Starting phenix.real_space_refine on Fri Sep 19 05:25:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vkh_43316/09_2025/8vkh_43316.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vkh_43316/09_2025/8vkh_43316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vkh_43316/09_2025/8vkh_43316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vkh_43316/09_2025/8vkh_43316.map" model { file = "/net/cci-nas-00/data/ceres_data/8vkh_43316/09_2025/8vkh_43316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vkh_43316/09_2025/8vkh_43316.cif" } resolution = 3.63 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= -0.001 sd= 0.024 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 Ca 14 9.91 5 P 14 5.49 5 S 142 5.16 5 C 14685 2.51 5 N 3961 2.21 5 O 4471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23287 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2934 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} 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: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "G" Number of atoms: 2812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 357, 2810 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 341} Conformer: "B" Number of residues, atoms: 357, 2810 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 341} bond proxies already assigned to first conformer: 2869 Chain: "H" Number of atoms: 2812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 357, 2810 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 341} Conformer: "B" Number of residues, atoms: 357, 2810 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 341} bond proxies already assigned to first conformer: 2869 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 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: {' CA': 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: {' CA': 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: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.78, per 1000 atoms: 0.29 Number of scatterers: 23287 At special positions: 0 Unit cell: (102.6, 141.48, 238.68, 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) Ca 14 19.99 S 142 16.00 P 14 15.00 O 4471 8.00 N 3961 7.00 C 14685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 45 sheets defined 43.1% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.732A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.891A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 125 removed outlier: 4.075A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.572A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.718A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.999A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.583A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.179A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.522A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) 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 347 removed outlier: 3.650A pdb=" N ILE A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.256A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.640A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.588A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.692A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 125 removed outlier: 4.443A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.535A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.643A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.632A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.910A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.318A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.004A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.943A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.582A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.871A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.549A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.641A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.588A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.871A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.984A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.605A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.670A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.583A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (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 348 removed outlier: 3.649A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.751A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.894A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.118A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.538A pdb=" N GLY D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.523A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.599A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.864A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.902A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.785A 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 295 removed outlier: 3.775A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 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 355 removed outlier: 3.880A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.084A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 91 removed outlier: 3.606A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 181 through 192 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 222 through 233 removed outlier: 3.781A pdb=" N GLU E 226 " --> pdb=" O ASP E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.855A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 285 removed outlier: 3.921A pdb=" N THR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 296 removed outlier: 3.678A pdb=" N LEU E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.775A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 removed outlier: 3.558A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.549A pdb=" N CYS E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 91 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.551A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 