Starting phenix.real_space_refine on Tue Jun 17 10:39:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zol_60297/06_2025/8zol_60297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zol_60297/06_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_60297/06_2025/8zol_60297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zol_60297/06_2025/8zol_60297.map" model { file = "/net/cci-nas-00/data/ceres_data/8zol_60297/06_2025/8zol_60297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zol_60297/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.79, per 1000 atoms: 0.71 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: 4.45 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: 6.07 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: 6.64 Time building geometry restraints manager: 5.29 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: 4.020 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 49.900 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 19972 Z= 0.283 Angle : 0.709 15.223 27385 Z= 0.406 Chirality : 0.048 0.454 3108 Planarity : 0.005 0.114 3350 Dihedral : 19.601 176.608 7564 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.10 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 Details of bonding type rmsd hydrogen bonds : bond 0.20653 ( 753) hydrogen bonds : angle 7.01302 ( 2115) covalent geometry : bond 0.00510 (19972) covalent geometry : angle 0.70902 (27385) *********************** 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 : 1.910 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: 1.2598 time to fit residues: 457.1599 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 : 1.874 ------------------------------------------------------------------------------- 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 = 0.210797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.182098 restraints weight = 30060.623| |-----------------------------------------------------------------------------| 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: 0.4129 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19972 Z= 0.126 Angle : 0.584 9.259 27385 Z= 0.303 Chirality : 0.040 0.186 3108 Planarity : 0.004 0.045 3350 Dihedral : 15.341 176.562 3495 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.07 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 102 TYR 0.017 0.001 TYR G 218 ARG 0.004 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 753) hydrogen bonds : angle 4.97880 ( 2115) covalent geometry : bond 0.00277 (19972) covalent geometry : angle 0.58411 (27385) *********************** 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 : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7238 (ptm160) cc_final: 0.6855 (ptp90) REVERT: F 62 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.5952 (ptp90) REVERT: F 103 MET cc_start: 0.5344 (OUTLIER) cc_final: 0.4593 (ptt) REVERT: F 241 VAL cc_start: 0.5742 (t) cc_final: 0.5190 (p) REVERT: H 4 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: H 82 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7532 (mm110) REVERT: J 98 LYS cc_start: 0.5778 (OUTLIER) cc_final: 0.5510 (mmtm) REVERT: K 332 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5813 (ttp-110) REVERT: G 218 TYR cc_start: 0.5736 (t80) cc_final: 0.4550 (t80) REVERT: G 365 LYS cc_start: 0.4078 (OUTLIER) cc_final: 0.3462 (mppt) REVERT: B 91 MET cc_start: 0.4795 (OUTLIER) cc_final: 0.4204 (tpp) outliers start: 73 outliers final: 31 residues processed: 339 average time/residue: 1.1916 time to fit residues: 460.6654 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 : 2.123 ------------------------------------------------------------------------------- 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: 0.7980 chunk 112 optimal weight: 0.5980 chunk 38 optimal weight: 0.0770 chunk 117 optimal weight: 0.8980 chunk 177 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 chunk 105 optimal weight: 0.5980 chunk 185 optimal weight: 8.9990 chunk 156 optimal weight: 0.0020 overall best weight: 0.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 264 ASN H 17 ASN H 50 ASN ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4665 r_free = 0.4665 target = 0.212339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.183116 restraints weight = 30120.530| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.14 r_work: 0.4270 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4161 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19972 Z= 0.101 Angle : 0.541 9.379 27385 Z= 0.278 Chirality : 0.039 0.172 3108 Planarity : 0.003 0.040 3350 Dihedral : 15.117 176.924 3476 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.61 % Favored : 93.18 % Rotamer: Outliers : 3.23 % Allowed : 26.94 % Favored : 69.83 % 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: -0.19 (0.18), residues: 2331 helix: 1.30 (0.20), residues: 785 sheet: 1.08 (0.24), residues: 408 loop : -1.70 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 78 HIS 0.004 0.001 HIS J 180 PHE 0.009 0.001 PHE B 82 TYR 0.016 0.001 TYR G 218 ARG 0.003 