Starting phenix.real_space_refine on Wed May 14 14:34:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oi6_16887/05_2025/8oi6_16887.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oi6_16887/05_2025/8oi6_16887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oi6_16887/05_2025/8oi6_16887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oi6_16887/05_2025/8oi6_16887.map" model { file = "/net/cci-nas-00/data/ceres_data/8oi6_16887/05_2025/8oi6_16887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oi6_16887/05_2025/8oi6_16887.cif" } resolution = 3.59 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= 0.214 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 83 5.16 5 C 7304 2.51 5 N 1945 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11573 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2767 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 18, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.34, per 1000 atoms: 0.72 Number of scatterers: 11573 At special positions: 0 Unit cell: (94.38, 89.54, 165.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 83 16.00 P 8 15.00 Mg 4 11.99 O 2229 8.00 N 1945 7.00 C 7304 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.6 seconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 22 sheets defined 49.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.569A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.864A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.699A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 214 removed outlier: 4.041A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.783A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.599A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 4.050A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.007A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.531A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.570A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.293A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.518A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.678A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.797A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.518A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.165A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.958A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.568A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.908A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.680A pdb=" N SER B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.500A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.691A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.810A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.507A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.549A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.733A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.430A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.501A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.916A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.585A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.567A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.652A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.585A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.746A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.513A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.851A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.550A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.658A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.602A pdb=" N MET D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.019A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 354 removed outlier: 4.011A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.565A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.839A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 7.171A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.667A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.698A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.574A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.654A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C 106 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.815A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.705A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.071A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR D 133 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.755A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 removed outlier: 5.947A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 529 