Starting phenix.real_space_refine on Thu Jan 23 07:18:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zol_60297/01_2025/8zol_60297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zol_60297/01_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_60297/01_2025/8zol_60297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zol_60297/01_2025/8zol_60297.map" model { file = "/net/cci-nas-00/data/ceres_data/8zol_60297/01_2025/8zol_60297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zol_60297/01_2025/8zol_60297.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP: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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP: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, 'PHE:plan': 1, 'GLN:plan1': 2} 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, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 1, 'ARG: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: 11.41, per 1000 atoms: 0.59 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: 4.75 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 6.09 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: 6.60 Time building geometry restraints manager: 5.52 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 46.360 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.630 ------------------------------------------------------------------------------- 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= 0.330 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 : 10.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (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 TRP 0.014 0.001 TRP K 78 HIS 0.005 0.001 HIS K 339 PHE 0.038 0.002 PHE K 215 TYR 0.016 0.001 TYR K 216 ARG 0.005 0.000 ARG B 128 *********************** 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 : 2.008 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: 1.2917 time to fit residues: 468.1944 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 : 2.003 ------------------------------------------------------------------------------- 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 201 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 187 optimal weight: 0.0570 chunk 72 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.210794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.182111 restraints weight = 30059.778| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.27 r_work: 0.4244 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19972 Z= 0.184 Angle : 0.584 9.261 27385 Z= 0.303 Chirality : 0.040 0.187 3108 Planarity : 0.004 0.045 3350 Dihedral : 15.341 176.562 3495 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.42 % Favored : 92.36 % Rotamer: Outliers : 3.87 % Allowed : 25.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2331 helix: 1.06 (0.20), residues: 786 sheet: 0.98 (0.24), residues: 387 loop : -1.75 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 78 HIS 0.003 0.001 HIS J 180 PHE 0.013 0.001 PHE H 260 TYR 0.017 0.001 TYR G 218 ARG 0.004 0.000 ARG B 128 *********************** 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 372 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 299 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7238 (ptm160) cc_final: 0.6854 (ptp90) REVERT: F 62 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.5952 (ptp90) REVERT: F 103 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.4581 (ptt) REVERT: F 241 VAL cc_start: 0.5741 (t) cc_final: 0.5187 (p) REVERT: H 4 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7078 (mt-10) REVERT: H 82 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7530 (mm110) REVERT: J 98 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.5499 (mmtm) REVERT: K 332 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5813 (ttp-110) REVERT: G 218 TYR cc_start: 0.5739 (t80) cc_final: 0.4551 (t80) REVERT: G 365 LYS cc_start: 0.4078 (OUTLIER) cc_final: 0.3461 (mppt) REVERT: B 91 MET cc_start: 0.4786 (OUTLIER) cc_final: 0.4199 (tpp) outliers start: 73 outliers final: 31 residues processed: 339 average time/residue: 1.2426 time to fit residues: 478.9469 Evaluate side-chains 325 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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 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 220 SER 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 J residue 99 MET Chi-restraints excluded: chain K residue 17 ASN 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 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 102 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 211 optimal weight: 0.0670 chunk 112 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 117 optimal weight: 0.6980 chunk 177 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 185 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 GLN J 82 GLN J 225 GLN K 164 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.210486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.180997 restraints weight = 29897.868| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 2.16 r_work: 0.4248 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.1338 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= 0.165 Angle : 0.559 