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 753) hydrogen bonds : angle 4.47109 ( 2115) covalent geometry : bond 0.00210 (19972) covalent geometry : angle 0.54066 (27385) *********************** 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 359 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 298 time to evaluate : 1.971 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6925 (ptp90) REVERT: F 187 ASP cc_start: 0.8388 (t0) cc_final: 0.8177 (t0) REVERT: H 115 VAL cc_start: 0.8330 (p) cc_final: 0.8114 (t) REVERT: I 49 SER cc_start: 0.8302 (p) cc_final: 0.7989 (p) REVERT: J 87 LYS cc_start: 0.4892 (OUTLIER) cc_final: 0.4454 (tttt) REVERT: J 98 LYS cc_start: 0.5491 (OUTLIER) cc_final: 0.5035 (mmtm) REVERT: K 315 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.5722 (t80) REVERT: K 332 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5903 (ttp-110) REVERT: K 333 TYR cc_start: 0.7533 (m-80) cc_final: 0.6965 (m-80) REVERT: G 218 TYR cc_start: 0.5676 (t80) cc_final: 0.4520 (t80) REVERT: B 91 MET cc_start: 0.4799 (OUTLIER) cc_final: 0.4392 (tpp) outliers start: 61 outliers final: 19 residues processed: 327 average time/residue: 1.1835 time to fit residues: 441.3495 Evaluate side-chains 299 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 52 PHE Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 228 LYS 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 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: 1.9990 chunk 41 optimal weight: 0.5980 chunk 206 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 205 optimal weight: 0.0070 chunk 11 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 ASN J 69 GLN J 225 GLN J 257 GLN K 164 ASN G 331 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.211141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.181727 restraints weight = 30409.436| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.18 r_work: 0.4256 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4145 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19972 Z= 0.111 Angle : 0.541 9.550 27385 Z= 0.279 Chirality : 0.039 0.179 3108 Planarity : 0.003 0.043 3350 Dihedral : 15.005 176.637 3463 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.04 % Favored : 92.75 % Rotamer: Outliers : 3.87 % Allowed : 26.88 % Favored : 69.25 % 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: -0.18 (0.18), residues: 2331 helix: 1.28 (0.20), residues: 799 sheet: 1.12 (0.24), residues: 403 loop : -1.71 (0.18), residues: 1129 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 0.011 0.001 PHE H 260 TYR 0.013 0.001 TYR K 360 ARG 0.003 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 753) hydrogen bonds : angle 4.36412 ( 2115) covalent geometry : bond 0.00240 (19972) covalent geometry : angle 0.54144 (27385) *********************** 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 351 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 278 time to evaluate : 1.859 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6108 (ptm160) REVERT: F 103 MET cc_start: 0.5076 (OUTLIER) cc_final: 0.4769 (ptt) REVERT: H 115 VAL cc_start: 0.8356 (p) cc_final: 0.8147 (t) REVERT: I 49 SER cc_start: 0.8338 (p) cc_final: 0.8006 (p) REVERT: I 103 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6690 (ppp) REVERT: J 87 LYS cc_start: 0.4837 (OUTLIER) cc_final: 0.4437 (tttt) REVERT: K 186 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.7022 (mp) REVERT: K 315 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.5702 (t80) REVERT: K 332 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5783 (ttp-110) REVERT: K 333 TYR cc_start: 0.7562 (m-80) cc_final: 0.6962 (m-80) REVERT: B 74 ARG cc_start: 0.3852 (OUTLIER) cc_final: 0.1471 (ttt180) REVERT: B 91 MET cc_start: 0.4813 (OUTLIER) cc_final: 0.4330 (tpp) REVERT: B 202 GLU cc_start: 0.1675 (OUTLIER) cc_final: 0.1093 (tp30) outliers start: 73 outliers final: 27 residues processed: 315 average time/residue: 1.1885 time to fit residues: 425.4585 Evaluate side-chains 308 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 103 MET 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 250 LYS Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 228 LYS 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 26 THR 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 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: 3.9990 chunk 130 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 92 ASN ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 257 GLN I 299 GLN I 349 ASN J 69 GLN J 82 GLN J 92 ASN J 225 GLN ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.202603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.173823 restraints weight = 29316.447| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.37 r_work: 0.4161 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4037 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 19972 Z= 0.246 Angle : 0.698 9.523 27385 Z= 0.366 Chirality : 0.045 0.228 3108 Planarity : 0.005 0.048 3350 Dihedral : 15.331 176.192 3463 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.79 % Favored : 90.99 % Rotamer: Outliers : 4.98 % Allowed : 27.04 % Favored : 67.97 % 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: -0.71 (0.17), residues: 2331 helix: 0.82 (0.19), residues: 785 sheet: 0.71 (0.24), residues: 380 loop : -1.88 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 326 HIS 0.006 0.001 HIS G 6 PHE 0.023 0.002 PHE G 210 TYR 0.015 0.002 TYR K 280 ARG 0.014 0.001 ARG K 113 Details of bonding type rmsd hydrogen bonds : bond 0.05304 ( 753) hydrogen bonds : angle 5.01868 ( 2115) covalent geometry : bond 0.00568 (19972) covalent geometry : angle 0.69765 (27385) *********************** 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 391 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 297 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6625 (ptm160) REVERT: F 62 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6099 (ptp-170) REVERT: F 103 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.4739 (ptt) REVERT: H 4 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6762 (mt-10) REVERT: H 150 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6425 (mt-10) REVERT: I 99 MET cc_start: 0.7598 (ttm) cc_final: 0.7341 (ttm) REVERT: J 87 LYS cc_start: 0.5003 (OUTLIER) cc_final: 0.4431 (tttt) REVERT: J 111 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5378 (mp) REVERT: J 312 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7276 (mpp80) REVERT: K 148 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7167 (ttt) REVERT: K 186 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6793 (mp) REVERT: K 216 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5777 (t80) REVERT: K 332 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.6029 (ttp-110) REVERT: K 333 TYR cc_start: 0.7694 (m-80) cc_final: 0.6952 (m-80) REVERT: G 218 TYR cc_start: 0.5945 (t80) cc_final: 0.5741 (t80) REVERT: B 74 ARG cc_start: 0.4330 (OUTLIER) cc_final: 0.1734 (ttt180) REVERT: B 91 MET cc_start: 0.4879 (OUTLIER) cc_final: 0.4293 (tpp) REVERT: B 202 GLU cc_start: 0.1940 (OUTLIER) cc_final: 0.1136 (tp30) outliers start: 94 outliers final: 44 residues processed: 348 average time/residue: 1.3992 time to fit residues: 558.6693 Evaluate side-chains 347 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 292 LYS 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 133 ILE Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 225 GLN Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 315 TYR Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 SER 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: 1.9990 chunk 17 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 183 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 195 optimal weight: 0.5980 chunk 235 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 ASN H 50 ASN H 339 HIS I 349 ASN J 69 GLN ** G 6 HIS ** 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 = 0.4595 r_free = 0.4595 target = 0.204393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.175612 restraints weight = 29399.969| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.10 r_work: 0.4197 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4083 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19972 Z= 0.147 Angle : 0.603 9.445 27385 Z= 0.313 Chirality : 0.041 0.196 3108 Planarity : 0.004 0.045 3350 Dihedral : 15.221 177.668 3463 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.34 % Favored : 92.49 % Rotamer: Outliers : 3.61 % Allowed : 28.79 % Favored : 67.60 % 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: -0.55 (0.17), residues: 2331 helix: 1.04 (0.19), residues: 789 sheet: 0.62 (0.23), residues: 400 loop : -1.83 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 326 HIS 0.019 0.001 HIS G 6 PHE 0.015 0.001 PHE F 260 TYR 0.012 0.001 TYR K 360 ARG 0.011 0.000 ARG K 113 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 753) hydrogen bonds : angle 4.69461 ( 2115) covalent geometry : bond 0.00336 (19972) covalent geometry : angle 0.60303 (27385) *********************** 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 361 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 293 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6393 (ptm160) REVERT: F 103 MET cc_start: 0.5227 (OUTLIER) cc_final: 0.4859 (ptt) REVERT: F 228 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.7008 (ttpt) REVERT: H 4 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6740 (mt-10) REVERT: H 115 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8132 (t) REVERT: I 99 MET cc_start: 0.7342 (ttm) cc_final: 0.7059 (ttm) REVERT: J 87 LYS cc_start: 0.4841 (OUTLIER) cc_final: 0.4317 (tttt) REVERT: K 148 MET cc_start: 0.7354 (ppp) cc_final: 0.7050 (ttt) REVERT: K 332 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5990 (ttp-110) REVERT: K 333 TYR cc_start: 0.7597 (m-80) cc_final: 0.6870 (m-80) REVERT: G 6 HIS cc_start: 0.6053 (OUTLIER) cc_final: 0.3269 (m170) REVERT: B 74 ARG cc_start: 0.4272 (OUTLIER) cc_final: 0.1804 (ttt180) REVERT: B 82 PHE cc_start: 0.3357 (t80) cc_final: 0.3040 (t80) REVERT: B 91 