Starting phenix.real_space_refine on Sat Aug 23 11:54:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oi6_16887/08_2025/8oi6_16887.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oi6_16887/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8oi6_16887/08_2025/8oi6_16887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oi6_16887/08_2025/8oi6_16887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oi6_16887/08_2025/8oi6_16887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oi6_16887/08_2025/8oi6_16887.map" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.214 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.84, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 540.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.38 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: 1.62 Time building geometry restraints manager: 1.25 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: 5.220 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.910 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.880 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (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 ARG 0.003 0.000 ARG A 116 TYR 0.028 0.001 TYR C 166 PHE 0.008 0.001 PHE A 124 TRP 0.014 0.001 TRP B 86 HIS 0.011 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00523 (11822) covalent geometry : angle 0.64020 (16045) hydrogen bonds : bond 0.30317 ( 525) hydrogen bonds : angle 8.74333 ( 1329) link_TRANS : bond 0.01252 ( 6) link_TRANS : angle 2.98562 ( 18) *********************** 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 : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 88 average time/residue: 0.0881 time to fit residues: 12.2698 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 : 0.328 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 173 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.075423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064679 restraints weight = 33999.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.066837 restraints weight = 17236.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.068270 restraints weight = 10580.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.069231 restraints weight = 7399.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069873 restraints weight = 5667.696| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11828 Z= 0.186 Angle : 0.628 6.475 16063 Z= 0.305 Chirality : 0.045 0.180 1795 Planarity : 0.004 0.035 2031 Dihedral : 12.003 178.747 1673 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.55 % Favored : 98.38 % Rotamer: Outliers : 1.71 % Allowed : 16.35 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.22), residues: 1418 helix: 0.33 (0.22), residues: 580 sheet: 0.48 (0.34), residues: 235 loop : 0.66 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.017 0.001 TYR B 143 PHE 0.015 0.001 PHE C 352 TRP 0.023 0.002 TRP I 1 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00417 (11822) covalent geometry : angle 0.62739 (16045) hydrogen bonds : bond 0.04269 ( 525) hydrogen bonds : angle 5.68816 ( 1329) link_TRANS : bond 0.00361 ( 6) link_TRANS : angle 0.73020 ( 18) *********************** 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 101 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.480 Fit side-chains REVERT: A 80 ASP cc_start: 0.7911 (t0) cc_final: 0.7643 (t0) REVERT: B 314 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: D 355 MET cc_start: 0.7747 (pmm) cc_final: 0.7064 (pmm) outliers start: 21 outliers final: 9 residues processed: 97 average time/residue: 0.0810 time to fit residues: 12.8435 Evaluate side-chains 87 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 300 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 112 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.063584 restraints weight = 33845.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065788 restraints weight = 17145.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067260 restraints weight = 10576.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068215 restraints weight = 7401.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.068881 restraints weight = 5698.214| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11828 Z= 0.139 Angle : 0.570 7.623 16063 Z= 0.268 Chirality : 0.044 0.200 1795 Planarity : 0.004 0.035 2031 Dihedral : 11.072 160.359 1668 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 2.20 % Allowed : 16.27 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.23), residues: 1418 helix: 0.54 (0.22), residues: 585 sheet: 0.44 (0.34), residues: 253 loop : 0.67 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 116 TYR 0.014 0.001 TYR B 143 PHE 0.012 0.001 PHE D 31 TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00321 (11822) covalent geometry : angle 0.57064 (16045) hydrogen bonds : bond 0.03606 ( 525) hydrogen bonds : angle 5.24404 ( 1329) link_TRANS : bond 0.00237 ( 6) link_TRANS : angle 0.37162 ( 18) *********************** 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 105 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.474 Fit side-chains REVERT: A 80 ASP cc_start: 0.7960 (t0) cc_final: 0.7522 (t0) REVERT: B 132 MET cc_start: 0.8150 (ttp) cc_final: 0.7508 (ttp) REVERT: B 314 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: D 305 MET cc_start: 0.8020 (tpp) cc_final: 0.7788 (tpp) REVERT: D 355 MET cc_start: 0.7706 (pmm) cc_final: 0.7139 (pmm) REVERT: I 5 CYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8034 (p) outliers start: 27 outliers final: 14 residues processed: 101 average time/residue: 0.0758 time to fit residues: 12.3295 Evaluate side-chains 93 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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 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 D residue 82 MET Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.069818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.058873 restraints weight = 34828.