9.337 27385 Z= 0.289 Chirality : 0.040 0.183 3108 Planarity : 0.003 0.042 3350 Dihedral : 15.158 176.799 3476 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.95 % Favored : 92.84 % Rotamer: Outliers : 3.45 % Allowed : 27.15 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2331 helix: 1.16 (0.19), residues: 791 sheet: 1.07 (0.24), residues: 397 loop : -1.75 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 78 HIS 0.003 0.001 HIS J 180 PHE 0.011 0.001 PHE H 260 TYR 0.014 0.001 TYR G 218 ARG 0.003 0.000 ARG B 128 *********************** 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 366 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 301 time to evaluate : 2.130 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6180 (ptm160) REVERT: F 103 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4518 (ptt) REVERT: F 187 ASP cc_start: 0.8479 (t0) cc_final: 0.8277 (t0) REVERT: H 4 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: H 115 VAL cc_start: 0.8359 (p) cc_final: 0.8125 (t) REVERT: J 87 LYS cc_start: 0.4883 (OUTLIER) cc_final: 0.4512 (tttt) REVERT: J 98 LYS cc_start: 0.5554 (OUTLIER) cc_final: 0.5061 (mmtm) REVERT: K 332 ARG cc_start: 0.6265 (OUTLIER) cc_final: 0.5900 (ttp-110) REVERT: K 333 TYR cc_start: 0.7581 (m-80) cc_final: 0.7002 (m-80) REVERT: G 218 TYR cc_start: 0.5727 (t80) cc_final: 0.4462 (t80) REVERT: B 91 MET cc_start: 0.4797 (OUTLIER) cc_final: 0.4341 (tpp) outliers start: 65 outliers final: 27 residues processed: 332 average time/residue: 1.2612 time to fit residues: 476.3928 Evaluate side-chains 320 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 68 ILE Chi-restraints excluded: chain H residue 75 THR 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 45 SER Chi-restraints excluded: chain I residue 165 THR 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 99 MET Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 315 TYR Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 91 MET 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 7 optimal weight: 0.0570 chunk 41 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 236 optimal weight: 4.9990 chunk 50 optimal weight: 0.0970 chunk 205 optimal weight: 0.0770 chunk 11 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 17 ASN H 50 ASN ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN J 69 GLN J 225 GLN K 164 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.211295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.182586 restraints weight = 30315.863| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.36 r_work: 0.4249 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19972 Z= 0.146 Angle : 0.537 9.535 27385 Z= 0.276 Chirality : 0.039 0.176 3108 Planarity : 0.003 0.040 3350 Dihedral : 15.043 176.830 3466 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.04 % Favored : 92.75 % Rotamer: Outliers : 4.08 % Allowed : 26.56 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2331 helix: 1.25 (0.20), residues: 801 sheet: 1.08 (0.24), residues: 404 loop : -1.73 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 78 HIS 0.004 0.001 HIS J 180 PHE 0.010 0.001 PHE B 82 TYR 0.013 0.001 TYR G 218 ARG 0.003 0.000 ARG B 128 *********************** 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 369 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 292 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6113 (ptm160) REVERT: F 103 MET cc_start: 0.5156 (OUTLIER) cc_final: 0.4774 (ptt) REVERT: F 187 ASP cc_start: 0.8441 (t0) cc_final: 0.8210 (t0) REVERT: H 4 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6978 (mt-10) REVERT: I 49 SER cc_start: 0.8368 (p) cc_final: 0.8057 (p) REVERT: J 87 LYS cc_start: 0.4847 (OUTLIER) cc_final: 0.4454 (tttt) REVERT: K 315 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5686 (t80) REVERT: K 332 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5807 (ttp-110) REVERT: K 333 TYR cc_start: 0.7556 (m-80) cc_final: 0.6983 (m-80) REVERT: G 218 TYR cc_start: 0.5750 (t80) cc_final: 0.4601 (t80) REVERT: B 74 ARG cc_start: 0.3868 (OUTLIER) cc_final: 0.1459 (ttt180) REVERT: B 91 MET cc_start: 0.4915 (OUTLIER) cc_final: 0.4428 (tpp) REVERT: B 202 GLU cc_start: 0.1674 (OUTLIER) cc_final: 0.1120 (tp30) outliers start: 77 outliers final: 30 residues processed: 328 average time/residue: 1.2311 time to fit residues: 459.5283 Evaluate side-chains 315 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 103 MET 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 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 167 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 165 THR 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 99 MET Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 315 TYR Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 265 TYR 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 134 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 233 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 90 optimal weight: 0.0020 chunk 71 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 ASN ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 257 GLN I 299 GLN J 69 GLN J 82 GLN J 92 ASN J 225 GLN ** J 257 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 = 0.4601 