181 through 192 Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 223 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.969A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 273 through 284 removed outlier: 3.991A pdb=" N THR F 278 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 294 Processing helix chain 'F' and resid 301 through 305 removed outlier: 3.544A pdb=" N MET F 305 " --> pdb=" O GLY F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.754A pdb=" N LEU F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 359 through 364 removed outlier: 3.519A pdb=" N GLU F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.283A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 35 removed outlier: 3.507A pdb=" N LEU G 33 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS G 34 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 94 through 112 Processing helix chain 'G' and resid 127 through 134 removed outlier: 3.536A pdb=" N TYR G 133 " --> pdb=" O THR G 129 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE G 134 " --> pdb=" O PHE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 183 removed outlier: 3.500A pdb=" N SER G 182 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 223 Processing helix chain 'G' and resid 240 through 248 Processing helix chain 'G' and resid 261 through 269 Processing helix chain 'G' and resid 297 through 299 No H-bonds generated for 'chain 'G' and resid 297 through 299' Processing helix chain 'G' and resid 324 through 343 removed outlier: 3.909A pdb=" N ILE G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR G 340 " --> pdb=" O SER G 336 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET G 342 " --> pdb=" O PHE G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 364 removed outlier: 3.729A pdb=" N GLN G 364 " --> pdb=" O PRO G 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 35 removed outlier: 3.552A pdb=" N LEU H 33 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS H 34 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 94 through 112 Processing helix chain 'H' and resid 127 through 134 removed outlier: 3.686A pdb=" N TYR H 133 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE H 134 " --> pdb=" O PHE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 183 Processing helix chain 'H' and resid 206 through 223 removed outlier: 3.574A pdb=" N ARG H 210 " --> pdb=" O ASN H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 248 Processing helix chain 'H' and resid 261 through 269 Processing helix chain 'H' and resid 295 through 299 Processing helix chain 'H' and resid 324 through 342 removed outlier: 3.756A pdb=" N ILE H 339 " --> pdb=" O ALA H 335 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR H 340 " --> pdb=" O SER H 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET H 342 " --> pdb=" O PHE H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 364 removed outlier: 3.625A pdb=" N GLN H 364 " --> pdb=" O PRO H 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.998A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 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 176 through 178 removed outlier: 3.588A pdb=" N SER A 155 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.578A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (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: 4.232A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 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 176 through 178 removed outlier: 6.480A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.672A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (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: 6.735A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 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 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.506A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.511A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.220A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 31 removed outlier: 6.486A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.238A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 6.388A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 51 through 53 removed outlier: 5.574A pdb=" N ALA G 67 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLU G 121 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR G 87 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 61 through 63 removed outlier: 6.922A pdb=" N PHE G 62 " --> pdb=" O LYS G 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 172 through 175 removed outlier: 3.697A pdb=" N ASN G 196 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE G 197 " --> pdb=" O HIS G 232 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER G 234 " --> pdb=" O ILE G 197 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLN G 199 " --> pdb=" O SER G 234 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 285 through 289 removed outlier: 6.713A pdb=" N LEU G 273 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE G 315 " --> pdb=" O SER G 351 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU G 353 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL G 317 " --> pdb=" O LEU G 353 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 294 through 295 removed outlier: 6.621A pdb=" N PHE G 294 " --> pdb=" O LYS G 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'H' and resid 51 through 52 Processing sheet with id=AE7, first strand: chain 'H' and resid 61 through 63 removed outlier: 6.931A pdb=" N PHE H 62 " --> pdb=" O LYS H 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'H' and resid 172 through 175 removed outlier: 6.188A pdb=" N ILE H 197 " --> pdb=" O HIS H 232 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N SER H 234 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLN H 199 " --> pdb=" O SER H 234 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 285 through 289 removed outlier: 6.792A pdb=" N LEU H 273 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE H 315 " --> pdb=" O SER H 351 