Starting phenix.real_space_refine on Sun Aug 24 12:24:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zol_60297/08_2025/8zol_60297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zol_60297/08_2025/8zol_60297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zol_60297/08_2025/8zol_60297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zol_60297/08_2025/8zol_60297.map" model { file = "/net/cci-nas-00/data/ceres_data/8zol_60297/08_2025/8zol_60297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zol_60297/08_2025/8zol_60297.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 573 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 58 5.49 5 S 74 5.16 5 C 12087 2.51 5 N 3404 2.21 5 O 3828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19451 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1258 Classifications: {'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 17, 'rna3p_pyr': 19} Link IDs: {'rna2p': 22, 'rna3p': 36} Chain breaks: 1 Chain: "F" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2797 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2822 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2775 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 350} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2773 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "K" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2591 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain breaks: 3 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1979 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 246} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1591 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 4.77, per 1000 atoms: 0.25 Number of scatterers: 19451 At special positions: 0 Unit cell: (115.37, 136.95, 168.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 58 15.00 O 3828 8.00 N 3404 7.00 C 12087 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 749.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4442 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 26 sheets defined 37.2% alpha, 18.4% beta 4 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 52 through 56 Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.574A pdb=" N LEU F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 86 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.899A pdb=" N LYS F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ARG F 113 " --> pdb=" O LYS F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 135 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 234 through 250 Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.764A pdb=" N ALA F 283 " --> pdb=" O TYR F 280 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE F 284 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 313 Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 49 through 53 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.748A pdb=" N LEU H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 89 Processing helix chain 'H' and resid 92 through 96 Processing helix chain 'H' and resid 107 through 116 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 139 through 146 Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 281 through 285 Processing helix chain 'H' and resid 295 through 315 Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 349 through 362 Processing helix chain 'H' and resid 365 through 371 Processing helix chain 'I' and resid 38 through 49 Processing helix chain 'I' and resid 50 through 56 removed outlier: 4.867A pdb=" N ALA I 54 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU I 56 " --> pdb=" O LYS I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 69 removed outlier: 3.927A pdb=" N LEU I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 89 removed outlier: 3.551A pdb=" N GLY I 89 " --> pdb=" O LEU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 116 Processing helix chain 'I' and resid 124 through 136 removed outlier: 3.640A pdb=" N ALA I 136 " --> pdb=" O VAL I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 146 Processing helix chain 'I' and resid 152 through 156 removed outlier: 3.695A pdb=" N LYS I 156 " --> pdb=" O ASP I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 230 Processing helix chain 'I' and resid 234 through 250 removed outlier: 3.723A pdb=" N ALA I 249 " --> pdb=" O LEU I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 285 removed outlier: 3.654A pdb=" N VAL I 285 " --> pdb=" O ASN I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 316 removed outlier: 3.577A pdb=" N GLN I 299 " --> pdb=" O ASP I 295 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR I 316 " --> pdb=" O ARG I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 332 Processing helix chain 'I' and resid 349 through 362 Processing helix chain 'I' and resid 365 through 370 Processing helix chain 'J' and resid 38 through 48 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 64 through 73 removed outlier: 3.645A pdb=" N GLY J 73 " --> pdb=" O GLN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 88 Processing helix chain 'J' and resid 92 through 96 Processing helix chain 'J' and resid 108 through 116 Processing helix chain 'J' and resid 122 through 136 removed outlier: 3.619A pdb=" N ALA J 136 " --> pdb=" O VAL J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 removed outlier: 4.013A pdb=" N LEU J 144 " --> pdb=" O PRO J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 230 Processing helix chain 'J' and resid 233 through 250 Processing helix chain 'J' and resid 280 through 285 Processing helix chain 'J' and resid 295 through 315 Processing helix chain 'J' and resid 329 through 332 Processing helix chain 'J' and resid 349 through 363 Processing helix chain 'J' and resid 365 through 370 removed outlier: 3.796A pdb=" N VAL J 369 " --> pdb=" O LYS J 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 16 removed outlier: 3.556A pdb=" N LEU K 16 " --> pdb=" O PRO K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 48 Processing helix chain 'K' and resid 52 through 56 removed outlier: 3.569A pdb=" N LEU K 56 " --> pdb=" O LYS K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 69 removed outlier: 3.992A pdb=" N GLN K 69 " --> pdb=" O ALA K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 89 removed outlier: 4.032A pdb=" N ASN K 86 " --> pdb=" O GLN K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 116 Processing helix chain 'K' and resid 121 through 133 Processing helix chain 'K' and resid 141 through 146 Processing helix chain 'K' and resid 223 through 230 Processing helix chain 'K' and resid 234 through 250 Processing helix chain 'K' and resid 280 through 284 removed outlier: 3.536A pdb=" N ALA K 283 " --> pdb=" O TYR K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 316 removed outlier: 4.022A pdb=" N TYR K 316 " --> pdb=" O ARG K 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 329 through 332 Processing helix chain 'K' and resid 349 through 362 removed outlier: 3.615A pdb=" N VAL K 354 " --> pdb=" O LEU K 350 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY K 355 " --> pdb=" O ASN K 351 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE K 361 " --> pdb=" O VAL K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 370 Processing helix chain 'G' and resid 38 through 43 removed outlier: 