MET cc_start: 0.4938 (OUTLIER) cc_final: 0.4356 (tpp) REVERT: B 202 GLU cc_start: 0.1953 (OUTLIER) cc_final: 0.0948 (tp30) outliers start: 68 outliers final: 37 residues processed: 333 average time/residue: 1.2313 time to fit residues: 465.5184 Evaluate side-chains 331 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 284 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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 228 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 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 323 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 95 ASP 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 227 VAL Chi-restraints excluded: chain K residue 228 LYS 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 G residue 6 HIS Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain 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 266 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 113 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 ASN I 349 ASN J 69 GLN J 225 GLN K 264 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.199988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.171209 restraints weight = 28715.328| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.10 r_work: 0.4152 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 19972 Z= 0.214 Angle : 0.683 10.073 27385 Z= 0.357 Chirality : 0.044 0.214 3108 Planarity : 0.005 0.048 3350 Dihedral : 15.410 177.328 3463 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.79 % Favored : 90.99 % Rotamer: Outliers : 4.98 % Allowed : 27.89 % Favored : 67.13 % 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: -0.84 (0.17), residues: 2331 helix: 0.79 (0.19), residues: 794 sheet: 0.50 (0.24), residues: 382 loop : -1.99 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 326 HIS 0.018 0.001 HIS G 6 PHE 0.021 0.002 PHE H 260 TYR 0.024 0.002 TYR I 316 ARG 0.009 0.001 ARG K 113 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 753) hydrogen bonds : angle 5.00538 ( 2115) covalent geometry : bond 0.00494 (19972) covalent geometry : angle 0.68287 (27385) *********************** 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 382 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 288 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6565 (ptm160) REVERT: F 62 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6017 (ptp-170) REVERT: F 103 MET cc_start: 0.5494 (OUTLIER) cc_final: 0.5251 (ptt) REVERT: F 111 LEU cc_start: 0.7500 (mp) cc_final: 0.7237 (tt) REVERT: H 4 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6747 (mt-10) REVERT: I 99 MET cc_start: 0.7335 (ttm) cc_final: 0.7107 (ttm) REVERT: J 62 ARG cc_start: 0.7359 (tpp-160) cc_final: 0.6886 (ttt180) REVERT: J 87 LYS cc_start: 0.4863 (OUTLIER) cc_final: 0.4281 (tttt) REVERT: J 111 LEU cc_start: 0.5624 (OUTLIER) cc_final: 0.5384 (mp) REVERT: K 148 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7135 (ttt) REVERT: K 332 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.6147 (ttp-110) REVERT: K 333 TYR cc_start: 0.7696 (m-80) cc_final: 0.6880 (m-80) REVERT: G 298 GLU cc_start: 0.7951 (tt0) cc_final: 0.7740 (pt0) REVERT: G 342 LEU cc_start: 0.4711 (OUTLIER) cc_final: 0.3906 (mt) REVERT: B 74 ARG cc_start: 0.4604 (OUTLIER) cc_final: 0.1936 (ttt180) REVERT: B 91 MET cc_start: 0.5019 (OUTLIER) cc_final: 0.4434 (tpp) REVERT: B 233 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5873 (tt) outliers start: 94 outliers final: 47 residues processed: 341 average time/residue: 1.2214 time to fit residues: 472.6427 Evaluate side-chains 343 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 285 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 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 293 GLU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 338 LYS 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 315 TYR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 148 MET 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 6 HIS Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 179 THR 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 211 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 47 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 9 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 ASN H 50 ASN H 131 ASN I 349 ASN J 69 GLN J 225 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.202451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.174033 restraints weight = 29234.466| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.11 r_work: 0.4182 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19972 Z= 0.134 Angle : 0.608 11.880 27385 Z= 0.315 Chirality : 0.041 0.189 3108 Planarity : 0.004 0.045 3350 Dihedral : 15.229 178.358 3463 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.04 % Favored : 92.79 % Rotamer: Outliers : 3.61 % Allowed : 29.32 % Favored : 67.07 % 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: -0.60 (0.17), residues: 2331 helix: 1.11 (0.19), residues: 789 sheet: 0.48 (0.24), residues: 397 loop : -1.89 