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU H 353 " --> pdb=" O ILE H 315 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL H 317 " --> pdb=" O LEU H 353 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2646 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: 4.89 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6416 1.34 - 1.46: 5272 1.46 - 1.58: 11840 1.58 - 1.71: 19 1.71 - 1.83: 246 Bond restraints: 23793 Sorted by residual: bond pdb=" C ASP G 371 " pdb=" N PRO G 372 " ideal model delta sigma weight residual 1.336 1.375 -0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.97e+00 ... (remaining 23788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 31378 3.00 - 6.00: 773 6.00 - 8.99: 91 8.99 - 11.99: 16 11.99 - 14.99: 8 Bond angle restraints: 32266 Sorted by residual: angle pdb=" N GLU B 364 " pdb=" CA GLU B 364 " pdb=" CB GLU B 364 " ideal model delta sigma weight residual 110.30 118.96 -8.66 1.54e+00 4.22e-01 3.16e+01 angle pdb=" CA GLN G 95 " pdb=" CB GLN G 95 " pdb=" CG GLN G 95 " ideal model delta sigma weight residual 114.10 124.41 -10.31 2.00e+00 2.50e-01 2.66e+01 angle pdb=" CB GLN G 95 " pdb=" CG GLN G 95 " pdb=" CD GLN G 95 " ideal model delta sigma weight residual 112.60 121.18 -8.58 1.70e+00 3.46e-01 2.55e+01 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 127.69 -14.99 3.00e+00 1.11e-01 2.50e+01 angle pdb=" CB MET A 283 " pdb=" CG MET A 283 " pdb=" SD MET A 283 " ideal model delta sigma weight residual 112.70 127.59 -14.89 3.00e+00 1.11e-01 2.46e+01 ... (remaining 32261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 12862 17.38 - 34.76: 1201 34.76 - 52.13: 206 52.13 - 69.51: 37 69.51 - 86.89: 18 Dihedral angle restraints: 14324 sinusoidal: 5829 harmonic: 8495 Sorted by residual: dihedral pdb=" CA THR B 120 " pdb=" C THR B 120 " pdb=" N GLN B 121 " pdb=" CA GLN B 121 " ideal model delta harmonic sigma weight residual -180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP D 286 " pdb=" C ASP D 286 " pdb=" N ILE D 287 " pdb=" CA ILE D 287 " ideal model delta harmonic sigma weight residual 180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ILE F 267 " pdb=" C ILE F 267 " pdb=" N GLY F 268 " pdb=" CA GLY F 268 " ideal model delta harmonic sigma weight residual 180.00 153.42 26.58 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 14321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3109 0.097 - 0.194: 403 0.194 - 0.291: 22 0.291 - 0.388: 4 0.388 - 0.485: 1 Chirality restraints: 3539 Sorted by residual: chirality pdb=" CG LEU D 140 " pdb=" CB LEU D 140 " pdb=" CD1 LEU D 140 " pdb=" CD2 LEU D 140 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3536 not shown) Planarity restraints: 4160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 86 " 0.053 2.00e-02 2.50e+03 4.89e-02 5.97e+01 pdb=" CG TRP D 86 " -0.129 2.00e-02 2.50e+03 pdb=" CD1 TRP D 86 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TRP D 86 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP D 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 86 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 86 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 86 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 86 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP D 86 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 86 " 0.000 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP F 86 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP F 86 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP F 86 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 86 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP F 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 86 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 86 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 86 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 86 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " -0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A 102 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.044 5.00e-02 4.00e+02 ... (remaining 4157 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 7127 2.84 - 3.35: 20312 3.35 - 3.87: 39204 3.87 - 4.38: 44995 4.38 - 4.90: 77439 Nonbonded interactions: 189077 Sorted by model distance: nonbonded pdb=" O ILE A 122 " pdb=" OG1 THR A 126 " model vdw 2.321 3.040 nonbonded pdb=" O GLN F 314 " pdb=" OG1 THR F 318 " model vdw 2.332 3.040 nonbonded pdb=" O ILE F 85 " pdb=" OG1 THR F 89 " model vdw 2.333 3.040 nonbonded pdb=" O GLN B 314 " pdb=" OG1 THR B 318 " model vdw 2.338 3.040 nonbonded pdb=" O GLY B 182 " pdb=" OG1 THR B 186 " model vdw 2.338 3.040 ... (remaining 189072 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 4 through 375 or resid 402)) selection = (chain 'B' and (resid 4 through 375 or resid 402)) selection = (chain 'C' and (resid 4 through 375 or resid 402)) selection = (chain 'D' and (resid 4 through 375 or resid 402)) selection = (chain 'E' and (resid 4 through 375 or resid 402)) selection = (chain 'F' and (resid 4 through 375 or resid 402)) } ncs_group { reference = (chain 'G' and (resid 24 through 206 or resid 208 through 804)) selection = (chain 'H' and (resid 24 through 206 or resid 208 through 804)) } 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=0.10 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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.400 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.006 0.093 23793 Z= 0.282 Angle : 1.113 14.990 32266 Z= 0.580 Chirality : 0.064 0.485 3539 Planarity : 0.008 0.081 4160 Dihedral : 13.867 86.891 8890 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.16 % Allowed : 0.40 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -1.79 (0.14), residues: 2917 helix: -2.11 (0.12), residues: 1044 sheet: 0.05 (0.21), residues: 578 loop : -0.77 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG D 290 TYR 0.048 0.003 TYR C 279 PHE 0.039 0.003 PHE G 316 TRP 0.129 0.004 TRP D 86 HIS 0.017 0.002 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00590 (23793) covalent geometry : angle 1.11286 (32266) hydrogen bonds : bond 0.18372 ( 