A 38 " pdb=" O GLN A 38 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.19e-02 7.06e+03 5.23e+01 bond pdb=" C GLU B 184 " pdb=" O GLU B 184 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.18e-02 7.18e+03 5.11e+01 ... (remaining 57937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.29: 79797 5.29 - 10.58: 605 10.58 - 15.87: 16 15.87 - 21.16: 12 21.16 - 26.45: 4 Bond angle restraints: 80434 Sorted by residual: angle pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " pdb=" PG ATP B 302 " ideal model delta sigma weight residual 139.87 113.42 26.45 1.00e+00 1.00e+00 7.00e+02 angle pdb=" PB ATP E 302 " pdb=" O3B ATP E 302 " pdb=" PG ATP E 302 " ideal model delta sigma weight residual 139.87 114.76 25.11 1.00e+00 1.00e+00 6.30e+02 angle pdb=" PB ATP F 302 " pdb=" O3B ATP F 302 " pdb=" PG ATP F 302 " ideal model delta sigma weight residual 139.87 115.25 24.62 1.00e+00 1.00e+00 6.06e+02 angle pdb=" PB ATP C 302 " pdb=" O3B ATP C 302 " pdb=" PG ATP C 302 " ideal model delta sigma weight residual 139.87 118.58 21.29 1.00e+00 1.00e+00 4.53e+02 angle pdb=" PB ATP I 302 " pdb=" O3B ATP I 302 " pdb=" PG ATP I 302 " ideal model delta sigma weight residual 139.87 119.92 19.95 1.00e+00 1.00e+00 3.98e+02 ... (remaining 80429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 33184 35.60 - 71.21: 1973 71.21 - 106.81: 158 106.81 - 142.41: 2 142.41 - 178.01: 11 Dihedral angle restraints: 35328 sinusoidal: 19034 harmonic: 16294 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 33.96 -68.96 1 8.00e+00 1.56e-02 9.62e+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 89.17 -89.17 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 29.48 -64.48 1 8.00e+00 1.56e-02 8.54e+01 ... (remaining 35325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 8947 0.216 - 0.431: 190 0.431 - 0.647: 14 0.647 - 0.862: 1 0.862 - 1.078: 1 Chirality restraints: 9153 Sorted by residual: chirality pdb=" CA GLU K 24 " pdb=" N GLU K 24 " pdb=" C GLU K 24 " pdb=" CB GLU K 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 K 22 " pdb=" N GLN K 22 " pdb=" C GLN K 22 " pdb=" CB GLN K 22 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" P DT 1 35 " pdb=" OP1 DT 1 35 " pdb=" OP2 DT 1 35 " pdb=" O5' DT 1 35 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 9150 not shown) Planarity restraints: 8462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 20 " -0.216 2.00e-02 2.50e+03 1.07e-01 2.86e+02 pdb=" CG TRP G 20 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP G 20 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TRP G 20 " 0.091 2.00e-02 2.50e+03 pdb=" NE1 TRP G 20 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 TRP G 20 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP G 20 " 0.137 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 20 " -0.130 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 20 " 0.049 2.00e-02 2.50e+03 pdb=" CH2 TRP G 20 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 367 " -1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG W 367 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG W 367 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG W 367 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG W 367 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 526 " -1.087 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG Y 526 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG Y 526 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 526 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 526 " -0.018 2.00e-02 2.50e+03 ... (remaining 8459 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 54 1.91 - 2.66: 1468 2.66 - 3.40: 73068 3.40 - 4.15: 143240 4.15 - 4.90: 236908 Nonbonded interactions: 454738 Sorted by model distance: nonbonded pdb=" OE2 GLU B 162 " pdb=" NH1 ARG B 189 " model vdw 1.162 3.120 nonbonded pdb=" NH1 ARG X 322 " pdb=" N3 DA 2 4 " model vdw 1.188 3.200 nonbonded pdb=" NH2 ARG W 380 " pdb=" O5' DT 5 3 " model vdw 1.232 3.120 nonbonded pdb=" OP2 DG 1 36 " pdb=" CE LYS I 119 " model vdw 1.236 3.440 nonbonded pdb=" NE2 GLN X 330 " pdb=" OP1 DA 2 6 " model vdw 1.269 3.120 ... (remaining 454733 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 or resid 29)) selection = (chain '5' and (resid 1 through 11 or resid 13 through 18 or resid 20 through 25 \ or resid 27 through 28)) } 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.120 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: 0.070 Extract box with map and model: 1.590 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 107.820 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.340 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 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 0.112 57942 Z= 0.842 Angle : 1.649 