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 78 HIS 0.009 0.001 HIS G 6 PHE 0.031 0.001 PHE G 29 TYR 0.013 0.001 TYR K 360 ARG 0.008 0.000 ARG K 113 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 753) hydrogen bonds : angle 4.69944 ( 2115) covalent geometry : bond 0.00299 (19972) covalent geometry : angle 0.60808 (27385) *********************** 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 365 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 297 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6385 (ptm160) REVERT: F 62 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6045 (ptp-170) REVERT: F 111 LEU cc_start: 0.7499 (mp) cc_final: 0.7261 (tt) REVERT: F 117 ASP cc_start: 0.6538 (m-30) cc_final: 0.6168 (m-30) REVERT: H 4 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6726 (mt-10) REVERT: H 150 GLU cc_start: 0.6342 (mt-10) cc_final: 0.6129 (mt-10) REVERT: I 99 MET cc_start: 0.7321 (ttm) cc_final: 0.7088 (ttm) REVERT: J 62 ARG cc_start: 0.7277 (tpp-160) cc_final: 0.6769 (ttt180) REVERT: J 87 LYS cc_start: 0.4787 (OUTLIER) cc_final: 0.4230 (tttt) REVERT: J 312 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7237 (mpp80) REVERT: K 148 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7092 (ttt) REVERT: G 298 GLU cc_start: 0.7958 (tt0) cc_final: 0.7724 (pt0) REVERT: B 74 ARG cc_start: 0.4432 (OUTLIER) cc_final: 0.1927 (ttt180) REVERT: B 91 MET cc_start: 0.5255 (OUTLIER) cc_final: 0.4959 (tpp) REVERT: B 233 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5814 (tt) outliers start: 68 outliers final: 39 residues processed: 332 average time/residue: 1.2288 time to fit residues: 463.2193 Evaluate side-chains 332 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 2.102 ------------------------------------------------------------------------------- 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 177 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 304 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 75 THR Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain 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 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 95 ASP 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 148 MET Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain 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: 0.8980 chunk 66 optimal weight: 0.0070 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 214 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 ASN H 50 ASN J 69 GLN J 225 GLN G 17 ASN ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.202871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.174621 restraints weight = 29225.633| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 2.12 r_work: 0.4189 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4074 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.3161 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= 0.125 Angle : 0.600 11.732 27385 Z= 0.309 Chirality : 0.041 0.181 3108 Planarity : 0.004 0.044 3350 Dihedral : 15.122 177.657 3463 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.98 % Favored : 91.85 % Rotamer: Outliers : 3.71 % Allowed : 29.22 % Favored : 67.07 % 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: 1.22 (0.19), residues: 792 sheet: 0.71 (0.24), residues: 391 loop : -1.85 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 78 HIS 0.008 0.001 HIS G 6 PHE 0.032 0.001 PHE G 29 TYR 0.022 0.001 TYR G 218 ARG 0.009 0.000 ARG K 332 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 753) hydrogen bonds : angle 4.56528 ( 2115) covalent geometry : bond 0.00279 (19972) covalent geometry : angle 0.60048 (27385) *********************** 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 354 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 284 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6274 (ptm160) REVERT: F 62 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.5946 (ptp-170) REVERT: F 111 LEU cc_start: 0.7463 (mp) cc_final: 0.7230 (tt) REVERT: F 117 ASP cc_start: 0.6447 (m-30) cc_final: 0.6046 (m-30) REVERT: H 4 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6733 (mt-10) REVERT: I 99 MET cc_start: 0.7188 (ttm) cc_final: 0.6985 (ttm) REVERT: I 103 MET cc_start: 0.7600 (pp-130) cc_final: 0.7357 (pp-130) REVERT: J 62 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.6761 (ttt180) REVERT: J 87 LYS cc_start: 0.4831 (OUTLIER) cc_final: 0.4301 (tttt) REVERT: J 111 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5101 (mp) REVERT: J 312 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7219 (mpp80) REVERT: K 148 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7042 (ttt) REVERT: G 298 GLU cc_start: 0.7985 (tt0) cc_final: 0.7720 (pt0) REVERT: B 74 ARG cc_start: 0.4381 (OUTLIER) cc_final: 0.1911 (ttt180) REVERT: B 91 MET cc_start: 0.5358 (OUTLIER) cc_final: 0.5065 (tpp) REVERT: B 233 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5852 (tt) outliers start: 70 outliers final: 40 residues processed: 324 average time/residue: 1.2942 time to fit residues: 476.7265 