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.060967 restraints weight = 18111.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.062382 restraints weight = 11331.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063321 restraints weight = 8033.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.063964 restraints weight = 6225.296| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.107 11828 Z= 0.379 Angle : 0.781 7.665 16063 Z= 0.379 Chirality : 0.050 0.223 1795 Planarity : 0.005 0.044 2031 Dihedral : 10.317 144.903 1668 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 2.69 % Allowed : 17.90 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.23), residues: 1418 helix: 0.20 (0.22), residues: 581 sheet: 0.20 (0.34), residues: 256 loop : 0.29 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 254 TYR 0.018 0.002 TYR C 143 PHE 0.022 0.002 PHE C 352 TRP 0.014 0.003 TRP C 340 HIS 0.009 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00879 (11822) covalent geometry : angle 0.78062 (16045) hydrogen bonds : bond 0.04372 ( 525) hydrogen bonds : angle 5.49714 ( 1329) link_TRANS : bond 0.00581 ( 6) link_TRANS : angle 0.72560 ( 18) *********************** 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 110 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.416 Fit side-chains REVERT: A 80 ASP cc_start: 0.8139 (t0) cc_final: 0.7550 (t0) REVERT: B 314 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: C 132 MET cc_start: 0.8340 (tmm) cc_final: 0.8140 (tmm) REVERT: D 305 MET cc_start: 0.8120 (tpp) cc_final: 0.7746 (tpp) REVERT: D 355 MET cc_start: 0.7880 (pmm) cc_final: 0.7262 (pmm) outliers start: 33 outliers final: 19 residues processed: 104 average time/residue: 0.0773 time to fit residues: 13.0258 Evaluate side-chains 94 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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 278 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 330 ILE 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 186 THR 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 282 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.073257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062321 restraints weight = 33930.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064529 restraints weight = 17244.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.065995 restraints weight = 10628.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066969 restraints weight = 7450.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067630 restraints weight = 5724.391| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11828 Z= 0.123 Angle : 0.570 8.473 16063 Z= 0.266 Chirality : 0.044 0.202 1795 Planarity : 0.004 0.038 2031 Dihedral : 9.690 139.585 1668 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.90 % Favored : 98.03 % Rotamer: Outliers : 2.03 % Allowed : 18.80 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.23), residues: 1418 helix: 0.68 (0.23), residues: 580 sheet: 0.25 (0.34), residues: 253 loop : 0.56 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 116 TYR 0.008 0.001 TYR A 169 PHE 0.012 0.001 PHE D 31 TRP 0.015 0.002 TRP C 340 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00278 (11822) covalent geometry : angle 0.57001 (16045) hydrogen bonds : bond 0.02972 ( 525) hydrogen bonds : angle 4.96192 ( 1329) link_TRANS : bond 0.00216 ( 6) link_TRANS : angle 0.37163 ( 18) *********************** 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 103 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.321 Fit side-chains REVERT: A 80 ASP cc_start: 0.7973 (t0) cc_final: 0.7446 (t0) REVERT: B 314 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: C 82 MET cc_start: 0.8399 (tpt) cc_final: 0.8172 (tpt) REVERT: D 305 MET cc_start: 0.8208 (tpp) cc_final: 0.7927 (tpp) REVERT: H 5 CYS cc_start: 0.6649 (t) cc_final: 0.5761 (m) REVERT: I 5 CYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8105 (p) REVERT: J 5 CYS cc_start: 0.7644 (m) cc_final: 0.7354 (t) outliers start: 25 outliers final: 11 residues processed: 100 average time/residue: 0.0741 time to fit residues: 12.2865 Evaluate side-chains 91 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 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 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 D residue 314 GLN 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 30 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 140 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.071341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060393 restraints weight = 34426.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062528 restraints weight = 17730.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.063960 restraints weight = 11053.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064923 restraints weight = 7811.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065580 restraints weight = 6022.564| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11828 Z= 0.232 Angle : 0.646 7.578 16063 Z= 0.303 Chirality : 0.046 0.211 1795 Planarity : 0.004 0.039 2031 Dihedral : 9.333 134.354 1668 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.25 % Rotamer: Outliers : 2.44 % Allowed : 18.