26.449 80434 Z= 1.166 Chirality : 0.086 1.078 9153 Planarity : 0.020 0.493 8462 Dihedral : 18.841 178.015 24792 Min Nonbonded Distance : 1.162 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.39 % Rotamer: Outliers : 0.29 % Allowed : 1.25 % Favored : 98.47 % Cbeta Deviations : 0.23 % 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: -1.04 (0.10), residues: 5554 helix: -1.16 (0.08), residues: 2863 sheet: 0.26 (0.21), residues: 559 loop : 0.06 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.216 0.022 TRP G 20 HIS 0.019 0.002 HIS X 258 PHE 0.074 0.009 PHE Q 56 TYR 0.159 0.017 TYR x 575 ARG 0.015 0.001 ARG J 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1323 time to evaluate : 4.384 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: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7977 (ttp80) REVERT: A 144 ASP cc_start: 0.8746 (t0) cc_final: 0.8542 (t0) REVERT: C 187 LEU cc_start: 0.9324 (tp) cc_final: 0.9062 (tp) REVERT: C 260 LEU cc_start: 0.5968 (mm) cc_final: 0.5685 (tp) REVERT: F 117 VAL cc_start: 0.8725 (t) cc_final: 0.8304 (m) REVERT: G 123 SER cc_start: 0.7790 (p) cc_final: 0.7098 (t) REVERT: G 229 MET cc_start: 0.7501 (mmm) cc_final: 0.7198 (mmt) REVERT: H 156 ASP cc_start: 0.7162 (m-30) cc_final: 0.6952 (m-30) REVERT: J 229 MET cc_start: 0.6539 (mmm) cc_final: 0.5983 (mmt) REVERT: L 64 THR cc_start: 0.8702 (p) cc_final: 0.8464 (p) REVERT: Q 156 MET cc_start: 0.6889 (ttp) cc_final: 0.6145 (ttt) REVERT: Z 233 TYR cc_start: 0.4961 (t80) cc_final: 0.4597 (t80) outliers start: 14 outliers final: 2 residues processed: 1335 average time/residue: 0.6232 time to fit residues: 1307.0970 Evaluate side-chains 546 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 543 time to evaluate : 4.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 251 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 502 optimal weight: 0.6980 chunk 450 optimal weight: 0.6980 chunk 250 optimal weight: 0.4980 chunk 154 optimal weight: 0.8980 chunk 304 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 466 optimal weight: 0.5980 chunk 180 optimal weight: 0.9990 chunk 283 optimal weight: 0.2980 chunk 347 optimal weight: 1.9990 chunk 540 optimal weight: 8.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN D 38 GLN F 38 GLN G 77 HIS G 269 GLN H 38 GLN I 80 GLN I 213 GLN J 38 GLN J 185 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 GLN K 269 GLN O 42 HIS O 61 GLN O 269 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 369 HIS O 370 HIS O 420 GLN O 603 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN W 217 HIS W 272 HIS X 217 HIS X 272 HIS Y 296 HIS Y 309 HIS Y 375 GLN Y 463 ASN Z 203 GLN ** Z 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 283 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 57942 Z= 0.204 Angle : 0.662 11.632 80434 Z= 0.356 Chirality : 0.040 0.225 9153 Planarity : 0.005 0.085 8462 Dihedral : 20.958 172.602 13194 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.08 % Allowed : 8.56 % Favored : 89.36 % 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: 0.87 (0.11), residues: 5554 helix: 0.92 (0.09), residues: 2938 sheet: 0.31 (0.22), residues: 526 loop : 0.37 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 20 HIS 0.008 0.001 HIS O 586 PHE 0.026 0.002 PHE Z 332 TYR 0.039 0.002 TYR y 575 ARG 0.010 0.001 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 632 time to evaluate : 4.397 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: E 210 MET cc_start: 0.6915 (mtp) cc_final: 0.6560 (ttm) REVERT: E 268 LEU cc_start: 0.9019 (tp) cc_final: 0.8784 (mt) REVERT: F 64 THR cc_start: 0.8605 (p) cc_final: 0.8392 (p) REVERT: F 159 ASP cc_start: 0.7083 (t70) cc_final: 0.6764 (t0) REVERT: G 229 MET cc_start: 0.7619 (mmm) cc_final: 0.7098 (mmt) REVERT: H 156 ASP cc_start: 0.7443 (m-30) cc_final: 0.7179 (m-30) REVERT: I 214 MET cc_start: 0.6846 (tpp) cc_final: 0.6646 (tpp) REVERT: I 269 GLN cc_start: 0.7969 (mm110) cc_final: 0.7662 (mm-40) REVERT: J 263 ILE cc_start: 0.8009 (mt) cc_final: 0.7759 (tt) REVERT: K 145 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7776 (mm-30) REVERT: K 214 MET cc_start: 0.7645 (mmm) cc_final: 0.7189 (mtt) REVERT: L 64 THR cc_start: 0.8395 (p) cc_final: 0.8117 (p) REVERT: Q 75 GLU cc_start: 0.7737 (mp0) cc_final: 0.7512 (mp0) REVERT: Q 147 GLU cc_start: 0.7310 (tt0) cc_final: 0.6884 (tt0) REVERT: Q 156 MET cc_start: 0.6651 (ttp) cc_final: 0.6406 (ttt) REVERT: S 71 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8774 (ttmt) REVERT: X 178 TRP cc_start: 0.6387 (m100) cc_final: 0.5762 (m100) REVERT: X 341 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8327 (t) outliers start: 102 outliers final: 61 residues processed: 712 average time/residue: 0.6090 time to fit residues: 718.7654 Evaluate side-chains 474 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 411 time to evaluate : 4.