Starting phenix.real_space_refine on Fri Jun 20 07:28:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vkh_43316/06_2025/8vkh_43316.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vkh_43316/06_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_43316/06_2025/8vkh_43316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vkh_43316/06_2025/8vkh_43316.map" model { file = "/net/cci-nas-00/data/ceres_data/8vkh_43316/06_2025/8vkh_43316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vkh_43316/06_2025/8vkh_43316.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.76, per 1000 atoms: 0.81 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: 5.32 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.71 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: 9.11 Time building geometry restraints manager: 6.37 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 380 or resid 801 throu \ gh 804)) selection = (chain 'H' and (resid 24 through 206 or resid 208 through 380 or resid 801 throu \ gh 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: 6.180 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: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 61.300 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.170 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.129 0.004 TRP D 86 HIS 0.017 0.002 HIS E 173 PHE 0.039 0.003 PHE G 316 TYR 0.048 0.003 TYR C 279 ARG 0.017 0.002 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.18372 ( 992) hydrogen bonds : angle 7.36218 ( 2646) covalent geometry : bond 0.00590 (23793) covalent geometry : angle 1.11286 (32266) *********************** 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 : 2.658 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: 0.3268 time to fit residues: 148.9869 Evaluate side-chains 177 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 228 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 265 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.062958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.048127 restraints weight = 108146.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049660 restraints weight = 53128.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050660 restraints weight = 32551.584| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23793 Z= 0.134 Angle : 0.621 9.785 32266 Z= 0.310 Chirality : 0.044 0.155 3539 Planarity : 0.005 0.072 4160 Dihedral : 7.352 79.647 3327 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.89 % Allowed : 5.31 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 2917 helix: -0.44 (0.15), residues: 1079 sheet: 0.25 (0.20), residues: 645 loop : -0.26 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 86 HIS 0.004 0.001 HIS A 161 PHE 0.017 0.001 PHE G 125 TYR 0.017 0.001 TYR G 87 ARG 0.007 0.001 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 992) hydrogen bonds : angle 5.10520 ( 2646) covalent geometry : bond 0.00312 (23793) covalent geometry : angle 0.62093 (32266) *********************** 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 215 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8441 (mp0) REVERT: A 355 MET cc_start: 0.8526 (mpp) cc_final: 0.8005 (mpp) REVERT: B 340 TRP cc_start: 0.8812 (t60) cc_final: 0.8132 (t60) REVERT: C 82 MET cc_start: 0.8468 (tpp) cc_final: 0.8222 (tpp) REVERT: C 176 MET cc_start: 0.8696 (tpp) cc_final: 0.8436 (mmt) REVERT: C 227 MET cc_start: 0.8623 (mmt) cc_final: 0.8250 (mmt) REVERT: D 82 MET cc_start: 0.9081 (tpp) cc_final: 0.7526 (tpp) REVERT: D 86 TRP cc_start: 0.8375 (m-90) cc_final: 0.8161 (m-90) REVERT: D 276 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7219 (tm-30) REVERT: E 82 MET cc_start: 0.9273 (tpt) cc_final: 0.8946 (mmm) REVERT: F 283 MET cc_start: 0.9089 (mmm) cc_final: 0.8869 (mmm) REVERT: F 355 MET cc_start: 0.9267 (mtp) cc_final: 0.8948 (ptp) REVERT: G 309 HIS cc_start: 0.8195 (t-90) cc_final: 0.7941 (t-90) REVERT: G 349 GLN cc_start: 0.8553 (tp-100) cc_final: 0.7809 (pp30) REVERT: H 125 PHE cc_start: 0.8357 (m-80) cc_final: 0.7965 (m-80) REVERT: H 304 CYS cc_start: 0.8552 (m) cc_final: 0.8324 (m) outliers start: 18 outliers final: 8 residues processed: 207 average time/residue: 0.3266 time to fit residues: 110.8817 Evaluate side-chains 179 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 2.887 ------------------------------------------------------------------------------- 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 122 ILE 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 159 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.0670 chunk 291 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- 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 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 162 ASN F 128 ASN F 314 GLN G 118 GLN ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.060599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.045635 restraints weight = 109409.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.047123 restraints weight = 53862.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.048060 restraints weight = 33216.305| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 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 = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2348 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= 0.174 Angle : 0.621 7.386 32266 Z= 0.310 Chirality : 0.045 0.152 3539 Planarity : 0.005 0.064 4160 Dihedral : 6.936 89.313 3327 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.85 % Allowed : 7.85 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2917 helix: 0.42 (0.16), residues: 1063 sheet: 0.19 (0.20), residues: 664 loop : 0.14 (0.19), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 86 HIS 0.007 0.001 HIS G 119 PHE 0.014 0.002 PHE D 255 TYR 0.024 0.002 TYR C 143 ARG 0.007 0.001 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 992) hydrogen bonds : angle 4.68997 ( 2646) covalent geometry : bond 0.00398 (23793) covalent geometry : angle 0.62087 (32266) *********************** 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 202 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 2.668 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: 0.9254 (mmm) cc_final: 0.8698 (tpp) REVERT: A 355 MET cc_start: 0.8795 (mpp) cc_final: 0.7986 (mpp) REVERT: B 47 MET cc_start: 0.8580 (mmm) cc_final: 0.8270 (mmt) REVERT: C 82 MET cc_start: 0.8512 (tpp) cc_final: 0.8230 (tpp) REVERT: C 176 MET cc_start: 0.8837 (tpp) cc_final: 0.8601 (mmt) REVERT: C 227 MET cc_start: 0.8641 (mmt) cc_final: 0.8199 (mmt) REVERT: D 82 MET cc_start: 0.9286 (tpp) cc_final: 0.7981 (tpp) REVERT: D 86 TRP cc_start: 0.8624 (m-10) cc_final: 0.8046 (m-90) REVERT: D 217 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8051 (m) REVERT: D 276 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7415 (tm-30) REVERT: E 82 MET cc_start: 0.9264 (tpt) cc_final: 0.8954 (mmm) REVERT: E 285 CYS cc_start: 0.8672 (m) cc_final: 0.8452 (t) REVERT: F 86 TRP cc_start: 0.8639 (m-10) cc_final: 0.8279 (m-10) REVERT: F 123 MET cc_start: 0.9097 (mmm) cc_final: 0.7968 (mmm) REVERT: F 294 TYR cc_start: 0.7600 (m-80) cc_final: 0.7394 (t80) REVERT: F 364 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: G 199 GLN cc_start: 0.8902 (tt0) cc_final: 0.8670 (tt0) REVERT: G 235 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8298 (mm-30) REVERT: G 309 HIS cc_start: 0.8173 (t-90) cc_final: 0.7871 (t-90) REVERT: G 315 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7745 (tp) REVERT: G 349 GLN cc_start: 0.8519 (tp-100) cc_final: 0.7917 (pp30) REVERT: H 125 PHE cc_start: 0.8457 (m-80) cc_final: 0.8035 (m-80) REVERT: H 342 MET cc_start: 0.8574 (mpp) cc_final: 0.8200 (mpp) outliers start: 17 outliers final: 8 residues processed: 195 average time/residue: 0.3153 time to fit residues: 102.9160 Evaluate side-chains 179 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain D residue 217 CYS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 187 ASP 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 315 ILE Chi-restraints excluded: chain H residue 364 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 253 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 257 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 HIS ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.060102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045082 restraints weight = 109822.