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.23), residues: 1418 helix: 0.60 (0.23), residues: 582 sheet: 0.16 (0.34), residues: 252 loop : 0.43 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.009 0.001 TYR A 198 PHE 0.013 0.002 PHE C 352 TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00543 (11822) covalent geometry : angle 0.64646 (16045) hydrogen bonds : bond 0.03328 ( 525) hydrogen bonds : angle 5.03193 ( 1329) link_TRANS : bond 0.00404 ( 6) link_TRANS : angle 0.53287 ( 18) *********************** 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 107 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.460 Fit side-chains REVERT: A 80 ASP cc_start: 0.8079 (t0) cc_final: 0.7569 (t0) REVERT: B 118 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7856 (tptt) REVERT: B 314 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: D 44 MET cc_start: 0.7234 (ttp) cc_final: 0.6748 (ttp) REVERT: D 305 MET cc_start: 0.8266 (tpp) cc_final: 0.7924 (tpp) REVERT: H 5 CYS cc_start: 0.7035 (t) cc_final: 0.5870 (m) REVERT: I 5 CYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8134 (p) REVERT: J 5 CYS cc_start: 0.7666 (m) cc_final: 0.7384 (t) outliers start: 30 outliers final: 21 residues processed: 103 average time/residue: 0.0754 time to fit residues: 12.7954 Evaluate side-chains 101 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 186 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 282 ILE Chi-restraints excluded: chain D residue 314 GLN 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 121 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.0870 chunk 68 optimal weight: 0.0070 chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.074423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063359 restraints weight = 33945.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.065545 restraints weight = 17364.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.067003 restraints weight = 10753.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.067983 restraints weight = 7564.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.068652 restraints weight = 5831.961| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11828 Z= 0.100 Angle : 0.560 8.191 16063 Z= 0.258 Chirality : 0.043 0.201 1795 Planarity : 0.004 0.037 2031 Dihedral : 8.945 133.281 1668 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.76 % Favored : 98.17 % Rotamer: Outliers : 1.63 % Allowed : 19.77 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.23), residues: 1418 helix: 0.76 (0.23), residues: 590 sheet: 0.15 (0.33), residues: 253 loop : 0.63 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.009 0.001 TYR A 143 PHE 0.013 0.001 PHE D 31 TRP 0.013 0.001 TRP C 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00226 (11822) covalent geometry : angle 0.56018 (16045) hydrogen bonds : bond 0.02723 ( 525) hydrogen bonds : angle 4.77614 ( 1329) link_TRANS : bond 0.00168 ( 6) link_TRANS : angle 0.31294 ( 18) *********************** 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 100 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8012 (t0) cc_final: 0.7409 (t0) REVERT: B 314 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: D 44 MET cc_start: 0.7095 (ttp) cc_final: 0.6640 (ttp) REVERT: D 305 MET cc_start: 0.8291 (tpp) cc_final: 0.7970 (tpp) REVERT: I 5 CYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8159 (p) REVERT: J 5 CYS cc_start: 0.7597 (m) cc_final: 0.7353 (t) outliers start: 20 outliers final: 12 residues processed: 98 average time/residue: 0.0713 time to fit residues: 11.4239 Evaluate side-chains 93 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 GLU 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 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 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 34 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.073875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062828 restraints weight = 34311.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.064987 restraints weight = 17543.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066442 restraints weight = 10894.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067401 restraints weight = 7678.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.068074 restraints weight = 5932.623| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11828 Z= 0.124 Angle : 0.579 9.535 16063 Z= 0.265 Chirality : 0.044 0.204 1795 Planarity : 0.003 0.037 2031 Dihedral : 8.684 136.883 1668 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.19 % Favored : 97.74 % Rotamer: Outliers : 1.87 % Allowed : 19.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.23), residues: 1418 helix: 0.79 (0.23), residues: 594 sheet: 0.18 (0.33), residues: 250 loop : 0.61 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.016 0.001 TYR C 166 PHE 0.012 0.001 PHE D 31 TRP 0.010 0.001 TRP C 340 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00289 (11822) covalent geometry : angle 0.57892 (16045) hydrogen bonds : bond 0.02746 ( 525) hydrogen bonds : angle 4.73482 ( 1329) link_TRANS : bond 0.00210 ( 6) link_TRANS : angle 0.33272 ( 18) *********************** 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 101 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7990 (t0) cc_final: 0.7490 (t0) REVERT: B 118 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7696 (tptm) REVERT: B 314 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: D 44 MET cc_start: 0.7178 (ttp) cc_final: 0.6696 (ttp) REVERT: D 305 MET cc_start: 0.8325 (tpp) cc_final: 0.7948 (tpp) REVERT: I 5 CYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8153 (p) REVERT: J 5 CYS cc_start: 0.7588 (m) cc_final: 0.7366 (t) outliers start: 23 outliers final: 16 residues processed: 98 average time/residue: 0.0771 time to fit residues: 12.0603 Evaluate side-chains 97 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 205 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 151 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 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 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 72 optimal weight: 6.9990 chunk 31 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 114 optimal weight: 0.0010 chunk 90 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 0.2980 chunk 140 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.3324 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.075046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.064033 restraints weight = 33663.