992) hydrogen bonds : angle 7.36218 ( 2646) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.8312 (mpp) cc_final: 0.7994 (mpp) REVERT: B 340 TRP cc_start: 0.8312 (t60) cc_final: 0.7814 (t60) REVERT: C 44 MET cc_start: 0.8650 (tpp) cc_final: 0.8445 (tpp) REVERT: C 176 MET cc_start: 0.8714 (tpp) cc_final: 0.8415 (mmt) REVERT: C 227 MET cc_start: 0.8769 (mmt) cc_final: 0.8503 (mmt) REVERT: D 276 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7730 (tm-30) REVERT: E 82 MET cc_start: 0.9195 (tpt) cc_final: 0.8806 (mmm) REVERT: E 227 MET cc_start: 0.8796 (mtp) cc_final: 0.8543 (mtp) REVERT: E 269 MET cc_start: 0.8910 (mmp) cc_final: 0.8570 (mtt) REVERT: E 325 MET cc_start: 0.5132 (ptm) cc_final: 0.4509 (ppp) REVERT: F 157 ASP cc_start: 0.7288 (t0) cc_final: 0.7028 (t0) REVERT: F 175 ILE cc_start: 0.8996 (mp) cc_final: 0.8604 (mm) REVERT: F 274 ILE cc_start: 0.8694 (pt) cc_final: 0.8454 (pt) REVERT: F 299 MET cc_start: 0.8132 (mmp) cc_final: 0.7894 (mtm) REVERT: G 305 PHE cc_start: 0.8664 (m-80) cc_final: 0.8042 (m-80) REVERT: G 306 ILE cc_start: 0.9436 (mp) cc_final: 0.9228 (pt) REVERT: G 309 HIS cc_start: 0.8183 (t-90) cc_final: 0.7857 (t-90) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.1545 time to fit residues: 70.8707 Evaluate side-chains 178 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 0.0370 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS B 101 HIS B 173 HIS B 296 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 115 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN F 92 ASN G 119 HIS G 232 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.062388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047492 restraints weight = 109128.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.049003 restraints weight = 53874.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050004 restraints weight = 33221.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050661 restraints weight = 23731.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051072 restraints weight = 18877.113| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23793 Z= 0.160 Angle : 0.636 9.102 32266 Z= 0.319 Chirality : 0.045 0.162 3539 Planarity : 0.005 0.072 4160 Dihedral : 7.372 80.777 3327 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.97 % Allowed : 5.31 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.49 (0.15), residues: 2917 helix: -0.48 (0.15), residues: 1097 sheet: 0.23 (0.20), residues: 645 loop : -0.26 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 372 TYR 0.017 0.001 TYR G 111 PHE 0.015 0.001 PHE G 125 TRP 0.052 0.002 TRP D 86 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00365 (23793) covalent geometry : angle 0.63610 (32266) hydrogen bonds : bond 0.03816 ( 992) hydrogen bonds : angle 5.12246 ( 2646) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: A 355 MET cc_start: 0.8529 (mpp) cc_final: 0.8023 (mpp) REVERT: B 340 TRP cc_start: 0.8837 (t60) cc_final: 0.8147 (t60) REVERT: C 44 MET cc_start: 0.8634 (tpp) cc_final: 0.8432 (tpp) REVERT: C 82 MET cc_start: 0.8463 (tpp) cc_final: 0.8209 (tpp) REVERT: C 176 MET cc_start: 0.8693 (tpp) cc_final: 0.8427 (mmt) REVERT: C 227 MET cc_start: 0.8609 (mmt) cc_final: 0.8209 (mmt) REVERT: D 276 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7194 (tm-30) REVERT: D 305 MET cc_start: 0.8549 (mmm) cc_final: 0.8274 (mmp) REVERT: E 82 MET cc_start: 0.9261 (tpt) cc_final: 0.8924 (mmm) REVERT: F 283 MET cc_start: 0.9093 (mmm) cc_final: 0.8873 (mmm) REVERT: F 355 MET cc_start: 0.9250 (mtp) cc_final: 0.8931 (ptp) REVERT: G 309 HIS cc_start: 0.8192 (t-90) cc_final: 0.7887 (t-90) REVERT: G 349 GLN cc_start: 0.8565 (tp-100) cc_final: 0.7854 (pp30) REVERT: H 125 PHE cc_start: 0.8377 (m-80) cc_final: 0.7982 (m-10) REVERT: H 304 CYS cc_start: 0.8490 (m) cc_final: 0.8289 (m) REVERT: H 342 MET cc_start: 0.8763 (mpp) cc_final: 0.8452 (mpp) outliers start: 20 outliers final: 10 residues processed: 201 average time/residue: 0.1591 time to fit residues: 52.7472 Evaluate side-chains 176 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 93 CYS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 364 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 40 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS B 49 GLN C 40 HIS ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 162 ASN F 314 GLN H 309 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.043823 restraints weight = 110620.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.045282 restraints weight = 53981.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046250 restraints weight = 33067.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.046889 restraints weight = 23646.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047293 restraints weight = 18801.717| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 23793 Z= 0.281 Angle : 0.715 7.575 32266 Z= 0.360 Chirality : 0.047 0.168 3539 Planarity : 0.005 0.064 4160 Dihedral : 7.181 82.874 3327 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.13 % Allowed : 8.21 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.04 (0.16), residues: 2917 helix: 0.18 (0.16), residues: 1078 sheet: 0.14 (0.20), residues: 636 loop : 0.05 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 116 TYR 0.030 0.002 TYR C 143 PHE 0.019 0.002 PHE A 124 TRP 0.029 0.002 TRP D 86 HIS 0.006 0.001 HIS G 119 Details of bonding type rmsd covalent geometry : bond 0.00623 (23793) covalent geometry : angle 0.71487 (32266) hydrogen bonds : bond 0.04023 ( 992) hydrogen bonds : angle 5.00906 ( 2646) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: A 227 MET cc_start: 0.9263 (mmm) cc_final: 0.8756 (tpp) REVERT: A 355 MET cc_start: 0.8825 (mpp) cc_final: 0.8032 (mpp) REVERT: B 227 MET cc_start: 0.9246 (tpp) cc_final: 0.9022 (tpt) REVERT: C 82 MET cc_start: 0.8606 (tpp) cc_final: 0.8330 (tpp) REVERT: C 176 MET cc_start: 0.8908 (tpp) cc_final: 0.8689 (mmt) REVERT: C 227 MET cc_start: 0.8745 (mmt) cc_final: 0.8351 (mmt) REVERT: D 82 MET cc_start: 0.9337 (tpp) cc_final: 0.9046 (tpp) REVERT: D 166 TYR cc_start: 0.8774 (t80) cc_final: 0.8531 (t80) REVERT: D 276 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7712 (tm-30) REVERT: E 82 MET cc_start: 0.9251 (tpt) cc_final: 0.8931 (mmm) REVERT: E 180 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8439 (pt) REVERT: F 86 TRP cc_start: 0.8843 (m-10) cc_final: 0.8502 (m-10) REVERT: F 123 MET cc_start: 0.9116 (mmm) cc_final: 0.8425 (mmm) REVERT: F 190 MET cc_start: 0.8530 (tpt) cc_final: 0.8280 (mmm) REVERT: F 283 MET cc_start: 0.9130 (mmm) cc_final: 0.8769 (mmm) REVERT: F 294 TYR cc_start: 0.7621 (m-80) cc_final: 0.7293 (t80) REVERT: F 355 MET cc_start: 0.9284 (mtp) cc_final: 0.9056 (ptm) REVERT: F 364 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: G 243 MET cc_start: 0.8902 (tpp) cc_final: 0.8452 (tpp) REVERT: G 309 HIS cc_start: 0.8181 (t-90) cc_final: 0.7888 (t-90) REVERT: G 349 GLN cc_start: 0.8571 (tp-100) cc_final: 0.7923 (pp30) REVERT: H 125 PHE cc_start: 0.8514 (m-80) cc_final: 0.8093 (m-10) REVERT: H 342 MET cc_start: 0.8812 (mpp) cc_final: 0.8497 (mpp) outliers start: 24 outliers final: 12 residues processed: 190 average time/residue: 0.1510 time to fit residues: 48.4908 Evaluate side-chains 173 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 93 CYS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain H residue 133 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 182 optimal weight: 9.9990 chunk 257 optimal weight: 0.0010 chunk 219 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN D 92 ASN F 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.059939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.045065 restraints weight = 109889.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.046539 restraints weight = 53568.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047515 restraints weight = 32894.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048152 restraints weight = 23456.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048561 restraints weight = 18665.110| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23793 Z= 0.135 Angle : 0.583 9.964 32266 Z= 0.288 Chirality : 0.044 0.156 3539 Planarity : 0.004 0.059 4160 Dihedral : 6.876 79.600 3327 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.09 % Allowed : 8.73 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.33 (0.16), residues: 2917 helix: 0.47 (0.16), residues: 1096 sheet: 0.22 (0.20), residues: 663 loop : 0.20 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 177 TYR 0.030 0.001 TYR C 279 PHE 0.014 0.001 PHE C 31 TRP 0.019 0.001 TRP D 86 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00315 (23793) covalent geometry : angle 0.58329 (32266) hydrogen bonds : bond 0.03142 ( 992) hydrogen bonds : angle 4.67821 ( 2646) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9188 (mmm) cc_final: 0.8662 (tpp) REVERT: A 325 MET cc_start: 0.9093 (mmm) cc_final: 0.8711 (tpp) REVERT: A 355 MET cc_start: 0.8840 (mpp) cc_final: 0.8019 (mpp) REVERT: C 176 MET cc_start: 0.8851 (tpp) cc_final: 0.8639 (mmt) REVERT: C 227 MET cc_start: 0.8642 (mmt) cc_final: 0.8375 (mmt) REVERT: C 354 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8571 (pp30) REVERT: D 82 MET cc_start: 0.9256 (tpp) cc_final: 0.8819 (tpp) REVERT: D 276 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7649 (tm-30) REVERT: E 82 MET cc_start: 0.9186 (tpt) cc_final: 0.8788 (mmm) REVERT: F 86 TRP cc_start: 0.8765 (m-10) cc_final: 0.8141 (m-10) REVERT: F 123 MET cc_start: 0.8973 (mmm) cc_final: 0.7968 (mmm) REVERT: F 190 MET cc_start: 0.8525 (tpt) cc_final: 0.8194 (mmm) REVERT: F 283 MET cc_start: 0.9099 (mmm) cc_final: 0.8893 (mmm) REVERT: F 294 TYR cc_start: 0.7508 (m-80) cc_final: 0.7251 (t80) REVERT: F 305 MET cc_start: 0.7700 (mmm) cc_final: 0.7474 (mmm) REVERT: F 355 MET cc_start: 0.9336 (mtp) cc_final: 0.9057 (ptm) REVERT: F 364 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: G 349 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8010 (pp30) REVERT: H 125 PHE cc_start: 0.8401 (m-80) cc_final: 0.7966 (m-80) outliers start: 23 outliers final: 10 residues processed: 186 average time/residue: 0.1289 time to fit residues: 41.1126 Evaluate side-chains 170 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 93 CYS Chi-restraints excluded: chain G residue 158 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 218 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 179 optimal weight: 0.1980 chunk 248 optimal weight: 2.9990 chunk 254 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.046855 restraints weight = 109484.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048436 restraints weight = 50320.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.049466 restraints weight = 30121.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.050125 restraints weight = 21222.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050554 restraints weight = 16844.513| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23793 Z= 0.159 Angle : 0.584 9.513 32266 Z= 0.288 Chirality : 0.044 0.277 3539 Planarity : 0.004 0.057 4160 Dihedral : 6.744 78.182 3327 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.25 % Allowed : 9.58 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.16), residues: 2917 helix: 0.64 (0.16), residues: 1096 sheet: 0.32 (0.20), residues: 651 loop : 0.26 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 335 TYR 0.017 0.001 TYR G 140 PHE 0.015 0.001 PHE F 223 TRP 0.011 0.001 TRP D 86 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00365 (23793) covalent geometry : angle 0.58445 (32266) hydrogen bonds : bond 0.03110 ( 992) hydrogen bonds : angle 4.63169 ( 2646) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9229 (mmm) cc_final: 0.8692 (tpp) REVERT: A 325 MET cc_start: 0.9122 (mmm) cc_final: 0.8702 (tpp) REVERT: A 355 MET cc_start: 0.8863 (mpp) cc_final: 0.7924 (mpp) REVERT: B 325 MET cc_start: 0.8947 (mmm) cc_final: 0.8289 (tpp) REVERT: B 337 TYR cc_start: 0.8896 (m-10) cc_final: 0.8658 (m-80) REVERT: C 44 MET cc_start: 0.8578 (mmm) cc_final: 0.8363 (mmm) REVERT: C 82 MET cc_start: 0.8627 (tpp) cc_final: 0.8200 (tpp) REVERT: C 176 MET cc_start: 0.8899 (tpp) cc_final: 0.8699 (mmt) REVERT: C 227 MET cc_start: 0.8721 (mmt) cc_final: 0.8396 (mmt) REVERT: C 325 MET cc_start: 0.7636 (mtt) cc_final: 0.7347 (mtt) REVERT: D 82 MET cc_start: 0.9307 (tpp) cc_final: 0.8957 (tpp) REVERT: D 166 TYR cc_start: 0.8797 (t80) cc_final: 0.8593 (t80) REVERT: D 276 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7711 (tm-30) REVERT: D 325 MET cc_start: 0.8675 (mmp) cc_final: 0.8453 (mmm) REVERT: E 82 MET cc_start: 0.9184 (tpt) cc_final: 0.8723 (mmm) REVERT: F 86 TRP cc_start: 0.8893 (m-10) cc_final: 0.8387 (m-10) REVERT: F 123 MET cc_start: 0.9116 (mmm) cc_final: 0.8708 (mmm) REVERT: F 190 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8325 (mmm) REVERT: F 283 MET cc_start: 0.9109 (mmm) cc_final: 0.8888 (mmm) REVERT: F 294 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.7324 (t80) REVERT: F 355 MET cc_start: 0.9298 (mtp) cc_final: 0.8995 (ptm) REVERT: F 364 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: G 199 GLN cc_start: 0.8788 (tt0) cc_final: 0.8557 (tt0) REVERT: H 125 PHE cc_start: 0.8465 (m-80) cc_final: 0.8032 (m-80) outliers start: 27 outliers final: 13 residues processed: 181 average time/residue: 0.1323 time to fit residues: 40.9191 Evaluate side-chains 173 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 93 CYS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 338 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 280 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 254 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.059984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045062 restraints weight = 109561.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.046562 restraints weight = 51572.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.047554 restraints weight = 31168.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048190 restraints weight = 22061.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.048602 restraints weight = 17523.764| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23793 Z= 0.189 Angle : 0.610 11.899 32266 Z= 0.299 Chirality : 0.045 0.207 3539 Planarity : 0.004 0.054 4160 Dihedral : 6.715 77.917 3327 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.13 % Allowed : 10.42 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.53 (0.16), residues: 2917 helix: 0.66 (0.16), residues: 1099 sheet: 0.31 (0.20), residues: 646 loop : 0.29 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 335 TYR 0.015 0.001 TYR G 274 PHE 0.016 0.001 PHE G 125 TRP 0.012 0.001 TRP B 79 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00432 (23793) covalent geometry : angle 0.60985 (32266) hydrogen bonds : bond 0.03192 ( 992) hydrogen bonds : angle 4.65905 ( 2646) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9227 (mmm) cc_final: 0.8713 (tpp) REVERT: A 355 MET cc_start: 0.8837 (mpp) cc_final: 0.8372 (mmt) REVERT: B 337 TYR cc_start: 0.8886 (m-10) cc_final: 0.8677 (m-80) REVERT: B 355 MET cc_start: 0.8277 (mtm) cc_final: 0.7925 (mtm) REVERT: C 44 MET cc_start: 0.8652 (mmm) cc_final: 0.8443 (mmm) REVERT: C 82 MET cc_start: 0.8676 (tpp) cc_final: 0.8305 (tpp) REVERT: C 227 MET cc_start: 0.8729 (mmt) cc_final: 0.8424 (mmt) REVERT: C 313 MET cc_start: 0.8977 (mmm) cc_final: 0.8762 (mtp) REVERT: C 325 MET cc_start: 0.7907 (mtt) cc_final: 0.7628 (mtt) REVERT: D 82 MET cc_start: 0.9298 (tpp) cc_final: 0.8942 (tpp) REVERT: D 276 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7732 (tm-30) REVERT: E 82 MET cc_start: 0.9188 (tpt) cc_final: 0.8731 (mmm) REVERT: E 269 MET cc_start: 0.8588 (mmm) cc_final: 0.8230 (mmm) REVERT: F 82 MET cc_start: 0.8799 (tpt) cc_final: 0.8069 (tpp) REVERT: F 190 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8387 (mmm) REVERT: F 283 MET cc_start: 0.9053 (mmm) cc_final: 0.8832 (mmm) REVERT: F 294 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7224 (t80) REVERT: F 299 MET cc_start: 0.7773 (mtp) cc_final: 0.7568 (mmp) REVERT: F 355 MET cc_start: 0.9285 (mtp) cc_final: 0.8959 (ptp) REVERT: F 364 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: G 85 LEU cc_start: 0.9179 (mm) cc_final: 0.8823 (mt) REVERT: H 125 PHE cc_start: 0.8493 (m-80) cc_final: 0.8061 (m-80) outliers start: 24 outliers final: 15 residues processed: 177 average time/residue: 0.1280 time to fit residues: 38.8279 Evaluate side-chains 174 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 93 CYS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain H residue 338 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 259 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 0.0870 chunk 26 optimal weight: 0.4980 chunk 176 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.060186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.045359 restraints weight = 107911.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046856 restraints weight = 51891.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047839 restraints weight = 31586.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048471 restraints weight = 22384.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048893 restraints weight = 17796.179| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23793 Z= 0.109 Angle : 0.567 10.941 32266 Z= 0.275 Chirality : 0.043 0.174 3539 Planarity : 0.004 0.054 4160 Dihedral : 6.530 79.299 3327 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.05 % Allowed : 11.27 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.64 (0.16), residues: 2917 helix: 0.74 (0.16), residues: 1109 sheet: 0.39 (0.20), residues: 651 loop : 0.34 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 62 TYR 0.028 0.001 TYR C 279 PHE 0.015 0.001 PHE D 223 TRP 0.010 0.001 TRP A 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00256 (23793) covalent geometry : angle 0.56691 (32266) hydrogen bonds : bond 0.02924 ( 992) hydrogen bonds : angle 4.49860 ( 2646) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9144 (mmm) cc_final: 0.8868 (mmt) REVERT: A 325 MET cc_start: 0.9058 (mmm) cc_final: 0.8519 (tpp) REVERT: A 355 MET cc_start: 0.8810 (mpp) cc_final: 0.8415 (mmt) REVERT: B 162 ASN cc_start: 0.8613 (t0) cc_final: 0.8219 (t0) REVERT: B 337 TYR cc_start: 0.8842 (m-10) cc_final: 0.8616 (m-80) REVERT: B 355 MET cc_start: 0.8249 (mtm) cc_final: 0.7926 (mtm) REVERT: C 44 MET cc_start: 0.8705 (mmm) cc_final: 0.7807 (mmt) REVERT: C 82 MET cc_start: 0.8591 (tpp) cc_final: 0.8220 (tpp) REVERT: C 227 MET cc_start: 0.8652 (mmt) cc_final: 0.8403 (mmt) REVERT: C 283 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7977 (mpp) REVERT: C 325 MET cc_start: 0.7780 (mtt) cc_final: 0.7566 (mtt) REVERT: D 82 MET cc_start: 0.9267 (tpp) cc_final: 0.8902 (tpp) REVERT: D 276 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7704 (tm-30) REVERT: E 82 MET cc_start: 0.9159 (tpt) cc_final: 0.8713 (mmm) REVERT: E 355 MET cc_start: 0.9120 (mmm) cc_final: 0.8662 (mmm) REVERT: F 86 TRP cc_start: 0.8795 (m-10) cc_final: 0.8517 (m-10) REVERT: F 123 MET cc_start: 0.8840 (mmm) cc_final: 0.8032 (mmm) REVERT: F 190 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8352 (mmm) REVERT: F 294 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.7290 (t80) REVERT: F 355 MET cc_start: 0.9382 (mtp) cc_final: 0.9066 (ptp) REVERT: F 364 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: G 85 LEU cc_start: 0.9117 (mm) cc_final: 0.8778 (mt) REVERT: H 125 PHE cc_start: 0.8420 (m-80) cc_final: 0.7989 (m-80) REVERT: H 224 GLU cc_start: 0.8432 (tt0) cc_final: 0.8195 (tt0) outliers start: 22 outliers final: 11 residues processed: 177 average time/residue: 0.1371 time to fit residues: 41.3935 Evaluate side-chains 170 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain H residue 338 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 35 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 231 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 229 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 280 optimal weight: 0.4980 chunk 176 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.059995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.045242 restraints weight = 109011.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.046707 restraints weight = 53008.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047668 restraints weight = 32515.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048312 restraints weight = 23205.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048721 restraints weight = 18439.617| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23793 Z= 0.125 Angle : 0.584 13.441 32266 Z= 0.281 Chirality : 0.044 0.165 3539 Planarity : 0.004 0.053 4160 Dihedral : 6.481 79.306 3327 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.05 % Allowed : 11.59 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.66 (0.16), residues: 2917 helix: 0.72 (0.16), residues: 1122 sheet: 0.35 (0.20), residues: 662 loop : 0.44 (0.20), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 62 TYR 0.025 0.001 TYR C 279 PHE 0.016 0.001 PHE G 125 TRP 0.008 0.001 TRP B 79 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00293 (23793) covalent geometry : angle 0.58368 (32266) hydrogen bonds : bond 0.02933 ( 992) hydrogen bonds : angle 4.48573 ( 2646) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9093 (mmm) cc_final: 0.8850 (mmt) REVERT: A 325 MET cc_start: 0.9015 (mmm) cc_final: 0.8483 (tpp) REVERT: A 355 MET cc_start: 0.8766 (mpp) cc_final: 0.8382 (mmt) REVERT: B 47 MET cc_start: 0.8173 (mmm) cc_final: 0.7874 (mmt) REVERT: B 162 ASN cc_start: 0.8578 (t0) cc_final: 0.8255 (t0) REVERT: B 337 TYR cc_start: 0.8785 (m-10) cc_final: 0.8559 (m-80) REVERT: B 355 MET cc_start: 0.8163 (mtm) cc_final: 0.7897 (mtm) REVERT: C 44 MET cc_start: 0.8732 (mmm) cc_final: 0.7927 (mmt) REVERT: C 82 MET cc_start: 0.8582 (tpp) cc_final: 0.8243 (tpp) REVERT: C 227 MET cc_start: 0.8663 (mmt) cc_final: 0.8345 (mmt) REVERT: C 283 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8019 (mpp) REVERT: C 325 MET cc_start: 0.7602 (mtt) cc_final: 0.7372 (mtt) REVERT: D 82 MET cc_start: 0.9252 (tpp) cc_final: 0.8905 (tpp) REVERT: D 276 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7670 (tm-30) REVERT: E 82 MET cc_start: 0.9175 (tpt) cc_final: 0.8736 (mmm) REVERT: E 269 MET cc_start: 0.8445 (mmm) cc_final: 0.8031 (mmm) REVERT: F 82 MET cc_start: 0.8873 (tpt) cc_final: 0.8310 (tpp) REVERT: F 86 TRP cc_start: 0.8731 (m-10) cc_final: 0.8244 (m-10) REVERT: F 123 MET cc_start: 0.8881 (mmm) cc_final: 0.8100 (mmm) REVERT: F 190 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8342 (mmm) REVERT: F 294 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7314 (t80) REVERT: F 355 MET cc_start: 0.9397 (mtp) cc_final: 0.9080 (ptp) REVERT: F 364 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: H 125 PHE cc_start: 0.8388 (m-80) cc_final: 0.7971 (m-80) outliers start: 22 outliers final: 10 residues processed: 176 average time/residue: 0.1300 time to fit residues: 39.2333 Evaluate side-chains 171 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 243 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.060413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045669 restraints weight = 109169.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047135 restraints weight = 52580.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048110 restraints weight = 32162.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048752 restraints weight = 22882.