Evaluate side-chains 334 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 ILE 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 220 SER Chi-restraints excluded: chain H residue 315 TYR 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 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 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 148 MET Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain 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: 2.9990 chunk 26 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 118 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 257 GLN I 349 ASN J 69 GLN J 225 GLN ** 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 = 0.4553 r_free = 0.4553 target = 0.199552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.171372 restraints weight = 28882.743| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.10 r_work: 0.4155 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19972 Z= 0.178 Angle : 0.665 14.715 27385 Z= 0.343 Chirality : 0.043 0.201 3108 Planarity : 0.004 0.044 3350 Dihedral : 15.197 178.065 3463 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.85 % Favored : 91.98 % Rotamer: Outliers : 3.18 % Allowed : 29.85 % Favored : 66.97 % 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: -0.66 (0.17), residues: 2331 helix: 1.01 (0.19), residues: 797 sheet: 0.57 (0.25), residues: 382 loop : -1.93 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 326 HIS 0.009 0.001 HIS G 6 PHE 0.020 0.002 PHE H 260 TYR 0.016 0.002 TYR F 315 ARG 0.014 0.001 ARG K 113 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 753) hydrogen bonds : angle 4.80738 ( 2115) covalent geometry : bond 0.00412 (19972) covalent geometry : angle 0.66494 (27385) ********************** 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 356 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 296 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6420 (ptm160) REVERT: F 62 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.5967 (ptp-170) REVERT: F 111 LEU cc_start: 0.7467 (mp) cc_final: 0.7256 (tt) REVERT: F 117 ASP cc_start: 0.6656 (m-30) cc_final: 0.6303 (m-30) REVERT: F 226 LEU cc_start: 0.5766 (tp) cc_final: 0.5444 (tp) REVERT: H 4 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6707 (mt-10) REVERT: I 103 MET cc_start: 0.7646 (pp-130) cc_final: 0.7375 (pp-130) REVERT: J 62 ARG cc_start: 0.7340 (tpp-160) cc_final: 0.6883 (ttt180) REVERT: J 87 LYS cc_start: 0.4890 (OUTLIER) cc_final: 0.4321 (tttt) REVERT: J 111 LEU cc_start: 0.5507 (OUTLIER) cc_final: 0.5201 (mp) REVERT: K 148 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7019 (ttt) REVERT: G 298 GLU cc_start: 0.8053 (tt0) cc_final: 0.7754 (pt0) REVERT: B 74 ARG cc_start: 0.4526 (OUTLIER) cc_final: 0.3821 (mtm-85) REVERT: B 91 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.5126 (tpp) REVERT: B 233 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6042 (tt) outliers start: 60 outliers final: 45 residues processed: 327 average time/residue: 1.5974 time to fit residues: 596.7668 Evaluate side-chains 346 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 293 time to evaluate : 4.181 ------------------------------------------------------------------------------- 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 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 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 231 LYS Chi-restraints excluded: chain H residue 315 TYR 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 68 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 107 LYS Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 193 ASP 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 148 MET Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 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: 0.9990 chunk 222 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 31 optimal weight: 0.0570 chunk 83 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.201936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.173844 restraints weight = 29225.710| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.11 r_work: 0.4183 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19972 Z= 0.125 Angle : 0.612 13.328 27385 Z= 0.314 Chirality : 0.041 0.182 3108 Planarity : 0.004 0.056 3350 Dihedral : 15.065 178.318 3463 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.25 % Favored : 92.58 % Rotamer: Outliers : 2.65 % Allowed : 30.59 % Favored : 66.76 % 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: 1.21 (0.19), residues: 790 sheet: 0.67 (0.25), residues: 387 loop : -1.84 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 78 HIS 0.006 0.001 HIS G 6 PHE 0.039 0.001 PHE G 29 TYR 0.022 0.001 TYR G 218 ARG 0.013 0.000 ARG K 113 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 753) hydrogen bonds : angle 4.59021 ( 2115) covalent geometry : bond 0.00280 (19972) covalent geometry : angle 0.61198 (27385) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27323.21 seconds wall clock time: 482 minutes 58.36 seconds (28978.36 seconds total)