3.685A pdb=" N ILE G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 229 Processing helix chain 'G' and resid 234 through 250 Processing helix chain 'G' and resid 280 through 284 removed outlier: 3.845A pdb=" N PHE G 284 " --> pdb=" O ALA G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 310 removed outlier: 3.511A pdb=" N GLY G 302 " --> pdb=" O GLU G 298 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 332 Processing helix chain 'G' and resid 349 through 361 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 59 through 66 removed outlier: 4.063A pdb=" N LEU B 63 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.819A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 185 through 193 removed outlier: 4.015A pdb=" N VAL B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 183 removed outlier: 3.611A pdb=" N LYS D 178 " --> pdb=" O TRP D 174 " (cutoff:3.500A) Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.556A pdb=" N LYS D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.595A pdb=" N GLY D 259 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 26 through 29 removed outlier: 5.895A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 37 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 26 through 29 removed outlier: 5.895A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 37 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY F 268 " --> pdb=" O ILE F 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 58 through 61 Processing sheet with id=AA4, first strand: chain 'F' and resid 185 through 187 Processing sheet with id=AA5, first strand: chain 'H' and resid 26 through 29 removed outlier: 3.620A pdb=" N VAL H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 26 through 29 removed outlier: 3.620A pdb=" N VAL H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE H 5 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY H 268 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE H 323 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY H 324 " --> pdb=" O ARG H 345 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ILE H 347 " --> pdb=" O GLY H 324 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP H 326 " --> pdb=" O ILE H 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 61 Processing sheet with id=AA8, first strand: chain 'H' and resid 185 through 187 Processing sheet with id=AA9, first strand: chain 'I' and resid 26 through 29 removed outlier: 3.596A pdb=" N VAL I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 177 " --> pdb=" O TYR I 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 26 through 29 removed outlier: 3.596A pdb=" N VAL I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 177 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY I 268 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG I 345 " --> pdb=" O GLY I 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 185 through 187 Processing sheet with id=AB3, first strand: chain 'J' and resid 26 through 29 removed outlier: 3.703A pdb=" N VAL J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER J 178 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 37 " --> pdb=" O ALA J 176 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE J 177 " --> pdb=" O TYR J 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 26 through 29 removed outlier: 3.703A pdb=" N VAL J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER J 178 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 37 " --> pdb=" O ALA J 176 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE J 177 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE J 323 " --> pdb=" O PHE J 273 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG J 345 " --> pdb=" O GLY J 324 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 58 through 60 Processing sheet with id=AB6, first strand: chain 'J' and resid 185 through 189 Processing sheet with id=AB7, first strand: chain 'K' and resid 171 through 173 removed outlier: 3.763A pdb=" N ALA K 213 " --> pdb=" O HIS K 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB9, first strand: chain 'K' and resid 58 through 61 removed outlier: 3.593A pdb=" N VAL K 59 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET K 103 " --> pdb=" O VAL K 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 171 through 173 removed outlier: 3.598A pdb=" N ILE G 221 " --> pdb=" O ILE G 3 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE G 3 " --> pdb=" O ILE G 221 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY G 324 " --> pdb=" O ARG G 345 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE G 347 " --> pdb=" O GLY G 324 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TRP G 326 " --> pdb=" O ILE G 347 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 26 through 29 Processing sheet with id=AC3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.712A pdb=" N GLU B 130 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA B 133 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU B 16 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 135 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 14 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 141 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 8 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 7 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 181 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE B 9 " --> pdb=" O PRO B 179 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 77 through 81 removed outlier: 7.170A pdb=" N SER B 136 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 73 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 142 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'D' and resid 184 through 197 removed outlier: 6.609A pdb=" N VAL D 235 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS D 189 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU D 233 " --> pdb=" O CYS D 189 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU D 191 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU D 231 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN D 193 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA D 229 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY D 195 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE D 227 " --> pdb=" O GLY D 195 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY D 234 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D 124 " --> pdb=" O GLY D 234 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 131 through 133 768 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3274 1.32 - 1.44: 5574 1.44 - 1.57: 10900 1.57 - 1.69: 115 1.69 - 1.81: 109 Bond restraints: 19972 Sorted by residual: bond pdb=" CA ALA J 54 " pdb=" C ALA J 54 " ideal model delta sigma weight residual 1.521 1.434 0.087 1.27e-02 6.20e+03 4.68e+01 bond pdb=" CA ASN F 86 " pdb=" C ASN F 86 " ideal model delta sigma weight residual 1.526 1.436 0.090 1.36e-02 5.41e+03 4.39e+01 bond pdb=" CA TRP F 78 " pdb=" C TRP F 78 " ideal model delta sigma weight residual 1.525 1.460 0.065 1.02e-02 9.61e+03 4.03e+01 bond pdb=" CA LEU J 55 " pdb=" C LEU J 55 " ideal model delta sigma weight residual 1.530 1.455 0.075 1.44e-02 4.82e+03 2.74e+01 bond pdb=" CA CYS I 77 " pdb=" C CYS I 77 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.34e-02 5.57e+03 