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.066235 restraints weight = 17196.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.067681 restraints weight = 10621.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.068661 restraints weight = 7463.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069314 restraints weight = 5748.232| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11828 Z= 0.090 Angle : 0.557 9.564 16063 Z= 0.255 Chirality : 0.043 0.199 1795 Planarity : 0.003 0.037 2031 Dihedral : 8.438 141.967 1668 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.97 % Favored : 97.95 % Rotamer: Outliers : 1.38 % Allowed : 20.02 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.23), residues: 1418 helix: 0.81 (0.22), residues: 600 sheet: 0.19 (0.33), residues: 250 loop : 0.65 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 210 TYR 0.008 0.001 TYR B 143 PHE 0.013 0.001 PHE D 31 TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00202 (11822) covalent geometry : angle 0.55773 (16045) hydrogen bonds : bond 0.02505 ( 525) hydrogen bonds : angle 4.64169 ( 1329) link_TRANS : bond 0.00120 ( 6) link_TRANS : angle 0.26125 ( 18) *********************** 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 99 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8014 (t0) cc_final: 0.7450 (t0) REVERT: B 314 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: D 44 MET cc_start: 0.7118 (ttp) cc_final: 0.6615 (ttp) REVERT: D 227 MET cc_start: 0.8873 (mmm) cc_final: 0.8568 (mmm) REVERT: D 305 MET cc_start: 0.8302 (tpp) cc_final: 0.7946 (tpp) REVERT: I 5 CYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8051 (p) REVERT: J 5 CYS cc_start: 0.7612 (m) cc_final: 0.7343 (t) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 0.0754 time to fit residues: 11.4457 Evaluate side-chains 95 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 205 GLU 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 370 VAL 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 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 115 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 133 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.064001 restraints weight = 34084.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.066175 restraints weight = 17328.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067608 restraints weight = 10691.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.068562 restraints weight = 7495.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.069227 restraints weight = 5760.163| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2685 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= 0.108 Angle : 0.566 10.216 16063 Z= 0.257 Chirality : 0.043 0.201 1795 Planarity : 0.003 0.037 2031 Dihedral : 8.275 143.568 1668 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.90 % Favored : 98.03 % Rotamer: Outliers : 1.55 % Allowed : 19.85 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.23), residues: 1418 helix: 0.82 (0.22), residues: 603 sheet: 0.20 (0.33), residues: 250 loop : 0.68 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.017 0.001 TYR C 166 PHE 0.012 0.001 PHE D 31 TRP 0.017 0.001 TRP A 86 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00251 (11822) covalent geometry : angle 0.56660 (16045) hydrogen bonds : bond 0.02555 ( 525) hydrogen bonds : angle 4.60759 ( 1329) link_TRANS : bond 0.00172 ( 6) link_TRANS : angle 0.30260 ( 18) ********************** 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 102 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8013 (t0) cc_final: 0.7500 (t0) REVERT: B 314 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: C 227 MET cc_start: 0.8947 (mmm) cc_final: 0.8680 (mmm) REVERT: D 44 MET cc_start: 0.7200 (ttp) cc_final: 0.6732 (ttp) REVERT: D 227 MET cc_start: 0.8840 (mmm) cc_final: 0.8529 (mmm) REVERT: D 305 MET cc_start: 0.8311 (tpp) cc_final: 0.7917 (tpp) REVERT: I 5 CYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8053 (p) REVERT: J 5 CYS cc_start: 0.7598 (m) cc_final: 0.7319 (t) outliers start: 19 outliers final: 15 residues processed: 99 average time/residue: 0.0772 time to fit residues: 12.4573 Evaluate side-chains 100 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 205 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 272 CYS 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 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR 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 106 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062957 restraints weight = 34235.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.065134 restraints weight = 17521.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.066580 restraints weight = 10868.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067542 restraints weight = 7658.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.068220 restraints weight = 5912.445| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11828 Z= 0.140 Angle : 0.581 10.017 16063 Z= 0.266 Chirality : 0.044 0.203 1795 Planarity : 0.003 0.037 2031 Dihedral : 8.193 143.619 1668 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.05 % Favored : 97.88 % Rotamer: Outliers : 1.63 % Allowed : 19.69 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.23), residues: 1418 helix: 0.80 (0.22), residues: 603 sheet: 0.18 (0.33), residues: 250 loop : 0.65 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.007 0.001 TYR B 143 PHE 0.011 0.001 PHE D 31 TRP 0.024 0.002 TRP A 86 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00328 (11822) covalent geometry : angle 0.58091 (16045) hydrogen bonds : bond 0.02713 ( 525) hydrogen bonds : angle 4.65157 ( 1329) link_TRANS : bond 0.00245 ( 6) link_TRANS : angle 0.35073 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1406.58 seconds wall clock time: 25 minutes 14.55 seconds (1514.55 seconds total)