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 420 GLN Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 597 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain w residue 570 ILE Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 411 MET Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 308 CYS Chi-restraints excluded: chain Y residue 479 THR Chi-restraints excluded: chain Z residue 236 CYS Chi-restraints excluded: chain Z residue 295 ASN Chi-restraints excluded: chain Z residue 435 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 300 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 449 optimal weight: 0.9980 chunk 367 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 541 optimal weight: 9.9990 chunk 584 optimal weight: 0.7980 chunk 482 optimal weight: 0.0670 chunk 536 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 434 optimal weight: 3.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 77 HIS B 38 GLN D 38 GLN F 38 GLN F 81 GLN J 38 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 GLN K 269 GLN L 213 GLN ** O 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 420 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 272 HIS ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 GLN Y 283 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 463 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 57942 Z= 0.201 Angle : 0.567 8.412 80434 Z= 0.307 Chirality : 0.038 0.191 9153 Planarity : 0.004 0.075 8462 Dihedral : 20.893 172.964 13188 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.02 % Allowed : 10.36 % Favored : 87.62 % 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: 1.32 (0.11), residues: 5554 helix: 1.38 (0.10), residues: 2962 sheet: 0.48 (0.23), residues: 505 loop : 0.43 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Z 225 HIS 0.007 0.001 HIS O 369 PHE 0.017 0.001 PHE A 190 TYR 0.023 0.001 TYR x 575 ARG 0.015 0.001 ARG Z 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 464 time to evaluate : 4.451 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: C 119 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7772 (mmmm) REVERT: E 210 MET cc_start: 0.6761 (mtp) cc_final: 0.6558 (ttm) REVERT: E 268 LEU cc_start: 0.8880 (tp) cc_final: 0.8668 (mt) REVERT: F 64 THR cc_start: 0.8617 (p) cc_final: 0.8373 (p) REVERT: G 229 MET cc_start: 0.7614 (mmm) cc_final: 0.7104 (mmt) REVERT: K 214 MET cc_start: 0.7636 (mmm) cc_final: 0.7266 (mtt) REVERT: L 64 THR cc_start: 0.8236 (p) cc_final: 0.7898 (p) REVERT: L 269 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8052 (mt0) REVERT: y 579 ARG cc_start: 0.7666 (ttm110) cc_final: 0.7232 (mtt180) REVERT: W 381 MET cc_start: 0.7938 (mmt) cc_final: 0.6963 (mmt) REVERT: X 178 TRP cc_start: 0.6392 (m100) cc_final: 0.5674 (m100) outliers start: 99 outliers final: 61 residues processed: 538 average time/residue: 0.5445 time to fit residues: 492.7388 Evaluate side-chains 438 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 377 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain O residue 222 GLU Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 597 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain w residue 570 ILE Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 210 ASP Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 283 HIS Chi-restraints excluded: chain Y residue 308 CYS Chi-restraints excluded: chain Z residue 435 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 534 optimal weight: 1.9990 chunk 406 optimal weight: 0.0870 chunk 280 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 chunk 363 optimal weight: 9.9990 chunk 543 optimal weight: 20.0000 chunk 575 optimal weight: 7.9990 chunk 283 optimal weight: 0.9980 chunk 514 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS F 38 GLN H 38 GLN H 213 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 ASN O 304 HIS O 369 HIS O 521 GLN O 613 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 272 HIS ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 463 ASN Y 464 ASN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 57942 Z= 0.251 Angle : 0.568 8.811 80434 Z= 0.308 Chirality : 0.038 0.189 9153 Planarity : 0.004 0.056 8462 Dihedral : 20.942 174.048 13188 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.55 % Allowed : 10.77 % Favored : 86.68 % 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: 1.47 (0.11), residues: 5554 helix: 1.55 (0.10), residues: 2961 sheet: 0.51 (0.23), residues: 501 loop : 0.42 (0.14), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Z 225 HIS 0.027 0.001 HIS Y 283 PHE 0.019 0.002 PHE A 190 TYR 0.018 0.002 TYR W 61 ARG 0.021 0.001 