2.28e+01 ... (remaining 19967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 27130 3.04 - 6.09: 220 6.09 - 9.13: 23 9.13 - 12.18: 10 12.18 - 15.22: 2 Bond angle restraints: 27385 Sorted by residual: angle pdb=" N ILE F 84 " pdb=" CA ILE F 84 " pdb=" C ILE F 84 " ideal model delta sigma weight residual 111.00 95.78 15.22 1.09e+00 8.42e-01 1.95e+02 angle pdb=" N CYS F 88 " pdb=" CA CYS F 88 " pdb=" C CYS F 88 " ideal model delta sigma weight residual 112.54 101.09 11.45 1.22e+00 6.72e-01 8.82e+01 angle pdb=" N LEU J 100 " pdb=" CA LEU J 100 " pdb=" C LEU J 100 " ideal model delta sigma weight residual 109.71 97.94 11.77 1.41e+00 5.03e-01 6.97e+01 angle pdb=" N ALA F 81 " pdb=" CA ALA F 81 " pdb=" C ALA F 81 " ideal model delta sigma weight residual 112.45 101.55 10.90 1.39e+00 5.18e-01 6.15e+01 angle pdb=" N ASP K 187 " pdb=" CA ASP K 187 " pdb=" C ASP K 187 " ideal model delta sigma weight residual 110.33 119.79 -9.46 1.29e+00 6.01e-01 5.38e+01 ... (remaining 27380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 11380 35.32 - 70.64: 574 70.64 - 105.96: 45 105.96 - 141.29: 3 141.29 - 176.61: 4 Dihedral angle restraints: 12006 sinusoidal: 5134 harmonic: 6872 Sorted by residual: dihedral pdb=" O4' U A 34 " pdb=" C1' U A 34 " pdb=" N1 U A 34 " pdb=" C2 U A 34 " ideal model delta sinusoidal sigma weight residual 200.00 41.40 158.60 1 1.50e+01 4.44e-03 8.24e+01 dihedral pdb=" O4' C A 6 " pdb=" C1' C A 6 " pdb=" N1 C A 6 " pdb=" C2 C A 6 " ideal model delta sinusoidal sigma weight residual 200.00 43.92 156.08 1 1.50e+01 4.44e-03 8.17e+01 dihedral pdb=" O4' U A 9 " pdb=" C1' U A 9 " pdb=" N1 U A 9 " pdb=" C2 U A 9 " ideal model delta sinusoidal sigma weight residual 200.00 61.84 138.16 1 1.50e+01 4.44e-03 7.45e+01 ... (remaining 12003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2930 0.091 - 0.182: 154 0.182 - 0.272: 14 0.272 - 0.363: 6 0.363 - 0.454: 4 Chirality restraints: 3108 Sorted by residual: chirality pdb=" CA ASN K 92 " pdb=" N ASN K 92 " pdb=" C ASN K 92 " pdb=" CB ASN K 92 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA LYS J 98 " pdb=" N LYS J 98 " pdb=" C LYS J 98 " pdb=" CB LYS J 98 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA LYS I 80 " pdb=" N LYS I 80 " pdb=" C LYS I 80 " pdb=" CB LYS I 80 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 3105 not shown) Planarity restraints: 3350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 183 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.06e+01 pdb=" N PRO K 184 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO K 184 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO K 184 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 79 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C LYS K 79 " -0.075 2.00e-02 2.50e+03 pdb=" O LYS K 79 " 0.029 2.00e-02 2.50e+03 pdb=" N LYS K 80 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER K 328 " -0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO K 329 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO K 329 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO K 329 " -0.044 5.00e-02 4.00e+02 ... (remaining 3347 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 137 2.55 - 3.14: 14345 3.14 - 3.73: 29352 3.73 - 4.31: 39705 4.31 - 4.90: 67225 Nonbonded interactions: 150764 Sorted by model distance: nonbonded pdb=" O ASN G 331 " pdb=" ND2 ASN G 331 " model vdw 1.968 3.120 nonbonded pdb=" O SER I 254 " pdb=" OG SER I 254 " model vdw 2.219 3.040 nonbonded pdb=" N GLY K 121 " pdb=" OE2 GLU K 124 " model vdw 2.223 3.120 nonbonded pdb=" OE2 GLU J 4 " pdb=" OH TYR J 218 " model vdw 2.224 3.040 nonbonded pdb=" OG SER F 212 " pdb=" O TYR H 28 " model vdw 2.250 3.040 ... (remaining 150759 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 'F' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 42 or (resid 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 52 or (resid 53 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 74 or (re \ sid 75 and (name N or name CA or name C or name O or name CB )) or resid 76 thro \ ugh 78 or (resid 79 through 81 and (name N or name CA or name C or name O or nam \ e CB )) or resid 82 through 86 or (resid 87 and (name N or name CA or name C or \ name O or name CB )) or resid 88 through 98 or (resid 99 and (name N or name CA \ or name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 117 or (r \ esid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 o \ r (resid 120 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 21 or (resid 122 through 126 and (name N or name CA or name C or name O or name \ CB )) or resid 127 through 134 or (resid 135 through 136 and (name N or name CA \ or name C or name O or name CB )) or resid 137 through 155 or (resid 156 and (na \ me N or name CA or name C or name O or name CB )) or resid 157 through 159 or (r \ esid 160 through 161 and (name N or name CA or name C or name O or name CB )) or \ resid 162 through 189 or resid 211 through 216 or (resid 217 and (name N or nam \ e CA or name C or name O or name CB )) or resid 218 through 225 or (resid 226 an \ d (name N or name CA or name C or name O or name CB )) or resid 227 or (resid 22 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 229 through \ 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) or re \ sid 232 through 249 or (resid 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 through 256 or resid 264 through 273 or (resid 274 and ( \ name N or name CA or name C or name O or name CB )) or resid 275 through 290 or \ resid 294 through 303 or (resid 304 and (name N or name CA or name C or name O o \ r name CB )) or resid 305 through 306 or (resid 307 and (name N or name CA or na \ me C or name O or name CB )) or resid 308 through 315 or (resid 316 through 319 \ and (name N or name CA or name C or name O or name CB )) or resid 320 through 32 \ 6 or (resid 327 and (name N or name CA or name C or name O or name CB )) or resi \ d 328 through 338 or (resid 339 and (name N or name CA or name C or name O or na \ me CB )) or resid 340 or (resid 341 and (name N or name CA or name C or name O o \ r name CB )) or resid 342 through 351 or (resid 352 and (name N or name CA or na \ me C or name O or name CB )) or resid 353 through 363 or (resid 364 through 365 \ and (name N or name CA or name C or name O or name CB )) or resid 366 through 36 \ 8 or (resid 369 through 371 and (name N or name CA or name C or name O or name C \ B )))) selection = (chain 'H' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 42 or (resid 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 52 or (resid 53 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 74 or (re \ sid 75 and (name N or name CA or name C or name O or name CB )) or resid 76 thro \ ugh 79 or (resid 80 through 81 and (name N or name CA or name C or name O or nam \ e CB )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or n \ ame CB )) or resid 84 through 90 or resid 97 or (resid 98 through 99 and (name N \ or name CA or name C or name O or name CB )) or resid 100 through 104 or (resid \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throu \ gh 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or \ resid 119 through 121 or (resid 122 through 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 134 or (resid 135 through 136 and \ (name N or name CA or name C or name O or name CB )) or resid 137 through 152 o \ r (resid 153 through 154 and (name N or name CA or name C or name O or name CB ) \ ) or resid 155 or (resid 156 and (name N or name CA or name C or name O or name \ CB )) or resid 157 through 159 or (resid 160 through 161 and (name N or name CA \ or name C or name O or name CB )) or resid 162 through 189 or resid 211 through \ 216 or (resid 217 and (name N or name CA or name C or name O or name CB )) or re \ sid 218 through 225 or (resid 226 and (name N or name CA or name C or name O or \ name CB )) or resid 227 or (resid 228 and (name N or name CA or name C or name O \ or name CB )) or resid 229 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 249 or (resid 250 and (name \ N or name CA or name C or name O or name CB )) or resid 251 through 256 or resid \ 264 through 290 or resid 294 through 303 or (resid 304 and (name N or name CA o \ r name C or name O or name CB )) or resid 305 through 311 or (resid 312 and (nam \ e N or name CA or name C or name O or name CB )) or resid 313 through 316 or (re \ sid 317 through 319 and (name N or name CA or name C or name O or name CB )) or \ resid 320 through 326 or (resid 327 and (name N or name CA or name C or name O o \ r name CB )) or resid 328 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 351 or (resid 352 and (nam \ e N or name CA or name C or name O or name CB )) or resid 353 through 363 or (re \ sid 364 through 365 and (name N or name CA or name C or name O or name CB )) or \ resid 366 through 367 or (resid 368 through 371 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'I' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 42 or (resid 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 52 or (resid 53 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 74 or (resid 75 and (n \ ame N or name CA or name C or name O or name CB )) or resid 76 through 82 or (re \ sid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 thro \ ugh 90 or resid 97 or (resid 98 through 99 and (name N or name CA or name C or n \ ame O or name CB )) or resid 100 through 104 or (resid 105 and (name N or name C \ A or name C or name O or name CB )) or resid 106 through 108 or (resid 109 and ( \ name N or name CA or name C or name O or name CB )) or resid 110 through 117 or \ (resid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 \ or (resid 120 and (name N or name CA or name C or name O or name CB )) or resid \ 121 through 134 or (resid 135 through 136 and (name N or name CA or name C or n \ ame O or name CB )) or resid 137 through 159 or (resid 160 through 161 and (name \ N or name CA or name C or name O or name CB )) or resid 162 through 189 or resi \ d 211 through 216 or (resid 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 225 or (resid 226 and (name N or name CA or name C \ or name O or name CB )) or resid 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 through 249 or (resid 250 and (name N \ or name CA or name C or name O or name CB )) or resid 251 through 256 or resid 2 \ 64 through 273 or (resid 274 and (name N or name CA or name C or name O or name \ CB )) or resid 275 through 290 or resid 294 through 303 or (resid 304 and (name \ N or name CA or name C or name O or name CB )) or resid 305 through 306 or (resi \ d 307 and (name N or name CA or name C or name O or name CB )) or resid 308 thro \ ugh 311 or (resid 312 and (name N or name CA or name C or name O or name CB )) o \ r resid 313 through 315 or (resid 316 through 319 and (name N or name CA or name \ C or name O or name CB )) or resid 320 through 326 or (resid 327 and (name N or \ name CA or name C or name O or name CB )) or resid 328 through 338 or (resid 33 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 351 or (resid 352 and (name N or name CA or name C or name O or name CB )) or re \ sid 353 through 363 or (resid 364 through 365 and (name N or name CA or name C o \ r name O or name CB )) or resid 366 through 367 or (resid 368 through 371 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'J' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 42 or (resid 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 52 or (resid 53 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 79 or (re \ sid 80 through 81 and (name N or name CA or name C or name O or name CB )) or re \ sid 82 through 86 or (resid 87 and (name N or name CA or name C or name O or nam \ e CB )) or resid 88 through 90 or resid 97 or (resid 98 through 99 and (name N o \ r name CA or name C or name O or name CB )) or resid 100 through 108 or (resid 1 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 110 through \ 122 or (resid 123 through 126 and (name N or name CA or name C or name O or nam \ e CB )) or resid 127 through 152 or (resid 153 through 154 and (name N or name C \ A or name C or name O or name CB )) or resid 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 or (resid 158 through 161 a \ nd (name N or name CA or name C or name O or name CB )) or resid 162 through 189 \ or resid 211 through 216 or (resid 217 and (name N or name CA or name C or name \ O or name CB )) or resid 218 through 225 or (resid 226 and (name N or name CA o \ r name C or name O or name CB )) or resid 227 through 230 or (resid 231 and (nam \ e N or name CA or name C or name O or name CB )) or resid 232 through 249 or (re \ sid 250 and (name N or name CA or name C or name O or name CB )) or resid 251 th \ rough 256 or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 290 or resid 294 through 303 or ( \ resid 304 and (name N or name CA or name C or name O or name CB )) or resid 305 \ through 306 or (resid 307 and (name N or name CA or name C or name O or name CB \ )) or resid 308 through 311 or (resid 312 and (name N or name CA or name C or na \ me O or name CB )) or resid 313 through 315 or (resid 316 through 319 and (name \ N or name CA or name C or name O or name CB )) or resid 320 through 326 or (resi \ d 327 and (name N or name CA or name C or name O or name CB )) or resid 328 thro \ ugh 351 or (resid 352 and (name N or name CA or name C or name O or name CB )) o \ r resid 353 through 367 or (resid 368 through 371 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'K' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 81 and (name N or name CA or name C or name O or name CB )) or resid 82 or (re \ sid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 thro \ ugh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or \ resid 88 through 90 or resid 97 or (resid 98 through 99 and (name N or name CA o \ r name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (nam \ e N or name CA or name C or name O or name CB )) or resid 106 through 108 or (re \ sid 109 and (name N or name CA or name C or name O or name CB )) or resid 110 th \ rough 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) \ or resid 119 or (resid 120 and (name N or name CA or name C or name O or name C \ B )) or resid 121 or (resid 122 through 126 and (name N or name CA or name C or \ name O or name CB )) or resid 127 through 134 or (resid 135 through 136 and (nam \ e N or name CA or name C or name O or name CB )) or resid 137 through 152 or (re \ sid 153 through 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 or (resid 156 and (name N or name CA or name C or name O or name CB )) \ or resid 157 through 159 or (resid 160 