r_free = 0.4601 target = 0.205320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.176438 restraints weight = 29726.295| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.42 r_work: 0.4183 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19972 Z= 0.273 Angle : 0.621 9.474 27385 Z= 0.324 Chirality : 0.042 0.203 3108 Planarity : 0.004 0.046 3350 Dihedral : 15.156 176.430 3466 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.89 % Favored : 91.89 % Rotamer: Outliers : 4.45 % Allowed : 26.78 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2331 helix: 1.09 (0.19), residues: 787 sheet: 0.94 (0.24), residues: 384 loop : -1.80 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 326 HIS 0.004 0.001 HIS J 263 PHE 0.020 0.002 PHE H 260 TYR 0.013 0.002 TYR K 360 ARG 0.003 0.000 ARG B 74 *********************** 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 378 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 294 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6333 (ptm160) REVERT: F 103 MET cc_start: 0.5403 (OUTLIER) cc_final: 0.4519 (ptt) REVERT: F 187 ASP cc_start: 0.8560 (t0) cc_final: 0.8315 (t0) REVERT: H 4 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: J 87 LYS cc_start: 0.4965 (OUTLIER) cc_final: 0.4469 (tttt) REVERT: J 98 LYS cc_start: 0.5498 (OUTLIER) cc_final: 0.5216 (mmtm) REVERT: J 111 LEU cc_start: 0.5462 (OUTLIER) cc_final: 0.5226 (mp) REVERT: J 312 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7276 (mpp80) REVERT: K 148 MET cc_start: 0.7419 (ppp) cc_final: 0.7051 (ttt) REVERT: K 167 VAL cc_start: 0.6317 (OUTLIER) cc_final: 0.6096 (p) REVERT: K 315 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.6390 (m-80) REVERT: K 332 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.5984 (ttp-110) REVERT: K 333 TYR cc_start: 0.7641 (m-80) cc_final: 0.6999 (m-80) REVERT: B 74 ARG cc_start: 0.4308 (OUTLIER) cc_final: 0.1747 (ttt180) REVERT: B 91 MET cc_start: 0.4971 (OUTLIER) cc_final: 0.4371 (tpp) REVERT: B 202 GLU cc_start: 0.1748 (OUTLIER) cc_final: 0.0987 (tp30) outliers start: 84 outliers final: 46 residues processed: 338 average time/residue: 1.2126 time to fit residues: 465.7161 Evaluate side-chains 338 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 279 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 97 THR 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 313 LEU Chi-restraints excluded: chain F residue 338 LYS 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 115 VAL 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 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 234 THR 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 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 99 MET Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 312 ARG 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 133 ILE Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 186 ILE 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 315 TYR Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 THR 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 175 HIS Chi-restraints excluded: chain G residue 179 THR 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 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 207 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 167 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 195 optimal weight: 0.0010 chunk 235 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 ASN H 339 HIS I 330 ASN J 69 GLN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.207100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.178280 restraints weight = 29747.691| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.10 r_work: 0.4224 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19972 Z= 0.179 Angle : 0.560 9.672 27385 Z= 0.289 Chirality : 0.040 0.183 3108 Planarity : 0.003 0.043 3350 Dihedral : 15.092 177.345 3466 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.95 % Favored : 92.88 % Rotamer: Outliers : 3.87 % Allowed : 27.94 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2331 helix: 1.27 (0.19), residues: 790 sheet: 0.81 (0.23), residues: 404 loop : -1.74 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 326 HIS 0.005 0.001 HIS G 175 PHE 0.012 0.001 PHE B 82 TYR 0.013 0.001 TYR I 316 ARG 0.003 0.000 ARG B 128 *********************** 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 352 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 279 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6241 (ptm160) REVERT: F 62 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6037 (ptp-170) REVERT: H 4 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: J 34 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7743 (mtt180) REVERT: J 53 LYS cc_start: 0.7376 (ptpp) cc_final: 0.7166 (ptpp) REVERT: J 87 LYS cc_start: 0.4771 (OUTLIER) cc_final: 0.4329 (tttt) REVERT: J 97 THR cc_start: 0.5907 (OUTLIER) cc_final: 0.5496 (t) REVERT: K 148 MET cc_start: 0.7340 (ppp) cc_final: 0.6949 (ttt) REVERT: K 167 VAL cc_start: 0.6324 (OUTLIER) cc_final: 0.6073 (p) REVERT: K 332 ARG cc_start: 0.6106 (OUTLIER) cc_final: 0.5905 (ttp-110) REVERT: K 333 TYR cc_start: 0.7551 (m-80) cc_final: 0.6920 (m-80) REVERT: G 218 TYR cc_start: 0.5932 (t80) cc_final: 