ARG Z 513 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 426 time to evaluate : 4.309 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: F 20 TRP cc_start: 0.5964 (OUTLIER) cc_final: 0.5026 (t60) REVERT: F 64 THR cc_start: 0.8709 (p) cc_final: 0.8492 (p) REVERT: G 210 MET cc_start: 0.7022 (tpp) cc_final: 0.6764 (ttt) REVERT: G 229 MET cc_start: 0.7640 (mmm) cc_final: 0.7092 (mmt) REVERT: I 80 GLN cc_start: 0.5966 (OUTLIER) cc_final: 0.5189 (mm-40) REVERT: K 61 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: K 196 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: L 64 THR cc_start: 0.8408 (p) cc_final: 0.8089 (p) REVERT: O 78 ARG cc_start: 0.2757 (mpt180) cc_final: 0.2497 (mmm-85) REVERT: Q 72 SER cc_start: 0.9328 (OUTLIER) cc_final: 0.8877 (t) REVERT: Q 74 VAL cc_start: 0.8964 (m) cc_final: 0.8707 (m) REVERT: Q 161 MET cc_start: 0.6597 (mmp) cc_final: 0.6250 (mmm) REVERT: S 22 THR cc_start: 0.6535 (p) cc_final: 0.6042 (m) REVERT: W 381 MET cc_start: 0.7805 (mmt) cc_final: 0.7387 (mmt) REVERT: W 488 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6945 (tm-30) REVERT: X 178 TRP cc_start: 0.6344 (m100) cc_final: 0.6040 (m100) REVERT: X 341 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8572 (t) REVERT: Y 381 MET cc_start: 0.0640 (ttm) cc_final: 0.0249 (ttm) REVERT: Z 244 PHE cc_start: 0.6222 (OUTLIER) cc_final: 0.5789 (t80) outliers start: 125 outliers final: 79 residues processed: 519 average time/residue: 0.5438 time to fit residues: 471.6601 Evaluate side-chains 434 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 348 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 293 TRP Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 597 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain w residue 570 ILE Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 237 ILE Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 445 ASN Chi-restraints excluded: chain Z residue 236 CYS Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 325 LYS Chi-restraints excluded: chain Z residue 401 ILE Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 520 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 478 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 428 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 490 optimal weight: 2.9990 chunk 397 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 516 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN H 38 GLN K 269 GLN L 269 GLN ** O 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 135 ASN y 577 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 428 ASN Y 463 ASN Y 464 ASN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 57942 Z= 0.308 Angle : 0.591 8.796 80434 Z= 0.319 Chirality : 0.040 0.191 9153 Planarity : 0.004 0.071 8462 Dihedral : 21.064 174.419 13188 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.73 % Rotamer: Outliers : 2.92 % Allowed : 11.32 % Favored : 85.76 % 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: 1.43 (0.11), residues: 5554 helix: 1.55 (0.10), residues: 2955 sheet: 0.53 (0.20), residues: 623 loop : 0.31 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP Z 225 HIS 0.009 0.001 HIS S 50 PHE 0.033 0.002 PHE X 426 TYR 0.023 0.002 TYR J 240 ARG 0.021 0.001 ARG O 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 380 time to evaluate : 4.423 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: A 37 GLN cc_start: 0.6802 (tp40) cc_final: 0.6524 (tp40) REVERT: C 121 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8758 (p) REVERT: F 20 TRP cc_start: 0.6114 (OUTLIER) cc_final: 0.5365 (t60) REVERT: G 210 MET cc_start: 0.7136 (tpp) cc_final: 0.6858 (ttt) REVERT: I 196 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8846 (m-10) REVERT: J 210 MET cc_start: 0.8002 (ttm) cc_final: 0.7783 (mtm) REVERT: K 37 GLN cc_start: 0.7147 (tp40) cc_final: 0.6935 (tp40) REVERT: K 61 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: K 196 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: L 64 THR cc_start: 0.8657 (p) cc_final: 0.8413 (p) REVERT: Q 72 SER cc_start: 0.9332 (OUTLIER) cc_final: 0.9002 (t) REVERT: Q 74 VAL cc_start: 0.8980 (m) cc_final: 0.8768 (m) REVERT: y 579 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7259 (mtt90) REVERT: W 381 MET cc_start: 0.7912 (mmt) cc_final: 0.7560 (mmt) REVERT: W 488 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6841 (tm-30) REVERT: X 341 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8622 (t) REVERT: Y 381 MET cc_start: 0.0834 (ttm) cc_final: -0.0136 (ttm) REVERT: Z 244 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5646 (t80) outliers start: 143 outliers final: 95 residues processed: 492 average time/residue: 0.5475 time to fit residues: 458.9992 Evaluate side-chains 439 