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046581 restraints weight = 53378.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047575 restraints weight = 32735.391| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 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 = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23793 Z= 0.170 Angle : 0.593 11.247 32266 Z= 0.293 Chirality : 0.044 0.155 3539 Planarity : 0.004 0.058 4160 Dihedral : 6.813 83.387 3327 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.93 % Allowed : 8.73 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2917 helix: 0.65 (0.16), residues: 1066 sheet: 0.22 (0.20), residues: 667 loop : 0.30 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 86 HIS 0.004 0.001 HIS D 371 PHE 0.015 0.001 PHE G 125 TYR 0.030 0.001 TYR C 279 ARG 0.005 0.000 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 992) hydrogen bonds : angle 4.61097 ( 2646) covalent geometry : bond 0.00388 (23793) covalent geometry : angle 0.59292 (32266) *********************** 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 186 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9273 (mmm) cc_final: 0.8687 (tpp) REVERT: A 355 MET cc_start: 0.8865 (mpp) cc_final: 0.7938 (mpp) REVERT: B 337 TYR cc_start: 0.8854 (m-10) cc_final: 0.8643 (m-80) REVERT: C 176 MET cc_start: 0.8906 (tpp) cc_final: 0.8693 (mmt) REVERT: C 227 MET cc_start: 0.8675 (mmt) cc_final: 0.8331 (mmt) REVERT: C 283 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.7845 (mpp) REVERT: C 325 MET cc_start: 0.7384 (mtt) cc_final: 0.7179 (mtt) REVERT: D 82 MET cc_start: 0.9352 (tpp) cc_final: 0.8946 (tpp) REVERT: D 217 CYS cc_start: 0.8609 (m) cc_final: 0.8252 (m) REVERT: D 276 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7672 (tm-30) REVERT: E 82 MET cc_start: 0.9242 (tpt) cc_final: 0.8767 (mmm) REVERT: F 86 TRP cc_start: 0.8777 (m-10) cc_final: 0.8259 (m-10) REVERT: F 123 MET cc_start: 0.9085 (mmm) cc_final: 0.8441 (mmm) REVERT: F 190 MET cc_start: 0.8341 (tpt) cc_final: 0.8091 (mmm) REVERT: F 227 MET cc_start: 0.9087 (mmm) cc_final: 0.8878 (mmm) REVERT: F 283 MET cc_start: 0.8978 (mmm) cc_final: 0.8721 (mmm) REVERT: F 294 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.7329 (t80) REVERT: F 297 ASN cc_start: 0.8650 (t0) cc_final: 0.8407 (m-40) REVERT: F 299 MET cc_start: 0.7733 (mtm) cc_final: 0.7488 (mmm) REVERT: F 355 MET cc_start: 0.9294 (mtp) cc_final: 0.9022 (ptm) REVERT: G 199 GLN cc_start: 0.8862 (tt0) cc_final: 0.8600 (tt0) REVERT: G 349 GLN cc_start: 0.8687 (tp-100) cc_final: 0.7897 (pp30) REVERT: H 125 PHE cc_start: 0.8450 (m-80) cc_final: 0.8041 (m-80) outliers start: 19 outliers final: 11 residues processed: 180 average time/residue: 0.3174 time to fit residues: 96.6939 Evaluate side-chains 174 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 364 GLU 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 364 GLU Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain G residue 93 CYS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN C 354 GLN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.062456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.047649 restraints weight = 108305.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.049239 restraints weight = 50277.