0.4757 (t80) REVERT: B 74 ARG cc_start: 0.4275 (OUTLIER) cc_final: 0.1773 (ttt180) REVERT: B 91 MET cc_start: 0.5151 (OUTLIER) cc_final: 0.4555 (tpp) REVERT: B 202 GLU cc_start: 0.1761 (OUTLIER) cc_final: 0.0957 (tp30) outliers start: 73 outliers final: 36 residues processed: 323 average time/residue: 1.2400 time to fit residues: 458.2102 Evaluate side-chains 325 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 2.083 ------------------------------------------------------------------------------- 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 116 LEU 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 313 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 75 THR 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 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 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 107 LYS Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 167 VAL 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 332 ARG Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 179 THR 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 202 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain D residue 159 LEU 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 113 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 233 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 ASN 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 299 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 = 0.4588 r_free = 0.4588 target = 0.203660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.174859 restraints weight = 29105.889| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.10 r_work: 0.4188 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4074 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19972 Z= 0.244 Angle : 0.612 9.692 27385 Z= 0.318 Chirality : 0.041 0.203 3108 Planarity : 0.004 0.045 3350 Dihedral : 15.161 177.061 3466 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.45 % Favored : 91.38 % Rotamer: Outliers : 4.14 % Allowed : 27.78 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2331 helix: 1.15 (0.19), residues: 797 sheet: 0.63 (0.24), residues: 398 loop : -1.82 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 326 HIS 0.018 0.001 HIS G 6 PHE 0.019 0.002 PHE H 260 TYR 0.015 0.001 TYR F 315 ARG 0.003 0.000 ARG J 183 *********************** 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 367 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 289 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6335 (ptm160) REVERT: F 62 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6016 (ptp-170) REVERT: F 111 LEU cc_start: 0.7499 (mp) cc_final: 0.7247 (tt) REVERT: F 228 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6982 (ttpt) REVERT: H 4 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6834 (mt-10) REVERT: I 99 MET cc_start: 0.7389 (ttm) cc_final: 0.7115 (ttm) REVERT: J 34 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7755 (mtt180) REVERT: J 53 LYS cc_start: 0.7451 (ptpp) cc_final: 0.7238 (ptpp) REVERT: J 87 LYS cc_start: 0.4865 (OUTLIER) cc_final: 0.4316 (tttt) REVERT: J 111 LEU cc_start: 0.5497 (OUTLIER) cc_final: 0.5161 (mp) REVERT: J 312 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7232 (mpp80) REVERT: K 148 MET cc_start: 0.7464 (ppp) cc_final: 0.7114 (ttt) REVERT: K 332 ARG cc_start: 0.6287 (OUTLIER) cc_final: 0.5991 (ttp-110) REVERT: K 333 TYR cc_start: 0.7624 (m-80) cc_final: 0.6817 (m-80) REVERT: B 74 ARG cc_start: 0.4342 (OUTLIER) cc_final: 0.1771 (ttt180) REVERT: B 91 MET cc_start: 0.4967 (OUTLIER) cc_final: 0.4306 (tpp) REVERT: B 202 GLU cc_start: 0.1944 (OUTLIER) cc_final: 0.0929 (tp30) outliers start: 78 outliers final: 51 residues processed: 337 average time/residue: 1.1996 time to fit residues: 461.0469 Evaluate side-chains 348 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 285 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 137 THR Chi-restraints excluded: chain F residue 177 ILE 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 338 LYS Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain H residue 4 GLU 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 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 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 116 LEU 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 95 ASP Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 186 ILE 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 323 ILE Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 290 VAL 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 202 GLU Chi-restraints excluded: chain B residue 211 VAL 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 47 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 20 optimal weight: 0.0050 chunk 9 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 223 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 174 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 ASN I 330 ASN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 264 ASN G 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.205868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.177079 restraints weight = 29684.606| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 