through 161 and (name N or name CA or na \ me C or name O or name CB )) or resid 162 through 227 or (resid 228 and (name N \ or name CA or name C or name O or name CB )) or resid 229 through 273 or (resid \ 274 and (name N or name CA or name C or name O or name CB )) or resid 275 throug \ h 306 or (resid 307 and (name N or name CA or name C or name O or name CB )) or \ resid 308 through 311 or (resid 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 through 316 or (resid 317 through 319 and (name N or n \ ame CA or name C or name O or name CB )) or resid 320 through 338 or (resid 339 \ and (name N or name CA or name C or name O or name CB )) or resid 340 or (resid \ 341 and (name N or name CA or name C or name O or name CB )) or resid 342 throug \ h 363 or (resid 364 through 365 and (name N or name CA or name C or name O or na \ me CB )) or resid 366 through 367 or (resid 368 through 371 and (name N or name \ CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.950 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 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 : 0.005 0.103 19972 Z= 0.283 Angle : 0.709 15.223 27385 Z= 0.406 Chirality : 0.048 0.454 3108 Planarity : 0.005 0.114 3350 Dihedral : 19.601 176.608 7564 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.32 % Favored : 91.21 % Rotamer: Outliers : 1.64 % Allowed : 27.36 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.18), residues: 2331 helix: 0.78 (0.19), residues: 796 sheet: 0.59 (0.24), residues: 410 loop : -1.83 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 128 TYR 0.016 0.001 TYR K 216 PHE 0.038 0.002 PHE K 215 TRP 0.014 0.001 TRP K 78 HIS 0.005 0.001 HIS K 339 Details of bonding type rmsd covalent geometry : bond 0.00510 (19972) covalent geometry : angle 0.70902 (27385) hydrogen bonds : bond 0.20653 ( 753) hydrogen bonds : angle 7.01302 ( 2115) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: B 91 MET cc_start: 0.3982 (tpt) cc_final: 0.3738 (tpp) outliers start: 31 outliers final: 10 residues processed: 321 average time/residue: 0.5773 time to fit residues: 209.1303 Evaluate side-chains 300 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 290 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 341 LYS Chi-restraints excluded: chain G residue 365 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 ASN J 69 GLN J 225 GLN ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 ASN K 264 ASN G 9 GLN G 331 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.208507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.178924 restraints weight = 30024.876| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.16 r_work: 0.4239 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19972 Z= 0.144 Angle : 0.599 9.233 27385 Z= 0.312 Chirality : 0.041 0.193 3108 Planarity : 0.004 0.046 3350 Dihedral : 15.361 176.449 3495 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.51 % Favored : 92.28 % Rotamer: Outliers : 4.14 % Allowed : 25.19 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.17), residues: 2331 helix: 0.96 (0.19), residues: 791 sheet: 0.91 (0.24), residues: 385 loop : -1.78 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 128 TYR 0.017 0.001 TYR K 360 PHE 0.015 0.002 PHE H 102 TRP 0.015 0.001 TRP K 78 HIS 0.003 0.001 HIS J 180 Details of bonding type rmsd covalent geometry : bond 0.00322 (19972) covalent geometry : angle 0.59875 (27385) hydrogen bonds : bond 0.04420 ( 753) hydrogen bonds : angle 5.03463 ( 2115) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 298 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7283 (ptm160) cc_final: 0.6852 (ptp90) REVERT: F 62 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.5957 (ptp90) REVERT: F 103 MET cc_start: 0.5404 (OUTLIER) cc_final: 0.4645 (ptt) REVERT: H 4 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: H 82 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7547 (mm110) REVERT: J 98 LYS cc_start: 0.5706 (OUTLIER) cc_final: 0.5322 (mmtm) REVERT: K 34 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6672 (mtt180) REVERT: K 332 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5786 (ttp-110) REVERT: G 218 TYR cc_start: 0.5745 (t80) cc_final: 0.4414 (t80) REVERT: G 365 LYS cc_start: 0.4074 (OUTLIER) cc_final: 0.3460 (mppt) REVERT: B 91 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.4130 (tpp) outliers start: 78 outliers final: 35 residues processed: 339 average time/residue: 0.5778 time to fit residues: 221.8107 Evaluate side-chains 329 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 285 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 315 TYR Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 340 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 365 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain D residue 159 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 48 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 257 GLN I 330 ASN J 69 GLN J 82 GLN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.207215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.178678 restraints weight = 29866.587| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.23 r_work: 0.4203 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4083 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 19972 Z= 0.159 Angle : 0.599 9.197 27385 Z= 0.311 Chirality : 0.041 0.196 3108 Planarity : 0.004 0.046 3350 Dihedral : 15.232 176.702 3473 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.68 % Favored : 92.11 % Rotamer: Outliers : 4.19 % Allowed : 26.30 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.17), residues: 2331 helix: 0.89 (0.19), residues: 801 sheet: 0.86 (0.24), residues: 395 loop : -1.83 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 36 TYR 0.014 0.001 TYR K 360 PHE 0.016 0.002 PHE H 260 TRP 0.014 0.001 TRP K 78 HIS 0.004 0.001 HIS J 6 Details of bonding type rmsd covalent geometry : bond 0.00358 (19972) covalent geometry : angle 0.59858 (27385) hydrogen bonds : bond 0.04412 ( 753) hydrogen bonds : angle 4.85727 ( 2115) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 303 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6381 (ptm160) REVERT: F 103 MET cc_start: 0.5298 (OUTLIER) cc_final: 0.4591 (ptt) REVERT: F 187 ASP cc_start: 0.8568 (t0) cc_final: 0.8333 (t0) REVERT: H 4 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: H 115 VAL cc_start: 0.8393 (p) cc_final: 0.8153 (t) REVERT: H 148 MET cc_start: 0.8282 (ttp) cc_final: 0.7949 (ttp) REVERT: J 87 LYS cc_start: 0.4971 (OUTLIER) cc_final: 0.4494 (tttt) REVERT: J 98 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.5222 (mmtm) REVERT: J 312 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7236 (mpp80) REVERT: K 34 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6464 (mtt180) REVERT: K 148 MET cc_start: 0.7537 (ppp) cc_final: 0.7013 (ttt) REVERT: K 332 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.6100 (ttp-110) REVERT: K 333 TYR cc_start: 0.7640 (m-80) cc_final: 0.7128 (m-80) REVERT: B 74 ARG cc_start: 0.4142 (OUTLIER) cc_final: 0.1586 (ttt180) REVERT: B 91 MET cc_start: 0.4928 (OUTLIER) cc_final: 0.4389 (tpp) REVERT: B 202 GLU cc_start: 0.1773 (OUTLIER) cc_final: 0.1138 (tp30) outliers start: 79 outliers final: 37 residues processed: 347 average time/residue: 0.5078 time to fit residues: 201.3021 Evaluate side-chains 