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.050258 restraints weight = 30109.386| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23793 Z= 0.111 Angle : 0.557 9.336 32266 Z= 0.271 Chirality : 0.043 0.152 3539 Planarity : 0.004 0.056 4160 Dihedral : 6.610 79.208 3327 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.93 % Allowed : 10.06 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.16), residues: 2917 helix: 0.77 (0.16), residues: 1089 sheet: 0.48 (0.20), residues: 637 loop : 0.41 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 86 HIS 0.003 0.001 HIS D 371 PHE 0.012 0.001 PHE C 31 TYR 0.023 0.001 TYR C 279 ARG 0.003 0.000 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 992) hydrogen bonds : angle 4.43808 ( 2646) covalent geometry : bond 0.00259 (23793) covalent geometry : angle 0.55653 (32266) *********************** 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 189 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 2.904 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 355 MET cc_start: 0.8895 (mpp) cc_final: 0.8003 (mpp) REVERT: B 325 MET cc_start: 0.8970 (mmm) cc_final: 0.7867 (tpp) REVERT: B 337 TYR cc_start: 0.8825 (m-10) cc_final: 0.8609 (m-80) REVERT: C 44 MET cc_start: 0.8627 (tpp) cc_final: 0.8329 (tpp) REVERT: C 82 MET cc_start: 0.8573 (tpp) cc_final: 0.8124 (tpp) REVERT: C 227 MET cc_start: 0.8668 (mmt) cc_final: 0.8338 (mmt) REVERT: C 283 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8059 (mpp) REVERT: D 82 MET cc_start: 0.9358 (tpp) cc_final: 0.8921 (tpp) REVERT: D 217 CYS cc_start: 0.8591 (m) cc_final: 0.8092 (m) REVERT: D 276 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7622 (tm-30) REVERT: E 82 MET cc_start: 0.9225 (tpt) cc_final: 0.8741 (mmm) REVERT: E 285 CYS cc_start: 0.8550 (t) cc_final: 0.8333 (m) REVERT: F 86 TRP cc_start: 0.8803 (m-10) cc_final: 0.8179 (m-10) REVERT: F 123 MET cc_start: 0.9069 (mmm) cc_final: 0.8565 (mmm) REVERT: F 283 MET cc_start: 0.9037 (mmm) cc_final: 0.8738 (mmm) REVERT: F 294 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.7260 (t80) REVERT: F 297 ASN cc_start: 0.8681 (t0) cc_final: 0.8439 (m-40) REVERT: F 299 MET cc_start: 0.7750 (mtm) cc_final: 0.7452 (mmm) REVERT: F 355 MET cc_start: 0.9266 (mtp) cc_final: 0.8949 (ptm) REVERT: F 364 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: H 125 PHE cc_start: 0.8401 (m-80) cc_final: 0.7994 (m-80) outliers start: 19 outliers final: 10 residues processed: 181 average time/residue: 0.3066 time to fit residues: 94.2616 Evaluate side-chains 175 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 364 GLU 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 H residue 338 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 17 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 108 optimal weight: 0.0870 chunk 205 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS D 92 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.061005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.046190 restraints weight = 109000.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.047720 restraints weight = 51267.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.048717 restraints weight = 30982.754| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 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 = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23793 Z= 0.201 Angle : 0.616 8.983 32266 Z= 0.303 Chirality : 0.045 0.232 3539 Planarity : 0.004 0.053 4160 Dihedral : 6.665 77.843 3327 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.17 % Allowed : 9.98 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 2917 helix: 0.84 (0.16), residues: 1066 sheet: 0.29 (0.20), residues: 667 loop : 0.42 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 79 HIS 0.004 0.001 HIS C 275 PHE 0.017 0.001 PHE G 125 TYR 0.020 0.001 TYR C 279 ARG 0.004 0.000 ARG H 225 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 992) hydrogen bonds : angle 4.57756 ( 2646) covalent geometry : bond 0.00457 (23793) covalent geometry : angle 0.61578 (32266) *********************** 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 185 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.8853 (mpp) cc_final: 0.8388 (mmt) REVERT: B 162 ASN cc_start: 0.8575 (t0) cc_final: 0.8186 (t0) REVERT: B 337 TYR cc_start: 0.8832 (m-10) cc_final: 0.8622 (m-80) REVERT: C 82 MET cc_start: 0.8723 (tpp) cc_final: 0.8391 (tpp) REVERT: C 227 MET cc_start: 0.8711 (mmt) cc_final: 0.8358 (mmt) REVERT: C 283 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8251 (mpp) REVERT: D 82 MET cc_start: 0.9341 (tpp) cc_final: 0.8904 (tpp) REVERT: D 217 CYS cc_start: 0.8576 (m) cc_final: 0.8130 (m) REVERT: D 276 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7678 (tm-30) REVERT: E 82 MET cc_start: 0.9244 (tpt) cc_final: 0.8801 (mmm) REVERT: E 269 MET cc_start: 0.8532 (mmm) cc_final: 0.8208 (mmm) REVERT: F 82 MET cc_start: 0.8848 (tpt) cc_final: 0.8151 (tpp) REVERT: F 86 TRP cc_start: 0.8857 (m-10) cc_final: 0.8522 (m-10) REVERT: F 123 MET cc_start: 0.9069 (mmm) cc_final: 0.8670 (mmt) REVERT: F 283 MET cc_start: 0.9022 (mmm) cc_final: 0.8714 (mmm) REVERT: F 294 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7402 (t80) REVERT: F 355 MET cc_start: 0.9291 (mtp) cc_final: 0.8983 (ptp) REVERT: F 364 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: G 85 LEU cc_start: 0.9174 (mm) cc_final: 0.8640 (mt) REVERT: H 125 PHE cc_start: 0.8464 (m-80) cc_final: 0.8037 (m-80) outliers start: 25 outliers final: 12 residues processed: 178 average time/residue: 0.3086 time to fit residues: 93.6674 Evaluate side-chains 167 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 2.925 ------------------------------------------------------------------------------- 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 201 VAL Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 364 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 113 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 197 optimal weight: 0.0770 chunk 254 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 1.7542 ------------------------------------------------------------------------------- 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** F 88 HIS ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.060606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.045677 restraints weight = 108791.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047203 restraints weight = 51452.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048195 restraints weight = 31152.713| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 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 = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3242 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= 0.142 Angle : 0.582 10.906 32266 Z= 0.284 Chirality : 0.044 0.195 3539 Planarity : 0.004 0.052 4160 Dihedral : 6.546 78.573 3327 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.09 % Allowed : 10.34 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2917 helix: 0.87 (0.16), residues: 1082 sheet: 0.39 (0.20), residues: 684 loop : 0.45 (0.20), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS D 371 PHE 0.033 0.001 PHE A 223 TYR 0.017 0.001 TYR G 140 ARG 0.003 0.000 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 992) hydrogen bonds : angle 4.48670 ( 2646) covalent geometry : bond 0.00330 (23793) covalent geometry : angle 0.58230 (32266) *********************** 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 183 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9156 (mmm) cc_final: 0.8877 (mmt) REVERT: A 325 MET cc_start: 0.8914 (mmm) cc_final: 0.8429 (tpp) REVERT: A 355 MET cc_start: 0.8864 (mpp) cc_final: 0.8410 (mmt) REVERT: B 162 ASN cc_start: 0.8570 (t0) cc_final: 0.8295 (t0) REVERT: B 337 TYR cc_start: 0.8859 (m-10) cc_final: 0.8642 (m-80) REVERT: C 44 MET cc_start: 0.8602 (mmm) cc_final: 0.7861 (mmt) REVERT: C 82 MET cc_start: 0.8640 (tpp) cc_final: 0.8256 (tpp) REVERT: C 227 MET cc_start: 0.8705 (mmt) cc_final: 0.8393 (mmt) REVERT: C 283 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8359 (mpp) REVERT: D 82 MET cc_start: 0.9319 (tpp) cc_final: 0.8853 (tpp) REVERT: D 217 CYS cc_start: 0.8642 (m) cc_final: 0.8123 (m) REVERT: D 276 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7685 (tm-30) REVERT: E 82 MET cc_start: 0.9202 (tpt) cc_final: 0.8750 (mmm) REVERT: E 355 MET cc_start: 0.9093 (mmm) cc_final: 0.8637 (mmm) REVERT: F 82 MET cc_start: 0.8857 (tpt) cc_final: 