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3734 1.34 - 1.46: 2694 1.46 - 1.58: 5233 1.58 - 1.70: 18 1.70 - 1.82: 143 Bond restraints: 11822 Sorted by residual: bond pdb=" N HYP I 6 " pdb=" CD HYP I 6 " ideal model delta sigma weight residual 1.473 1.636 -0.163 1.40e-02 5.10e+03 1.36e+02 bond pdb=" N HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.473 1.635 -0.162 1.40e-02 5.10e+03 1.35e+02 bond pdb=" N HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.473 1.635 -0.162 1.40e-02 5.10e+03 1.33e+02 bond pdb=" CG HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.530 1.371 0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" CG HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.530 1.372 0.158 2.00e-02 2.50e+03 6.23e+01 ... (remaining 11817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 15688 1.80 - 3.60: 254 3.60 - 5.39: 66 5.39 - 7.19: 30 7.19 - 8.99: 7 Bond angle restraints: 16045 Sorted by residual: angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.42 -4.42 1.10e+00 8.26e-01 1.61e+01 angle pdb=" N HYP H 6 " pdb=" CD HYP H 6 " pdb=" CG HYP H 6 " ideal model delta sigma weight residual 103.20 109.04 -5.84 1.50e+00 4.44e-01 1.52e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 116.88 -6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N HYP J 6 " pdb=" CA HYP J 6 " pdb=" CB HYP J 6 " ideal model delta sigma weight residual 103.00 106.86 -3.86 1.10e+00 8.26e-01 1.23e+01 angle pdb=" N HYP I 6 " pdb=" CA HYP I 6 " pdb=" CB HYP I 6 " ideal model delta sigma weight residual 103.00 106.84 -3.84 1.10e+00 8.26e-01 1.22e+01 ... (remaining 16040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 6878 33.98 - 67.96: 224 67.96 - 101.94: 17 101.94 - 135.92: 4 135.92 - 169.90: 3 Dihedral angle restraints: 7126 sinusoidal: 2885 harmonic: 4241 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 130.10 169.90 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 131.78 168.22 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 137.14 162.86 1 2.00e+01 2.50e-03 4.69e+01 ... (remaining 7123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1562 0.061 - 0.122: 226 0.122 - 0.184: 4 0.184 - 0.245: 0 0.245 - 0.306: 3 Chirality restraints: 1795 Sorted by residual: chirality pdb=" CA HYP I 6 " pdb=" N HYP I 6 " pdb=" C HYP I 6 " pdb=" CB HYP I 6 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA HYP J 6 " pdb=" N HYP J 6 " pdb=" C HYP J 6 " pdb=" CB HYP J 6 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA HYP H 6 " pdb=" N HYP H 6 " pdb=" C HYP H 6 " pdb=" CB HYP H 6 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1792 not shown) Planarity restraints: 2037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 117 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" CD GLU A 117 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 117 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 117 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 166 " -0.011 2.00e-02 2.50e+03 1.15e-02 2.63e+00 pdb=" CG TYR C 166 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 166 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 166 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 166 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 166 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 166 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 166 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 366 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 367 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.022 5.00e-02 4.00e+02 ... (remaining 2034 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 45 2.43 - 3.04: 7139 3.04 - 3.66: 17282 3.66 - 4.28: 26390 4.28 - 4.90: 43999 Nonbonded interactions: 94855 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.808 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.810 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.820 3.620 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.126 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.137 2.170 ... (remaining 94850 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 'A' and (resid 6 through 362 or resid 401 through 402)) selection = (chain 'B' and (resid 6 through 362 or resid 401 through 402)) selection = (chain 'C' and (resid 6 through 362 or resid 401 through 402)) selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.080 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 0.163 11828 Z= 0.303 Angle : 0.648 10.099 16063 Z= 0.305 Chirality : 0.043 0.306 1795 Planarity : 0.003 0.040 2031 Dihedral : 16.973 169.900 4386 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 0.24 % Allowed : 17.74 % Favored : 82.02 % 