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 336 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 597 ILE Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 222 SER Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 445 ASN Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 236 CYS Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 325 LYS Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Chi-restraints excluded: chain Z residue 520 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 193 optimal weight: 5.9990 chunk 517 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 575 optimal weight: 6.9990 chunk 477 optimal weight: 5.9990 chunk 266 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 302 optimal weight: 0.6980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS H 38 GLN L 269 GLN O 116 ASN ** O 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 303 GLN Y 206 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 57942 Z= 0.264 Angle : 0.565 10.159 80434 Z= 0.305 Chirality : 0.039 0.194 9153 Planarity : 0.004 0.051 8462 Dihedral : 21.087 174.615 13188 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.88 % Rotamer: Outliers : 2.72 % Allowed : 12.36 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.11), residues: 5554 helix: 1.62 (0.10), residues: 2948 sheet: 0.43 (0.20), residues: 629 loop : 0.32 (0.15), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 20 HIS 0.005 0.001 HIS S 50 PHE 0.024 0.001 PHE A 190 TYR 0.019 0.001 TYR W 61 ARG 0.013 0.000 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 385 time to evaluate : 4.391 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: A 37 GLN cc_start: 0.6857 (tp40) cc_final: 0.6639 (tp40) REVERT: C 33 ILE cc_start: 0.9264 (mp) cc_final: 0.9062 (mm) REVERT: F 20 TRP cc_start: 0.6107 (OUTLIER) cc_final: 0.5300 (t60) REVERT: F 210 MET cc_start: 0.7099 (mpp) cc_final: 0.6796 (mtm) REVERT: H 61 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: I 80 GLN cc_start: 0.5824 (OUTLIER) cc_final: 0.4948 (mm-40) REVERT: I 196 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8830 (m-10) REVERT: J 263 ILE cc_start: 0.7753 (mt) cc_final: 0.7519 (tt) REVERT: K 61 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: K 196 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: L 64 THR cc_start: 0.8741 (p) cc_final: 0.8481 (p) REVERT: O 78 ARG cc_start: 0.3051 (mpt180) cc_final: 0.2347 (mmm-85) REVERT: Q 72 SER cc_start: 0.9307 (OUTLIER) cc_final: 0.8982 (t) REVERT: S 35 GLN cc_start: 0.7885 (mm110) cc_final: 0.7336 (mm-40) REVERT: W 164 LEU cc_start: 0.8713 (mm) cc_final: 0.8481 (mt) REVERT: W 381 MET cc_start: 0.8015 (mmt) cc_final: 0.7621 (mmt) REVERT: W 488 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6922 (tm-30) REVERT: X 341 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8599 (t) REVERT: Z 244 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5712 (t80) outliers start: 133 outliers final: 96 residues processed: 490 average time/residue: 0.5999 time to fit residues: 498.9060 Evaluate side-chains 445 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 340 time to evaluate : 4.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 554 VAL Chi-restraints excluded: chain O residue 597 ILE Chi-restraints excluded: chain O residue 609 GLU Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 308 CYS Chi-restraints excluded: chain Y residue 445 ASN Chi-restraints excluded: chain Y residue 494 LEU Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 249 SER Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 325 LYS Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Chi-restraints excluded: chain Z residue 520 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 555 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 420 optimal weight: 7.9990 chunk 325 optimal weight: 0.6980 chunk 484 optimal weight: 0.9980 chunk 321 optimal weight: 0.0870 chunk 573 optimal weight: 0.9980 chunk 358 optimal weight: 0.0970 chunk 349 optimal weight: 7.9990 chunk 264 optimal weight: 0.5980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS H 38 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 269 GLN L 269 GLN ** O 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 613 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 463 ASN W 475 GLN Y 206 HIS Y 504 GLN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 57942 Z= 0.152 Angle : 0.520 8.562 80434 Z= 0.282 Chirality : 0.036 0.194 9153 Planarity : 0.004 0.043 8462 Dihedral : 20.974 173.880 13188 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.82 % Favored : 98.16 % Rotamer: Outliers : 1.86 % Allowed : 13.75 % Favored : 84.39 % 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: 1.79 (0.12), residues: 5554 helix: 