331 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 52 PHE Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 315 TYR Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain D residue 159 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 99 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 227 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN I 299 GLN I 330 ASN J 69 GLN J 92 ASN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.203153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.174150 restraints weight = 29247.316| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.10 r_work: 0.4180 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4065 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19972 Z= 0.185 Angle : 0.642 9.260 27385 Z= 0.335 Chirality : 0.043 0.210 3108 Planarity : 0.004 0.051 3350 Dihedral : 15.338 177.089 3463 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.07 % Favored : 91.72 % Rotamer: Outliers : 6.10 % Allowed : 26.09 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.17), residues: 2331 helix: 0.72 (0.19), residues: 802 sheet: 0.67 (0.24), residues: 387 loop : -1.89 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 60 TYR 0.015 0.002 TYR K 360 PHE 0.019 0.002 PHE H 260 TRP 0.011 0.001 TRP K 223 HIS 0.004 0.001 HIS J 180 Details of bonding type rmsd covalent geometry : bond 0.00422 (19972) covalent geometry : angle 0.64213 (27385) hydrogen bonds : bond 0.04687 ( 753) hydrogen bonds : angle 4.90248 ( 2115) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 301 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6566 (ptm160) REVERT: F 62 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6156 (ptp-170) REVERT: F 103 MET cc_start: 0.5389 (OUTLIER) cc_final: 0.4587 (ptt) REVERT: F 228 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6987 (ttpt) REVERT: F 304 LEU cc_start: 0.7956 (tp) cc_final: 0.7696 (tm) REVERT: F 347 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7434 (mt) REVERT: H 4 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: I 82 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7871 (mm-40) REVERT: J 50 ASN cc_start: 0.6284 (m-40) cc_final: 0.5952 (m-40) REVERT: J 87 LYS cc_start: 0.4905 (OUTLIER) cc_final: 0.4373 (tttt) REVERT: J 98 LYS cc_start: 0.5537 (OUTLIER) cc_final: 0.5095 (mmtm) REVERT: J 111 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5336 (mp) REVERT: K 148 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7042 (ttt) REVERT: K 216 TYR cc_start: 0.6075 (OUTLIER) cc_final: 0.5791 (t80) REVERT: K 332 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5933 (ttp-110) REVERT: K 333 TYR cc_start: 0.7622 (m-80) cc_final: 0.6850 (m-80) REVERT: B 74 ARG cc_start: 0.4438 (OUTLIER) cc_final: 0.1793 (ttt180) REVERT: B 91 MET cc_start: 0.4955 (OUTLIER) cc_final: 0.4361 (tpp) REVERT: B 202 GLU cc_start: 0.1980 (OUTLIER) cc_final: 0.0945 (tp30) REVERT: B 233 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5609 (tt) outliers start: 115 outliers final: 50 residues processed: 367 average time/residue: 0.5077 time to fit residues: 212.3965 Evaluate side-chains 357 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 228 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 306 ASN Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 79 TRP Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 55 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 264 ASN H 50 ASN H 82 GLN ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 ASN J 69 GLN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 264 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.201775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.173022 restraints weight = 28950.617| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.10 r_work: 0.4169 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4054 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19972 Z= 0.188 Angle : 0.635 9.578 27385 Z= 0.331 Chirality : 0.043 0.206 3108 Planarity : 0.004 0.051 3350 Dihedral : 15.356 177.781 3463 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.89 % Favored : 91.89 % Rotamer: Outliers : 5.09 % Allowed : 27.20 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.17), residues: 2331 helix: 0.80 (0.19), residues: 794 sheet: 0.59 (0.24), residues: 387 loop : -1.88 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 36 TYR 0.019 0.002 TYR F 315 PHE 0.018 0.002 PHE F 260 TRP 0.010 0.001 TRP K 162 HIS 0.025 0.001 HIS G 6 Details of bonding type rmsd covalent geometry : bond 0.00434 (19972) covalent geometry : angle 0.63454 (27385) hydrogen bonds : bond 0.04531 ( 753) hydrogen bonds : angle 4.86923 ( 2115) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 299 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6521 (ptm160) REVERT: F 103 MET cc_start: 0.5385 (OUTLIER) cc_final: 0.4978 (ptt) REVERT: F 111 LEU cc_start: 0.7469 (mp) cc_final: 0.7168 (tt) REVERT: H 4 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6872 (mt-10) REVERT: H 115 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.8081 (t) REVERT: H 116 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7398 (mp) REVERT: J 34 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7832 (mtt180) REVERT: J 87 LYS cc_start: 0.4902 (OUTLIER) cc_final: 0.4313 (tttt) REVERT: J 98 LYS cc_start: 0.5514 (OUTLIER) cc_final: 0.5092 (mmtm) REVERT: J 111 LEU cc_start: 0.5561 (OUTLIER) cc_final: 0.5250 (mp) REVERT: K 34 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6490 (mtt180) REVERT: K 148 MET cc_start: 0.7440 (ppp) cc_final: 0.7110 (ttt) REVERT: K 216 TYR cc_start: 0.5980 (OUTLIER) cc_final: 0.5708 (t80) REVERT: K 332 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.6080 (ttp-110) REVERT: K 333 TYR cc_start: 0.7648 (m-80) cc_final: 0.6887 (m-80) REVERT: G 342 LEU cc_start: 0.4697 (OUTLIER) cc_final: 0.3912 (mt) REVERT: B 74 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.1802 (ttt180) REVERT: B 82 PHE cc_start: 0.3556 (t80) cc_final: 0.3118 (t80) REVERT: B 91 MET cc_start: 0.5134 (OUTLIER) cc_final: 0.4724 (tpp) outliers start: 96 outliers final: 51 residues processed: 355 average time/residue: 0.5411 time to fit residues: 218.4502 Evaluate side-chains 357 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 209 MET Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 52 optimal weight: 0.0070 chunk 154 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 177 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 ASN H 17 ASN H 50 ASN H 339 HIS I 330 ASN J 69 GLN J 86 ASN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.202633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.174487 restraints weight = 29255.382| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.26 r_work: 0.4162 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19972 Z= 0.142 Angle : 0.597 12.046 27385 Z= 0.310 Chirality : 0.041 0.193 3108 Planarity : 0.004 0.050 3350 Dihedral : 15.259 177.898 3463 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.55 % Favored : 92.28 % Rotamer: Outliers : 5.30 % Allowed : 27.78 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.17), residues: 2331 helix: 1.01 (0.19), residues: 794 sheet: 0.59 (0.24), residues: 396 loop : -1.85 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 128 TYR 0.023 0.001 TYR G 218 PHE 0.014 0.001 PHE F 260 TRP 0.008 0.001 