2.16 r_work: 0.4212 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4097 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2686 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= 0.164 Angle : 0.560 9.781 27385 Z= 0.289 Chirality : 0.040 0.177 3108 Planarity : 0.003 0.042 3350 Dihedral : 15.042 177.596 3466 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.91 % Favored : 92.92 % Rotamer: Outliers : 3.87 % Allowed : 28.10 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2331 helix: 1.40 (0.19), residues: 785 sheet: 0.77 (0.24), residues: 404 loop : -1.75 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 78 HIS 0.007 0.001 HIS G 6 PHE 0.010 0.001 PHE F 260 TYR 0.014 0.001 TYR K 360 ARG 0.003 0.000 ARG B 128 *********************** 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 354 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 281 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6132 (ptm160) REVERT: F 62 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6002 (ptp-170) REVERT: F 111 LEU cc_start: 0.7456 (mp) cc_final: 0.7250 (tt) REVERT: H 4 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: J 34 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7732 (mtt180) REVERT: J 53 LYS cc_start: 0.7461 (ptpp) cc_final: 0.7229 (ptpp) REVERT: J 87 LYS cc_start: 0.4778 (OUTLIER) cc_final: 0.4310 (tttt) REVERT: J 312 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7198 (mpp80) REVERT: K 148 MET cc_start: 0.7479 (ppp) cc_final: 0.7091 (ttt) REVERT: G 218 TYR cc_start: 0.6061 (t80) cc_final: 0.5817 (t80) REVERT: B 74 ARG cc_start: 0.4238 (OUTLIER) cc_final: 0.1697 (ttt180) REVERT: B 82 PHE cc_start: 0.3596 (t80) cc_final: 0.3273 (t80) REVERT: B 91 MET cc_start: 0.5187 (OUTLIER) cc_final: 0.4572 (tpp) REVERT: B 202 GLU cc_start: 0.1780 (OUTLIER) cc_final: 0.0730 (tp30) REVERT: B 233 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5625 (tt) outliers start: 73 outliers final: 41 residues processed: 324 average time/residue: 1.2256 time to fit residues: 451.4005 Evaluate side-chains 323 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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 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 F residue 347 ILE Chi-restraints excluded: chain H residue 4 GLU 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 181 ILE Chi-restraints excluded: chain H residue 220 SER 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 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 99 MET Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 35 SER 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 332 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 359 ASP 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 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 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 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 16 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 214 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 192 optimal weight: 0.4980 chunk 92 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 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 B 201 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.205048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.176385 restraints weight = 29409.756| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.17 r_work: 0.4202 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4086 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2814 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= 0.180 Angle : 0.585 14.278 27385 Z= 0.298 Chirality : 0.040 0.178 3108 Planarity : 0.003 0.041 3350 Dihedral : 15.012 177.232 3466 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.32 % Rotamer: Outliers : 3.39 % Allowed : 28.53 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2331 helix: 1.43 (0.19), residues: 783 sheet: 0.71 (0.24), residues: 410 loop : -1.73 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 78 HIS 0.011 0.001 HIS G 175 PHE 0.017 0.001 PHE K 219 TYR 0.018 0.001 TYR K 333 ARG 0.003 0.000 ARG B 128 *********************** 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 343 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 279 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6128 (ptm160) REVERT: F 62 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.5952 (ptp-170) REVERT: F 111 LEU cc_start: 0.7417 (mp) cc_final: 0.7153 (tt) REVERT: F 228 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.7000 (ttpt) REVERT: J 34 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7713 (mtt180) REVERT: J 87 LYS cc_start: 0.4787 (OUTLIER) cc_final: 0.4320 (tttt) REVERT: J 312 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7208 (mpp80) REVERT: K 148 MET cc_start: 0.7494 (ppp) cc_final: 0.7117 (ttt) REVERT: K 332 ARG cc_start: 0.6200 (OUTLIER) cc_final: 0.5959 (ttp-110) REVERT: G 342 LEU cc_start: 0.4616 (OUTLIER) cc_final: 0.3791 (mt) REVERT: B 74 ARG cc_start: 0.4239 (OUTLIER) cc_final: 0.1682 (ttt180) REVERT: B 82 PHE cc_start: 0.3653 (t80) cc_final: 0.3244 (t80) REVERT: B 91 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4700 (tpp) REVERT: B 233 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5698 (tt) outliers