1.91 (0.10), residues: 2935 sheet: 0.56 (0.20), residues: 633 loop : 0.45 (0.15), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 20 HIS 0.005 0.001 HIS Y 206 PHE 0.022 0.001 PHE A 204 TYR 0.015 0.001 TYR W 61 ARG 0.011 0.000 ARG y 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 391 time to evaluate : 4.331 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: C 33 ILE cc_start: 0.9222 (mp) cc_final: 0.8995 (mm) REVERT: C 127 ASP cc_start: 0.7376 (m-30) cc_final: 0.7158 (m-30) REVERT: F 268 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8187 (tp) REVERT: I 37 GLN cc_start: 0.7743 (tp40) cc_final: 0.7425 (tp40) REVERT: I 80 GLN cc_start: 0.5730 (OUTLIER) cc_final: 0.4865 (mm-40) REVERT: I 196 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8620 (m-10) REVERT: J 263 ILE cc_start: 0.7527 (mt) cc_final: 0.7297 (tt) REVERT: K 61 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: K 196 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: L 64 THR cc_start: 0.8468 (p) cc_final: 0.8180 (p) REVERT: O 78 ARG cc_start: 0.2699 (mpt180) cc_final: 0.2388 (mmm-85) REVERT: O 481 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5510 (pt) REVERT: Q 72 SER cc_start: 0.9279 (OUTLIER) cc_final: 0.8959 (t) REVERT: S 35 GLN cc_start: 0.7964 (mm110) cc_final: 0.7463 (mm-40) REVERT: W 381 MET cc_start: 0.7941 (mmt) cc_final: 0.7579 (mmt) REVERT: W 488 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6852 (tm-30) REVERT: Z 244 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5580 (t80) outliers start: 91 outliers final: 57 residues processed: 463 average time/residue: 0.5369 time to fit residues: 418.0765 Evaluate side-chains 411 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 346 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 481 LEU Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 163 LYS Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 412 LYS Chi-restraints excluded: chain Y residue 445 ASN Chi-restraints excluded: chain Y residue 453 ILE Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 249 SER Chi-restraints excluded: chain Z residue 325 LYS Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 354 optimal weight: 7.9990 chunk 229 optimal weight: 0.9980 chunk 342 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 112 optimal weight: 0.0980 chunk 111 optimal weight: 4.9990 chunk 364 optimal weight: 20.0000 chunk 390 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 450 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS L 269 GLN O 420 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 57942 Z= 0.157 Angle : 0.530 11.104 80434 Z= 0.284 Chirality : 0.036 0.189 9153 Planarity : 0.004 0.058 8462 Dihedral : 20.919 173.680 13188 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.94 % Favored : 98.04 % Rotamer: Outliers : 1.63 % Allowed : 14.32 % Favored : 84.04 % 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: 1.88 (0.12), residues: 5554 helix: 1.97 (0.10), residues: 2936 sheet: 0.55 (0.20), residues: 638 loop : 0.51 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP Z 225 HIS 0.010 0.001 HIS Y 200 PHE 0.017 0.001 PHE A 190 TYR 0.016 0.001 TYR W 61 ARG 0.010 0.000 ARG y 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 376 time to evaluate : 4.513 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: B 61 GLU cc_start: 0.7073 (tp30) cc_final: 0.6651 (mm-30) REVERT: C 33 ILE cc_start: 0.9219 (mp) cc_final: 0.9004 (mm) REVERT: G 255 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8405 (t) REVERT: I 37 GLN cc_start: 0.7740 (tp40) cc_final: 0.7397 (tp40) REVERT: I 80 GLN cc_start: 0.5727 (OUTLIER) cc_final: 0.4933 (mm-40) REVERT: I 196 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8693 (m-10) REVERT: J 263 ILE cc_start: 0.7508 (mt) cc_final: 0.7281 (tt) REVERT: K 61 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: K 196 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8725 (m-80) REVERT: L 64 THR cc_start: 0.8336 (p) cc_final: 0.8040 (p) REVERT: O 78 ARG cc_start: 0.2656 (mpt180) cc_final: 0.2412 (mmm-85) REVERT: O 551 MET cc_start: 0.6017 (pmm) cc_final: 0.5623 (pmm) REVERT: Q 161 MET cc_start: 0.6799 (mmt) cc_final: 0.6595 (mmm) REVERT: S 35 GLN cc_start: 0.7986 (mm110) cc_final: 0.7445 (mm-40) REVERT: W 76 LEU cc_start: 0.5320 (tp) cc_final: 0.4996 (tp) REVERT: W 164 LEU cc_start: 0.8641 (mm) cc_final: 0.8320 (mt) REVERT: W 381 MET cc_start: 0.7963 (mmt) cc_final: 0.7595 (mmt) REVERT: W 413 GLN cc_start: 0.7328 (pp30) cc_final: 0.6981 (pp30) REVERT: W 488 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6789 (tm-30) REVERT: Y 445 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7720 (p0) REVERT: Z 244 PHE cc_start: 0.6029 (OUTLIER) cc_final: 0.5525 (t80) REVERT: Z 430 MET cc_start: 