TRP B 199 HIS 0.013 0.001 HIS G 6 Details of bonding type rmsd covalent geometry : bond 0.00322 (19972) covalent geometry : angle 0.59694 (27385) hydrogen bonds : bond 0.04049 ( 753) hydrogen bonds : angle 4.69127 ( 2115) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 291 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6379 (ptm160) REVERT: F 62 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6074 (ptp-170) REVERT: F 103 MET cc_start: 0.5254 (OUTLIER) cc_final: 0.5010 (ptt) REVERT: F 111 LEU cc_start: 0.7466 (mp) cc_final: 0.7187 (tt) REVERT: F 117 ASP cc_start: 0.6488 (m-30) cc_final: 0.6150 (m-30) REVERT: F 347 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7513 (mt) REVERT: H 116 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7381 (mp) REVERT: J 34 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7820 (mtt180) REVERT: J 87 LYS cc_start: 0.4886 (OUTLIER) cc_final: 0.4301 (tttt) REVERT: J 111 LEU cc_start: 0.5497 (OUTLIER) cc_final: 0.5087 (mp) REVERT: K 34 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6386 (mtt180) REVERT: K 148 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7152 (ttt) REVERT: K 216 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5672 (t80) REVERT: K 332 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.6037 (ttp-110) REVERT: K 333 TYR cc_start: 0.7668 (m-80) cc_final: 0.6879 (m-80) REVERT: G 6 HIS cc_start: 0.6302 (OUTLIER) cc_final: 0.5838 (t-170) REVERT: G 342 LEU cc_start: 0.4527 (OUTLIER) cc_final: 0.3733 (mt) REVERT: B 74 ARG cc_start: 0.4557 (OUTLIER) cc_final: 0.1772 (ttt180) REVERT: B 82 PHE cc_start: 0.3744 (t80) cc_final: 0.3197 (t80) REVERT: B 91 MET cc_start: 0.5228 (OUTLIER) cc_final: 0.4903 (tpp) REVERT: B 233 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5891 (tt) outliers start: 100 outliers final: 45 residues processed: 352 average time/residue: 0.5189 time to fit residues: 208.0751 Evaluate side-chains 348 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 286 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 209 MET Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 51 optimal weight: 1.9990 chunk 205 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 233 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 ASN J 69 GLN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.201040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.172618 restraints weight = 29112.330| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.39 r_work: 0.4148 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4020 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19972 Z= 0.165 Angle : 0.633 14.408 27385 Z= 0.326 Chirality : 0.042 0.196 3108 Planarity : 0.004 0.051 3350 Dihedral : 15.274 177.792 3463 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.98 % Favored : 91.85 % Rotamer: Outliers : 5.14 % Allowed : 27.62 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.17), residues: 2331 helix: 0.98 (0.19), residues: 800 sheet: 0.64 (0.25), residues: 381 loop : -1.89 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 183 TYR 0.015 0.001 TYR F 315 PHE 0.019 0.002 PHE K 219 TRP 0.008 0.001 TRP G 326 HIS 0.011 0.001 HIS G 6 Details of bonding type rmsd covalent geometry : bond 0.00377 (19972) covalent geometry : angle 0.63311 (27385) hydrogen bonds : bond 0.04342 ( 753) hydrogen bonds : angle 4.75362 ( 2115) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 288 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6421 (ptm160) REVERT: F 62 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6124 (ptp-170) REVERT: F 111 LEU cc_start: 0.7483 (mp) cc_final: 0.7225 (tt) REVERT: F 117 ASP cc_start: 0.6572 (m-30) cc_final: 0.6218 (m-30) REVERT: F 228 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7110 (ttpt) REVERT: H 116 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7506 (mp) REVERT: J 34 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7781 (mtt180) REVERT: J 87 LYS cc_start: 0.4930 (OUTLIER) cc_final: 0.4324 (tttt) REVERT: J 111 LEU cc_start: 0.5656 (OUTLIER) cc_final: 0.5283 (mp) REVERT: K 148 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7136 (ttt) REVERT: K 216 TYR cc_start: 0.5998 (OUTLIER) cc_final: 0.5739 (t80) REVERT: B 74 ARG cc_start: 0.4614 (OUTLIER) cc_final: 0.1914 (ttt180) REVERT: B 91 MET cc_start: 0.5301 (OUTLIER) cc_final: 0.5020 (tpp) REVERT: B 233 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.5986 (tt) outliers start: 97 outliers final: 55 residues processed: 347 average time/residue: 0.5793 time to fit residues: 229.2898 Evaluate side-chains 349 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 282 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 228 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 209 MET Chi-restraints excluded: chain I residue 306 ASN Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 160 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 209 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 216 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 206 optimal weight: 0.0270 chunk 212 optimal weight: 0.0040 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 ASN J 69 GLN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.203390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.175726 restraints weight = 29517.943| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.22 r_work: 0.4176 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4054 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19972 Z= 0.113 Angle : 0.580 12.161 27385 Z= 0.297 Chirality : 0.040 0.177 3108 Planarity : 0.004 0.046 3350 Dihedral : 15.140 177.943 3463 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.99 % Favored : 92.84 % Rotamer: Outliers : 3.34 % Allowed : 29.75 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.18), residues: 2331 helix: 1.17 (0.19), residues: 801 sheet: 0.71 (0.24), residues: 402 loop : -1.79 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 332 TYR 0.025 0.001 TYR G 218 PHE 0.015 0.001 PHE I 52 TRP 0.011 0.001 TRP H 78 HIS 0.009 0.001 HIS G 6 Details of bonding type rmsd covalent geometry : bond 0.00248 (19972) covalent geometry : angle 0.58006 (27385) hydrogen bonds : bond 0.03550 ( 753) hydrogen bonds : angle 4.52218 ( 2115) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 297 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6222 (ptm160) REVERT: F 62 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.5897 (ptp-170) REVERT: F 111 LEU cc_start: 0.7471 (mp) cc_final: 0.7266 (tt) REVERT: F 117 ASP cc_start: 0.6501 (m-30) cc_final: 0.6052 (m-30) REVERT: F 226 LEU cc_start: 0.5895 (tp) cc_final: 0.5483 (tp) REVERT: I 49 SER cc_start: 0.8349 (p) cc_final: 0.8075 (p) REVERT: J 34 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7684 (mtt180) REVERT: J 50 ASN cc_start: 0.6216 (m-40) cc_final: 0.5941 (m-40) REVERT: J 53 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7316 (ptpp) REVERT: J 87 LYS cc_start: 0.4815 (OUTLIER) cc_final: 0.4283 (tttt) REVERT: J 111 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5099 (mp) REVERT: K 34 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6442 (mtt180) REVERT: K 148 MET cc_start: 0.7510 (ppp) cc_final: 0.7097 (ttt) REVERT: K 216 TYR cc_start: 0.6007 (OUTLIER) cc_final: 0.5766 (t80) REVERT: B 74 ARG cc_start: 0.4430 (OUTLIER) cc_final: 0.1828 (ttt180) REVERT: B 91 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.5038 (tpp) REVERT: B 233 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5944 (tt) outliers start: 63 outliers final: 31 residues processed: 333 average time/residue: 0.5768 time to fit residues: 217.9264 Evaluate side-chains 327 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 209 MET Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 54 optimal weight: 0.8980 chunk 204 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 219 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 201 optimal weight: 0.0770 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 ASN I 299 GLN J 69 GLN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.204218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.176256 restraints weight = 29497.628| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 2.11 r_work: 0.4205 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4090 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19972 Z= 0.109 Angle : 0.571 11.785 27385 Z= 0.292 Chirality : 0.040 0.172 3108 Planarity : 0.004 0.046 3350 Dihedral : 15.031 177.324 3463 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.91 % Favored : 92.88 % Rotamer: Outliers : 2.76 % Allowed : 30.33 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.18), residues: 2331 helix: 1.22 (0.19), residues: 803 sheet: 0.92 (0.25), residues: 392 loop : -1.70 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 312 TYR 0.017 0.001 TYR K 333 PHE 0.009 0.001 PHE F 260 TRP 0.009 0.001 TRP H 366 HIS 0.008 0.001 HIS G 6 Details of bonding type rmsd covalent geometry : bond 0.00234 (19972) covalent geometry : angle 0.57126 (27385) hydrogen bonds : bond 0.03447 ( 753) hydrogen bonds : angle 4.40705 ( 2115) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6728 (ptp90) REVERT: F 111 LEU cc_start: 0.7433 (mp) cc_final: 0.7175 (tt) REVERT: F 115 VAL cc_start: 0.5735 (p) cc_final: 0.5510 (t) REVERT: F 117 ASP cc_start: 0.6306 (m-30) cc_final: 0.5836 (m-30) REVERT: I 49 SER cc_start: 0.8318 (p) cc_final: 0.8002 (p) REVERT: I 99 MET cc_start: 0.7447 (ttt) cc_final: 0.7226 (ttm) REVERT: J 34 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7653 (mtt180) REVERT: J 52 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6966 (t80) REVERT: J 87 LYS cc_start: 0.4803 (OUTLIER) cc_final: 0.4313 (tttt) REVERT: J 111 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.5024 (mt) REVERT: K 34 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6440 (mtt180) REVERT: K 148 MET cc_start: 0.7438 (ppp) cc_final: 0.7042 (ttt) REVERT: K 216 TYR cc_start: 0.5900 (OUTLIER) cc_final: 0.5680 (t80) REVERT: G 342 LEU cc_start: 0.2250 (OUTLIER) cc_final: 0.1989 (pp) REVERT: B 74 ARG cc_start: 0.4211 (OUTLIER) cc_final: 0.3510 (mtm-85) REVERT: B 91 MET cc_start: 0.5324 (OUTLIER) cc_final: 0.5057 (tpp) REVERT: B 233 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5852 (tt) outliers start: 52 outliers final: 30 residues processed: 327 average time/residue: 0.5809 time to fit residues: 214.8304 Evaluate side-chains 330 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 52 PHE Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 69 GLN Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 155 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 0.1980 chunk 56 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 201 optimal weight: 0.2980 chunk 185 optimal weight: 7.9990 chunk 66 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 ASN H 50 ASN I 330 ASN J 69 GLN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.204224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.176259 restraints weight = 29502.885| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.12 r_work: 0.4207 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 19972 Z= 0.111 Angle : 0.588 12.657 27385 Z= 0.299 Chirality : 0.040 0.197 3108 Planarity : 0.004 0.060 3350 Dihedral : 14.978 177.319 3463 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.08 % Favored : 92.71 % Rotamer: Outliers : 2.76 % Allowed : 31.02 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.18), residues: 2331 helix: 1.26 (0.19), residues: 799 sheet: 0.94 (0.25), residues: 393 loop : -1.68 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 113 TYR 0.027 0.001 TYR G 218 PHE 0.020 0.001 PHE J 327 TRP 0.009 0.001 TRP H 78 HIS 0.009 0.001 HIS G 6 Details of bonding type rmsd covalent geometry : bond 0.00247 (19972) covalent geometry : angle 0.58762 (27385) hydrogen bonds : bond 0.03439 ( 753) hydrogen bonds : angle 4.40554 ( 2115) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.5851 (ptm160) REVERT: F 111 LEU cc_start: 0.7437 (mp) cc_final: 0.7184 (tt) REVERT: F 115 VAL cc_start: 0.5662 (p) cc_final: 0.5459 (t) REVERT: F 117 ASP cc_start: 0.6235 (m-30) cc_final: 0.5662 (m-30) REVERT: F 226 LEU cc_start: 0.5767 (tp) cc_final: 0.5372 (tp) REVERT: I 49 SER cc_start: 0.8319 (p) cc_final: 0.8005 (p) REVERT: I 99 MET cc_start: 0.7419 (ttt) cc_final: 0.7204 (ttm) REVERT: J 34 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7633 (mtt180) REVERT: J 87 LYS cc_start: 0.4694 (OUTLIER) cc_final: 0.4218 (tttt) REVERT: J 111 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.5088 (mt) REVERT: K 34 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6389 (mtt180) REVERT: K 148 MET cc_start: 0.7370 (ppp) cc_final: 0.6997 (ttt) REVERT: K 216 TYR cc_start: 0.5898 (OUTLIER) cc_final: 0.5684 (t80) REVERT: G 342 LEU cc_start: 0.2257 (OUTLIER) cc_final: 0.1987 (pp) REVERT: B 74 ARG cc_start: 0.4172 (OUTLIER) cc_final: 0.3489 (mtm-85) REVERT: B 91 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.5089 (tpp) REVERT: B 233 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5874 (tt) outliers start: 52 outliers final: 32 residues processed: 317 average time/residue: 0.5654 time to fit residues: 202.5904 Evaluate side-chains 326 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 80 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 228 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 204 optimal weight: 0.4980 chunk 177 optimal weight: 0.0770 chunk 117 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 210 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.204015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.176049 restraints weight = 29481.460| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.29 r_work: 0.4188 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19972 Z= 0.114 Angle : 0.585 11.491 27385 Z= 0.299 Chirality : 0.040 0.193 3108 Planarity : 0.004 0.046 3350 Dihedral : 14.921 177.466 3463 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.12 % Favored : 92.71 % Rotamer: Outliers : 2.55 % Allowed : 31.34 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.18), residues: 2331 helix: 1.29 (0.19), residues: 799 sheet: 0.95 (0.25), residues: 392 loop : -1.63 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 113 TYR 0.017 0.001 TYR K 333 PHE 0.017 0.001 PHE J 327 TRP 0.012 0.001 TRP H 366 HIS 0.009 0.001 HIS G 6 Details of bonding type rmsd covalent geometry : bond 0.00256 (19972) covalent geometry : angle 0.58450 (27385) hydrogen bonds : bond 0.03486 ( 753) hydrogen bonds : angle 4.38428 ( 2115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9428.41 seconds wall clock time: 160 minutes 40.29 seconds (9640.29 seconds total)