start: 64 outliers final: 43 residues processed: 318 average time/residue: 1.2770 time to fit residues: 460.6528 Evaluate side-chains 329 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 2.083 ------------------------------------------------------------------------------- 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 195 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 228 LYS 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 105 LYS 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 322 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 63 ARG 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 95 ASP Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 35 SER 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 332 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 359 ASP 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 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 265 VAL 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 79 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 217 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 ASN H 82 GLN I 349 ASN J 69 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 175 HIS ** 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 = 0.4562 r_free = 0.4562 target = 0.200552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.172227 restraints weight = 28874.324| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.10 r_work: 0.4164 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4048 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19972 Z= 0.291 Angle : 0.675 13.349 27385 Z= 0.349 Chirality : 0.043 0.207 3108 Planarity : 0.004 0.045 3350 Dihedral : 15.209 177.766 3466 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.15 % Favored : 91.68 % Rotamer: Outliers : 3.34 % Allowed : 28.79 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2331 helix: 1.03 (0.19), residues: 796 sheet: 0.55 (0.24), residues: 384 loop : -1.87 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 326 HIS 0.011 0.001 HIS G 6 PHE 0.020 0.002 PHE H 260 TYR 0.023 0.002 TYR G 218 ARG 0.013 0.001 ARG K 113 ********************** 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 350 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 287 time to evaluate : 2.156 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6270 (ptm160) REVERT: F 62 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.5994 (ptp-170) REVERT: F 111 LEU cc_start: 0.7499 (mp) cc_final: 0.7222 (tt) REVERT: I 99 MET cc_start: 0.7357 (ttm) cc_final: 0.7118 (ttm) REVERT: J 4 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7583 (mm-30) REVERT: J 34 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7788 (mtt180) REVERT: J 87 LYS cc_start: 0.4898 (OUTLIER) cc_final: 0.4337 (tttt) REVERT: J 312 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7269 (mpp80) REVERT: K 148 MET cc_start: 0.7498 (ppp) cc_final: 0.7126 (ttt) REVERT: G 29 PHE cc_start: 0.7003 (t80) cc_final: 0.6791 (t80) REVERT: B 74 ARG cc_start: 0.4511 (OUTLIER) cc_final: 0.1939 (ttt180) REVERT: B 91 MET cc_start: 0.5305 (OUTLIER) cc_final: 0.5026 (tpp) REVERT: B 233 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5930 (tt) outliers start: 63 outliers final: 41 residues processed: 322 average time/residue: 1.2589 time to fit residues: 458.8323 Evaluate side-chains 331 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 282 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 195 VAL Chi-restraints excluded: chain F residue 205 ILE 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 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 231 LYS 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 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 99 MET Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 186 ILE 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 K residue 359 ASP Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 290 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 85 optimal weight: 0.6980 chunk 222 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 330 ASN J 69 GLN J 225 GLN ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 175 HIS ** 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 = 0.4572 r_free = 0.4572 target = 0.201498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.173315 restraints weight = 29110.243| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.10 r_work: 0.4176 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4060 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19972 Z= 0.226 Angle : 0.634 13.428 27385 Z= 0.325 Chirality : 0.042 0.188 3108 Planarity : 0.004 0.053 3350 Dihedral : 15.128 178.252 3466 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.59 % Favored : 92.24 % Rotamer: Outliers : 3.02 % Allowed : 29.43 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2331 helix: 1.18 (0.19), residues: 790 sheet: 0.58 (0.24), residues: 392 loop : -1.83 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 78 HIS 0.009 0.001 HIS G 6 PHE 0.014 0.001 PHE H 260 TYR 0.018 0.001 TYR K 315 ARG 0.013 0.000 ARG K 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19032.61 seconds wall clock time: 335 minutes 45.81 seconds (20145.81 seconds total)