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: 0.35 (0.23), residues: 1418 helix: 0.06 (0.22), residues: 538 sheet: 0.56 (0.37), residues: 212 loop : 0.49 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 86 HIS 0.011 0.001 HIS B 371 PHE 0.008 0.001 PHE A 124 TYR 0.028 0.001 TYR C 166 ARG 0.003 0.000 ARG A 116 Details of bonding type rmsd link_TRANS : bond 0.01252 ( 6) link_TRANS : angle 2.98562 ( 18) hydrogen bonds : bond 0.30317 ( 525) hydrogen bonds : angle 8.74333 ( 1329) covalent geometry : bond 0.00523 (11822) covalent geometry : angle 0.64020 (16045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 88 average time/residue: 0.2037 time to fit residues: 28.1210 Evaluate side-chains 84 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 225 GLN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.072961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.062003 restraints weight = 33811.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064124 restraints weight = 17411.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065578 restraints weight = 10898.272| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11828 Z= 0.269 Angle : 0.691 7.003 16063 Z= 0.337 Chirality : 0.047 0.175 1795 Planarity : 0.004 0.038 2031 Dihedral : 11.989 176.450 1673 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.97 % Favored : 97.95 % Rotamer: Outliers : 2.28 % Allowed : 16.60 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1418 helix: 0.19 (0.22), residues: 581 sheet: 0.45 (0.34), residues: 250 loop : 0.54 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 1 HIS 0.005 0.002 HIS B 101 PHE 0.018 0.002 PHE C 352 TYR 0.017 0.002 TYR B 143 ARG 0.003 0.001 ARG A 183 Details of bonding type rmsd link_TRANS : bond 0.00530 ( 6) link_TRANS : angle 0.89183 ( 18) hydrogen bonds : bond 0.05094 ( 525) hydrogen bonds : angle 5.82805 ( 1329) covalent geometry : bond 0.00622 (11822) covalent geometry : angle 0.69055 (16045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 1.333 Fit side-chains REVERT: A 80 ASP cc_start: 0.7978 (t0) cc_final: 0.7650 (t0) REVERT: B 123 MET cc_start: 0.8284 (mmm) cc_final: 0.7967 (mmt) REVERT: B 314 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: C 330 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9206 (tp) REVERT: D 355 MET cc_start: 0.7588 (pmm) cc_final: 0.7279 (pmm) outliers start: 28 outliers final: 13 residues processed: 102 average time/residue: 0.1798 time to fit residues: 29.7285 Evaluate side-chains 91 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 194 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 80 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063362 restraints weight = 33971.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065569 restraints weight = 17210.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.067045 restraints weight = 10612.990| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11828 Z= 0.124 Angle : 0.568 7.157 16063 Z= 0.267 Chirality : 0.044 0.202 1795 Planarity : 0.004 0.036 2031 Dihedral : 10.944 160.464 1668 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.90 % Favored : 98.03 % Rotamer: Outliers : 1.71 % Allowed : 17.82 % Favored : 80.47 % 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 (0.23), residues: 1418 helix: 0.51 (0.22), residues: 582 sheet: 0.41 (0.34), residues: 253 loop : 0.65 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.003 0.001 HIS D 87 PHE 0.013 0.001 PHE D 31 TYR 0.014 0.001 TYR B 143 ARG 0.003 0.000 ARG C 116 Details of bonding type rmsd link_TRANS : bond 0.00202 ( 6) link_TRANS : angle 0.37637 ( 18) hydrogen bonds : bond 0.03550 ( 525) hydrogen bonds : angle 5.26337 ( 1329) covalent geometry : bond 0.00282 (11822) covalent geometry : angle 0.56822 (16045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 1.380 Fit side-chains REVERT: A 80 ASP cc_start: 0.7998 (t0) cc_final: 0.7544 (t0) REVERT: B 132 MET cc_start: 0.8121 (ttp) cc_final: 0.7469 (ttp) REVERT: B 314 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: C 82 MET cc_start: 0.8527 (tpt) cc_final: 0.8307 (tpt) outliers start: 21 outliers final: 10 residues processed: 100 average time/residue: 0.1941 time to fit residues: 30.8316 Evaluate side-chains 89 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 chunk 109 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS B 12 ASN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN D 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.059811 restraints weight = 34397.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061920 restraints weight = 17813.