0.7698 (mmm) cc_final: 0.7350 (tpt) outliers start: 80 outliers final: 59 residues processed: 442 average time/residue: 0.5446 time to fit residues: 405.0808 Evaluate side-chains 410 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 344 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain O residue 420 GLN Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 609 GLU Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 261 LEU Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 385 THR Chi-restraints excluded: chain Y residue 445 ASN Chi-restraints excluded: chain Y residue 453 ILE Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 236 CYS Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 249 SER Chi-restraints excluded: chain Z residue 325 LYS Chi-restraints excluded: chain Z residue 327 LEU Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 521 optimal weight: 5.9990 chunk 549 optimal weight: 8.9990 chunk 501 optimal weight: 0.9990 chunk 534 optimal weight: 9.9990 chunk 321 optimal weight: 0.3980 chunk 232 optimal weight: 0.3980 chunk 419 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 482 optimal weight: 8.9990 chunk 505 optimal weight: 0.9990 chunk 532 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS L 213 GLN L 269 GLN O 420 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 57942 Z= 0.181 Angle : 0.549 35.794 80434 Z= 0.290 Chirality : 0.037 0.187 9153 Planarity : 0.004 0.063 8462 Dihedral : 20.907 173.531 13188 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.07 % Favored : 97.91 % Rotamer: Outliers : 1.70 % Allowed : 14.40 % Favored : 83.90 % 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: 1.93 (0.12), residues: 5554 helix: 2.02 (0.10), residues: 2930 sheet: 0.57 (0.20), residues: 641 loop : 0.52 (0.15), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP Z 225 HIS 0.008 0.001 HIS Y 200 PHE 0.023 0.001 PHE Z 306 TYR 0.015 0.001 TYR W 61 ARG 0.013 0.000 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 351 time to evaluate : 4.402 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: B 61 GLU cc_start: 0.7099 (tp30) cc_final: 0.6686 (mm-30) REVERT: C 33 ILE cc_start: 0.9231 (mp) cc_final: 0.8903 (mm) REVERT: D 188 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: G 255 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8385 (t) REVERT: I 37 GLN cc_start: 0.7754 (tp40) cc_final: 0.7441 (tp40) REVERT: I 80 GLN cc_start: 0.5713 (OUTLIER) cc_final: 0.4906 (mm-40) REVERT: I 196 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8662 (m-10) REVERT: J 263 ILE cc_start: 0.7520 (mt) cc_final: 0.7289 (tt) REVERT: K 61 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: K 196 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: L 64 THR cc_start: 0.8366 (p) cc_final: 0.8070 (p) REVERT: O 78 ARG cc_start: 0.2950 (mpt180) cc_final: 0.2485 (mmm-85) REVERT: O 481 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5407 (pt) REVERT: O 551 MET cc_start: 0.5968 (pmm) cc_final: 0.5476 (pmm) REVERT: Q 161 MET cc_start: 0.6820 (mmt) cc_final: 0.6594 (mmm) REVERT: S 35 GLN cc_start: 0.7997 (mm110) cc_final: 0.7448 (mm-40) REVERT: W 76 LEU cc_start: 0.5331 (tp) cc_final: 0.5005 (tp) REVERT: W 381 MET cc_start: 0.7999 (mmt) cc_final: 0.7623 (mmt) REVERT: W 488 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6799 (tm-30) REVERT: Y 445 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7775 (p0) REVERT: Z 244 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5519 (t80) outliers start: 83 outliers final: 58 residues processed: 418 average time/residue: 0.5410 time to fit residues: 383.8939 Evaluate side-chains 402 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 335 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 414 THR Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 481 LEU Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 609 GLU Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 222 SER Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 385 THR Chi-restraints excluded: chain Y residue 445 ASN Chi-restraints excluded: chain Y residue 453 ILE Chi-restraints excluded: chain Y residue 492 ARG Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 236 CYS Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 249 SER Chi-restraints excluded: chain Z residue 325 LYS Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 350 optimal weight: 6.9990 chunk 565 optimal weight: 9.9990 chunk 344 optimal weight: 0.9980 chunk 268 optimal weight: 0.2980 chunk 392 optimal weight: 3.9990 chunk 592 optimal weight: 4.9990 chunk 545 optimal weight: 8.9990 chunk 472 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 364 optimal weight: 20.0000 chunk 289 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS O 38 GLN ** O 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 ASN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 57942 Z= 0.164 Angle : 0.559 39.734 80434 Z= 0.292 Chirality : 0.037 0.189 9153 Planarity : 0.004 0.059 8462 Dihedral : 20.862 173.267 13188 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.88 % Rotamer: Outliers : 1.72 % Allowed : 14.67 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.12), residues: 5554 helix: 2.19 (0.10), residues: 2822 sheet: 0.60 (0.20), residues: 635 loop : 0.46 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP Z 225 HIS 0.008 0.001 HIS Y 200 PHE 0.036 0.001 PHE A 204 TYR 0.015 0.001 TYR W 61 ARG 0.013 0.000 ARG G 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 357 time to evaluate : 4.356 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: C 33 ILE cc_start: 0.9229 (mp) cc_final: 0.8904 (mm) REVERT: D 188 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: D 210 MET cc_start: 0.7630 (tpp) cc_final: 0.7187 (ttt) REVERT: F 20 TRP cc_start: 0.5950 (OUTLIER) cc_final: 0.5303 (t60) REVERT: G 255 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8379 (t) REVERT: H 159 ASP cc_start: 0.6526 (m-30) cc_final: 0.6295 (m-30) REVERT: I 37 GLN cc_start: 0.7741 (tp40) cc_final: 0.7466 (tp40) REVERT: I 80 GLN cc_start: 0.5669 (OUTLIER) cc_final: 0.4857 (mm-40) REVERT: I 196 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8660 (m-10) REVERT: J 263 ILE cc_start: 0.7463 (mt) cc_final: 0.7239 (tt) REVERT: K 196 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: L 64 THR cc_start: 0.8267 (p) cc_final: 0.7970 (p) REVERT: O 481 LEU cc_start: 0.5735 (OUTLIER) cc_final: 0.5402 (pt) REVERT: O 551 MET cc_start: 0.5852 (pmm) cc_final: 0.5347 (pmm) REVERT: S 35 GLN cc_start: 0.7958 (mm110) cc_final: 0.7432 (mm-40) REVERT: W 76 LEU cc_start: 0.5288 (tp) cc_final: 0.4978 (tp) REVERT: W 381 MET cc_start: 0.7999 (mmt) cc_final: 0.7594 (mmt) REVERT: W 488 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6839 (tm-30) REVERT: Y 445 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7757 (p0) REVERT: Z 244 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5479 (t80) outliers start: 84 outliers final: 60 residues processed: 427 average time/residue: 0.5394 time to fit residues: 390.8452 Evaluate side-chains 402 residues out of total 4897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 333 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 125 PHE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 414 THR Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 481 LEU Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 609 GLU Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 261 LEU Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 222 SER Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 385 THR Chi-restraints excluded: chain Y residue 445 ASN Chi-restraints excluded: chain Y residue 453 ILE Chi-restraints excluded: chain Y residue 492 ARG Chi-restraints excluded: chain Y residue 494 LEU Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 236 CYS Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 325 LYS Chi-restraints excluded: chain Z residue 327 LEU Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 374 optimal weight: 6.9990 chunk 502 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 435 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 472 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 485 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS O 85 HIS ** O 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN Q 125 HIS ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 328 ASN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.112783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079344 restraints weight = 140564.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080379 restraints weight = 89178.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.080654 restraints weight = 69807.010| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 57942 Z= 0.304 Angle : 0.606 12.888 80434 Z= 0.323 Chirality : 0.039 0.201 9153 Planarity : 0.004 0.103 8462 Dihedral : 21.011 173.539 13188 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.59 % Favored : 97.39 % Rotamer: Outliers : 1.78 % Allowed : 14.85 % Favored : 83.37 % 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: 1.67 (0.11), residues: 5554 helix: 1.83 (0.10), residues: 2934 sheet: 0.38 (0.20), residues: 638 loop : 0.39 (0.15), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP Z 225 HIS 0.008 0.001 HIS O 42 PHE 0.034 0.002 PHE A 204 TYR 0.020 0.002 TYR J 240 ARG 0.013 0.001 ARG J 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9960.41 seconds wall clock time: 176 minutes 56.46 seconds (10616.46 seconds total)