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.049148 restraints weight = 18178.031| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23793 Z= 0.105 Angle : 0.580 12.329 32266 Z= 0.277 Chirality : 0.043 0.175 3539 Planarity : 0.004 0.053 4160 Dihedral : 6.378 79.659 3327 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.97 % Allowed : 11.79 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.70 (0.16), residues: 2917 helix: 0.73 (0.16), residues: 1123 sheet: 0.44 (0.20), residues: 654 loop : 0.45 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.022 0.001 TYR C 279 PHE 0.017 0.001 PHE F 223 TRP 0.009 0.001 TRP A 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00249 (23793) covalent geometry : angle 0.57969 (32266) hydrogen bonds : bond 0.02826 ( 992) hydrogen bonds : angle 4.42096 ( 2646) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9103 (mmm) cc_final: 0.8855 (mmt) REVERT: A 325 MET cc_start: 0.9038 (mmm) cc_final: 0.8498 (tpp) REVERT: A 355 MET cc_start: 0.8753 (mpp) cc_final: 0.8362 (mmt) REVERT: B 47 MET cc_start: 0.8184 (mmm) cc_final: 0.7969 (mmt) REVERT: B 162 ASN cc_start: 0.8572 (t0) cc_final: 0.8252 (t0) REVERT: B 355 MET cc_start: 0.8186 (mtm) cc_final: 0.7920 (mtm) REVERT: C 44 MET cc_start: 0.8779 (mmm) cc_final: 0.7955 (mmt) REVERT: C 82 MET cc_start: 0.8568 (tpp) cc_final: 0.8226 (tpp) REVERT: C 227 MET cc_start: 0.8657 (mmt) cc_final: 0.8343 (mmt) REVERT: C 283 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8104 (mpp) REVERT: D 82 MET cc_start: 0.9245 (tpp) cc_final: 0.8896 (tpp) REVERT: D 276 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7626 (tm-30) REVERT: E 82 MET cc_start: 0.9170 (tpt) cc_final: 0.8711 (mmm) REVERT: E 269 MET cc_start: 0.8473 (mmm) cc_final: 0.8025 (mmm) REVERT: F 82 MET cc_start: 0.8882 (tpt) cc_final: 0.8299 (tpp) REVERT: F 86 TRP cc_start: 0.8755 (m-10) cc_final: 0.8248 (m-10) REVERT: F 123 MET cc_start: 0.8965 (mmm) cc_final: 0.8314 (mmm) REVERT: F 190 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8393 (mmm) REVERT: F 294 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7344 (t80) REVERT: F 299 MET cc_start: 0.7615 (mtm) cc_final: 0.7380 (mmp) REVERT: F 355 MET cc_start: 0.9402 (mtp) cc_final: 0.9077 (ptp) REVERT: F 364 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: H 125 PHE cc_start: 0.8381 (m-80) cc_final: 0.7958 (m-80) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 0.1447 time to fit residues: 42.3259 Evaluate side-chains 173 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 243 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 161 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 185 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.045042 restraints weight = 109278.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046526 restraints weight = 52514.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047498 restraints weight = 31987.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048142 restraints weight = 22772.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048540 restraints weight = 18093.116| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23793 Z= 0.145 Angle : 0.596 11.717 32266 Z= 0.287 Chirality : 0.044 0.173 3539 Planarity : 0.004 0.052 4160 Dihedral : 6.393 78.854 3327 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.01 % Allowed : 11.71 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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 (0.16), residues: 2917 helix: 0.79 (0.16), residues: 1105 sheet: 0.34 (0.21), residues: 639 loop : 0.47 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 254 TYR 0.021 0.001 TYR C 279 PHE 0.016 0.001 PHE G 125 TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00337 (23793) covalent geometry : angle 0.59612 (32266) hydrogen bonds : bond 0.02987 ( 992) hydrogen bonds : angle 4.44860 ( 2646) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9147 (mmm) cc_final: 0.8869 (mmt) REVERT: A 325 MET cc_start: 0.9087 (mmm) cc_final: 0.8527 (tpp) REVERT: A 355 MET cc_start: 0.8765 (mpp) cc_final: 0.8310 (mmt) REVERT: B 162 ASN cc_start: 0.8577 (t0) cc_final: 0.8315 (t0) REVERT: B 355 MET cc_start: 0.8289 (mtm) cc_final: 0.7914 (mtm) REVERT: C 44 MET cc_start: 0.8882 (mmm) cc_final: 0.8043 (mmt) REVERT: C 82 MET cc_start: 0.8650 (tpp) cc_final: 0.8291 (tpp) REVERT: C 227 MET cc_start: 0.8694 (mmt) cc_final: 0.8374 (mmt) REVERT: C 283 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8319 (mpp) REVERT: D 82 MET cc_start: 0.9220 (tpp) cc_final: 0.8855 (tpp) REVERT: D 276 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7699 (tm-30) REVERT: E 82 MET cc_start: 0.9187 (tpt) cc_final: 0.8699 (mmm) REVERT: E 269 MET cc_start: 0.8536 (mmm) cc_final: 0.8037 (mmm) REVERT: F 82 MET cc_start: 0.8881 (tpt) cc_final: 0.8309 (tpp) REVERT: F 123 MET cc_start: 0.9009 (mmm) cc_final: 0.8560 (mmm) REVERT: F 190 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8392 (mmm) REVERT: F 299 MET cc_start: 0.7705 (mtm) cc_final: 0.7370 (mmp) REVERT: F 355 MET cc_start: 0.9344 (mtp) cc_final: 0.8992 (ptp) REVERT: F 364 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: H 125 PHE cc_start: 0.8439 (m-80) cc_final: 0.8010 (m-80) outliers start: 21 outliers final: 13 residues processed: 169 average time/residue: 0.1421 time to fit residues: 41.2271 Evaluate side-chains 171 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 243 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 4 optimal weight: 0.0370 chunk 103 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 48 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.060773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046036 restraints weight = 109653.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047539 restraints weight = 53069.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048516 restraints weight = 32411.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049172 restraints weight = 23055.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049591 restraints weight = 18283.393| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23793 Z= 0.093 Angle : 0.570 11.603 32266 Z= 0.273 Chirality : 0.043 0.179 3539 Planarity : 0.004 0.053 4160 Dihedral : 6.262 79.679 3327 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.85 % Allowed : 11.95 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.79 (0.16), residues: 2917 helix: 0.77 (0.16), residues: 1123 sheet: 0.60 (0.21), residues: 636 loop : 0.45 (0.20), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 225 TYR 0.020 0.001 TYR C 279 PHE 0.013 0.001 PHE C 31 TRP 0.010 0.001 TRP F 86 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00220 (23793) covalent geometry : angle 0.57035 (32266) hydrogen bonds : bond 0.02759 ( 992) hydrogen bonds : angle 4.36167 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4506.87 seconds wall clock time: 78 minutes 42.32 seconds (4722.32 seconds total)