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063338 restraints weight = 11125.052| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 11828 Z= 0.318 Angle : 0.702 6.953 16063 Z= 0.339 Chirality : 0.048 0.210 1795 Planarity : 0.004 0.040 2031 Dihedral : 10.258 145.945 1668 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.11 % Rotamer: Outliers : 3.09 % Allowed : 17.82 % Favored : 79.09 % 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: 0.36 (0.23), residues: 1418 helix: 0.34 (0.22), residues: 584 sheet: 0.25 (0.34), residues: 253 loop : 0.36 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.013 0.002 HIS B 371 PHE 0.019 0.002 PHE C 352 TYR 0.016 0.002 TYR B 143 ARG 0.006 0.001 ARG B 290 Details of bonding type rmsd link_TRANS : bond 0.00525 ( 6) link_TRANS : angle 0.65861 ( 18) hydrogen bonds : bond 0.04000 ( 525) hydrogen bonds : angle 5.33155 ( 1329) covalent geometry : bond 0.00738 (11822) covalent geometry : angle 0.70192 (16045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 1.262 Fit side-chains REVERT: A 80 ASP cc_start: 0.8133 (t0) cc_final: 0.7573 (t0) REVERT: B 132 MET cc_start: 0.8380 (ttp) cc_final: 0.7793 (ttp) REVERT: B 314 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: D 180 LEU cc_start: 0.7728 (tp) cc_final: 0.7508 (tp) REVERT: I 5 CYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8159 (p) outliers start: 38 outliers final: 21 residues processed: 110 average time/residue: 0.1795 time to fit residues: 31.4847 Evaluate side-chains 99 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.073464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062578 restraints weight = 33623.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.064768 restraints weight = 17103.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066228 restraints weight = 10556.266| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11828 Z= 0.126 Angle : 0.566 7.197 16063 Z= 0.264 Chirality : 0.044 0.200 1795 Planarity : 0.004 0.037 2031 Dihedral : 9.739 140.865 1668 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.90 % Favored : 98.03 % Rotamer: Outliers : 1.63 % Allowed : 19.28 % Favored : 79.09 % 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: 0.72 (0.23), residues: 1418 helix: 0.69 (0.23), residues: 580 sheet: 0.28 (0.34), residues: 253 loop : 0.59 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 340 HIS 0.008 0.001 HIS B 371 PHE 0.012 0.001 PHE D 31 TYR 0.008 0.001 TYR A 143 ARG 0.003 0.000 ARG D 147 Details of bonding type rmsd link_TRANS : bond 0.00223 ( 6) link_TRANS : angle 0.36445 ( 18) hydrogen bonds : bond 0.02935 ( 525) hydrogen bonds : angle 4.92835 ( 1329) covalent geometry : bond 0.00288 (11822) covalent geometry : angle 0.56607 (16045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.449 Fit side-chains REVERT: A 80 ASP cc_start: 0.7989 (t0) cc_final: 0.7382 (t0) REVERT: A 283 MET cc_start: 0.8782 (mmm) cc_final: 0.8576 (mmm) REVERT: B 314 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: C 82 MET cc_start: 0.8407 (tpt) cc_final: 0.8194 (tpt) REVERT: D 180 LEU cc_start: 0.7615 (tp) cc_final: 0.7313 (tp) REVERT: H 5 CYS cc_start: 0.6751 (t) cc_final: 0.5825 (m) REVERT: I 5 CYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8045 (p) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 0.1891 time to fit residues: 29.6469 Evaluate side-chains 93 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 10 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.073181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.062304 restraints weight = 33956.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064484 restraints weight = 17253.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.065945 restraints weight = 10644.171| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11828 Z= 0.127 Angle : 0.565 6.533 16063 Z= 0.260 Chirality : 0.044 0.201 1795 Planarity : 0.003 0.036 2031 Dihedral : 9.206 135.213 1668 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.67 % Rotamer: Outliers : 1.95 % Allowed : 19.28 % Favored : 78.76 % 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: 0.76 (0.23), residues: 1418 helix: 0.73 (0.23), residues: 592 sheet: 0.26 (0.33), residues: 253 loop : 0.63 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.007 0.001 HIS B 371 PHE 0.011 0.001 PHE D 31 TYR 0.008 0.001 TYR C 294 ARG 0.003 0.000 ARG D 147 Details of bonding type rmsd link_TRANS : bond 0.00226 ( 6) link_TRANS : angle 0.33843 ( 18) hydrogen bonds : bond 0.02832 ( 525) hydrogen bonds : angle 4.82733 ( 1329) covalent geometry : bond 0.00296 (11822) covalent geometry : angle 0.56495 (16045) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 1.288 Fit side-chains REVERT: A 80 ASP cc_start: 0.8007 (t0) cc_final: 0.7508 (t0) REVERT: B 118 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7706 (tptm) REVERT: B 132 MET cc_start: 0.8081 (ttp) cc_final: 0.7475 (ttp) REVERT: B 314 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: D 180 LEU cc_start: 0.7568 (tp) cc_final: 0.7230 (tp) REVERT: H 5 CYS cc_start: 0.6878 (t) cc_final: 0.5898 (m) REVERT: I 5 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8057 (p) REVERT: J 5 CYS cc_start: 0.7673 (m) cc_final: 0.7412 (t) outliers start: 24 outliers final: 13 residues processed: 100 average time/residue: 0.1829 time to fit residues: 29.2609 Evaluate side-chains 95 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 116 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.073310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.062352 restraints weight = 34563.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.064495 restraints weight = 17612.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065940 restraints weight = 10894.857| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11828 Z= 0.163 Angle : 0.594 7.499 16063 Z= 0.275 Chirality : 0.044 0.205 1795 Planarity : 0.003 0.037 2031 Dihedral : 8.945 133.697 1668 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.67 % Rotamer: Outliers : 2.52 % Allowed : 19.04 % Favored : 78.44 % 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 (0.23), residues: 1418 helix: 0.71 (0.23), residues: 593 sheet: 0.20 (0.33), residues: 253 loop : 0.58 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 340 HIS 0.007 0.001 HIS B 371 PHE 0.011 0.001 PHE D 31 TYR 0.015 0.001 TYR C 166 ARG 0.004 0.000 ARG C 116 Details of bonding type rmsd link_TRANS : bond 0.00287 ( 6) link_TRANS : angle 0.38272 ( 18) hydrogen bonds : bond 0.02929 ( 525) hydrogen bonds : angle 4.81335 ( 1329) covalent geometry : bond 0.00382 (11822) covalent geometry : angle 0.59387 (16045) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8072 (t0) cc_final: 0.7543 (t0) REVERT: B 118 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7704 (tptm) REVERT: B 132 MET cc_start: 0.8167 (ttp) cc_final: 0.7519 (ttp) REVERT: B 314 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: H 5 CYS cc_start: 0.6962 (t) cc_final: 0.5951 (m) REVERT: I 5 CYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8210 (p) REVERT: J 5 CYS cc_start: 0.7666 (m) cc_final: 0.7384 (t) outliers start: 31 outliers final: 22 residues processed: 108 average time/residue: 0.1894 time to fit residues: 33.0336 Evaluate side-chains 104 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.073239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062194 restraints weight = 34469.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064341 restraints weight = 17684.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.065792 restraints weight = 10976.786| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11828 Z= 0.156 Angle : 0.589 7.757 16063 Z= 0.273 Chirality : 0.044 0.204 1795 Planarity : 0.003 0.037 2031 Dihedral : 8.751 140.138 1668 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.40 % Favored : 97.53 % Rotamer: Outliers : 2.20 % Allowed : 19.37 % Favored : 78.44 % 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: 0.73 (0.23), residues: 1418 helix: 0.75 (0.23), residues: 593 sheet: 0.19 (0.34), residues: 250 loop : 0.57 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.006 0.001 HIS B 371 PHE 0.012 0.001 PHE D 31 TYR 0.012 0.001 TYR B 143 ARG 0.002 0.000 ARG D 147 Details of bonding type rmsd link_TRANS : bond 0.00271 ( 6) link_TRANS : angle 0.37949 ( 18) hydrogen bonds : bond 0.02896 ( 525) hydrogen bonds : angle 4.79150 ( 1329) covalent geometry : bond 0.00364 (11822) covalent geometry : angle 0.58901 (16045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8085 (t0) cc_final: 0.7585 (t0) REVERT: B 118 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7792 (tptm) REVERT: B 132 MET cc_start: 0.8155 (ttp) cc_final: 0.7513 (ttp) REVERT: B 314 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: H 5 CYS cc_start: 0.6998 (t) cc_final: 0.6050 (m) REVERT: I 5 CYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8177 (p) REVERT: J 5 CYS cc_start: 0.7624 (m) cc_final: 0.7383 (t) outliers start: 27 outliers final: 21 residues processed: 103 average time/residue: 0.1791 time to fit residues: 29.5926 Evaluate side-chains 102 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 111 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062881 restraints weight = 34262.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065021 restraints weight = 17569.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066438 restraints weight = 10907.567| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11828 Z= 0.127 Angle : 0.579 9.383 16063 Z= 0.266 Chirality : 0.044 0.202 1795 Planarity : 0.003 0.036 2031 Dihedral : 8.566 144.220 1668 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.90 % Favored : 98.03 % Rotamer: Outliers : 2.03 % Allowed : 19.53 % Favored : 78.44 % 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: 0.80 (0.23), residues: 1418 helix: 0.81 (0.23), residues: 593 sheet: 0.14 (0.33), residues: 253 loop : 0.67 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.006 0.001 HIS B 371 PHE 0.012 0.001 PHE D 31 TYR 0.017 0.001 TYR C 166 ARG 0.002 0.000 ARG D 147 Details of bonding type rmsd link_TRANS : bond 0.00216 ( 6) link_TRANS : angle 0.34583 ( 18) hydrogen bonds : bond 0.02754 ( 525) hydrogen bonds : angle 4.72367 ( 1329) covalent geometry : bond 0.00296 (11822) covalent geometry : angle 0.57915 (16045) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8008 (t0) cc_final: 0.7513 (t0) REVERT: B 118 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7676 (tptm) REVERT: B 314 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: D 227 MET cc_start: 0.8901 (mmm) cc_final: 0.8600 (mmm) REVERT: I 5 CYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8162 (p) REVERT: J 5 CYS cc_start: 0.7659 (m) cc_final: 0.7361 (t) outliers start: 25 outliers final: 20 residues processed: 99 average time/residue: 0.1864 time to fit residues: 29.5680 Evaluate side-chains 101 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 107 optimal weight: 0.0370 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.063812 restraints weight = 34027.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065969 restraints weight = 17208.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067400 restraints weight = 10562.723| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11828 Z= 0.110 Angle : 0.565 8.315 16063 Z= 0.259 Chirality : 0.043 0.201 1795 Planarity : 0.003 0.036 2031 Dihedral : 8.374 147.400 1668 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.90 % Favored : 98.03 % Rotamer: Outliers : 1.63 % Allowed : 20.02 % Favored : 78.36 % 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: 0.76 (0.23), residues: 1418 helix: 0.78 (0.22), residues: 603 sheet: 0.17 (0.33), residues: 253 loop : 0.60 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS B 371 PHE 0.013 0.001 PHE D 31 TYR 0.007 0.001 TYR A 143 ARG 0.002 0.000 ARG D 147 Details of bonding type rmsd link_TRANS : bond 0.00175 ( 6) link_TRANS : angle 0.30931 ( 18) hydrogen bonds : bond 0.02596 ( 525) hydrogen bonds : angle 4.64671 ( 1329) covalent geometry : bond 0.00255 (11822) covalent geometry : angle 0.56495 (16045) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8043 (t0) cc_final: 0.7484 (t0) REVERT: B 118 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7631 (tptm) REVERT: B 132 MET cc_start: 0.7973 (ttp) cc_final: 0.7232 (ttp) REVERT: B 314 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: D 227 MET cc_start: 0.8889 (mmm) cc_final: 0.8569 (mmm) REVERT: I 5 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8123 (p) REVERT: J 5 CYS cc_start: 0.7725 (m) cc_final: 0.7435 (t) outliers start: 20 outliers final: 16 residues processed: 95 average time/residue: 0.1997 time to fit residues: 30.2137 Evaluate side-chains 98 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 117 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.074645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063666 restraints weight = 34053.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065858 restraints weight = 17343.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067307 restraints weight = 10719.172| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11828 Z= 0.103 Angle : 0.559 8.607 16063 Z= 0.255 Chirality : 0.043 0.199 1795 Planarity : 0.003 0.037 2031 Dihedral : 8.141 145.976 1668 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.76 % Favored : 98.17 % Rotamer: Outliers : 1.71 % Allowed : 20.10 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1418 helix: 0.88 (0.22), residues: 600 sheet: 0.27 (0.32), residues: 271 loop : 0.68 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 86 HIS 0.005 0.001 HIS B 371 PHE 0.012 0.001 PHE D 31 TYR 0.018 0.001 TYR C 166 ARG 0.002 0.000 ARG D 147 Details of bonding type rmsd link_TRANS : bond 0.00160 ( 6) link_TRANS : angle 0.28972 ( 18) hydrogen bonds : bond 0.02519 ( 525) hydrogen bonds : angle 4.59777 ( 1329) covalent geometry : bond 0.00239 (11822) covalent geometry : angle 0.55897 (16045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2947.19 seconds wall clock time: 53 minutes 11.56 seconds (3191.56 seconds total)