0.8180 (tpp) REVERT: F 86 TRP cc_start: 0.8916 (m-10) cc_final: 0.8178 (m-10) REVERT: F 123 MET cc_start: 0.9133 (mmm) cc_final: 0.8754 (mmm) REVERT: F 227 MET cc_start: 0.8981 (mmm) cc_final: 0.8750 (mmm) REVERT: F 294 TYR cc_start: 0.7649 (m-80) cc_final: 0.7349 (t80) REVERT: F 299 MET cc_start: 0.7766 (mtm) cc_final: 0.7558 (mmm) REVERT: F 355 MET cc_start: 0.9330 (mtp) cc_final: 0.8990 (ptp) REVERT: F 364 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: G 85 LEU cc_start: 0.9146 (mm) cc_final: 0.8600 (mt) REVERT: H 25 MET cc_start: 0.7223 (tpt) cc_final: 0.6827 (tmm) REVERT: H 125 PHE cc_start: 0.8472 (m-80) cc_final: 0.8042 (m-80) outliers start: 23 outliers final: 11 residues processed: 174 average time/residue: 0.3105 time to fit residues: 91.7832 Evaluate side-chains 170 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 2.949 ------------------------------------------------------------------------------- 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 D residue 355 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 364 GLU 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 158 VAL Chi-restraints excluded: chain G residue 174 THR 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 157 optimal weight: 8.9990 chunk 76 optimal weight: 0.0270 chunk 170 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 269 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.7644 ------------------------------------------------------------------------------- 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** ** H 368 ASN ** 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 = 0.3401 r_free = 0.3401 target = 0.060583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.045669 restraints weight = 108988.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.047189 restraints weight = 51488.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048179 restraints weight = 31149.197| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 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 = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3370 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= 0.143 Angle : 0.580 11.283 32266 Z= 0.282 Chirality : 0.044 0.180 3539 Planarity : 0.004 0.051 4160 Dihedral : 6.469 78.946 3327 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.05 % Allowed : 10.46 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 2917 helix: 0.86 (0.16), residues: 1093 sheet: 0.41 (0.20), residues: 686 loop : 0.48 (0.20), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.003 0.001 HIS D 371 PHE 0.016 0.001 PHE G 125 TYR 0.017 0.001 TYR C 279 ARG 0.003 0.000 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 992) hydrogen bonds : angle 4.46369 ( 2646) covalent geometry : bond 0.00332 (23793) covalent geometry : angle 0.58046 (32266) *********************** 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 180 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 3.088 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: 0.9311 (mtp) cc_final: 0.8859 (tpp) REVERT: A 305 MET cc_start: 0.9154 (mmm) cc_final: 0.8869 (mmt) REVERT: A 325 MET cc_start: 0.8931 (mmm) cc_final: 0.8400 (tpp) REVERT: A 355 MET cc_start: 0.8837 (mpp) cc_final: 0.8412 (mmt) REVERT: B 162 ASN cc_start: 0.8566 (t0) cc_final: 0.8302 (t0) REVERT: B 337 TYR cc_start: 0.8904 (m-10) cc_final: 0.8672 (m-80) REVERT: B 355 MET cc_start: 0.8402 (mtm) cc_final: 0.8112 (mtm) REVERT: C 44 MET cc_start: 0.8734 (mmm) cc_final: 0.7920 (mmt) REVERT: C 82 MET cc_start: 0.8674 (tpp) cc_final: 0.8294 (tpp) REVERT: C 227 MET cc_start: 0.8708 (mmt) cc_final: 0.8398 (mmt) REVERT: C 283 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8419 (mpp) REVERT: D 82 MET cc_start: 0.9297 (tpp) cc_final: 0.8851 (tpp) REVERT: D 217 CYS cc_start: 0.8645 (m) cc_final: 0.8166 (m) REVERT: D 276 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7677 (tm-30) REVERT: E 82 MET cc_start: 0.9201 (tpt) cc_final: 0.8733 (mmm) REVERT: E 269 MET cc_start: 0.8553 (mmm) cc_final: 0.8190 (mmm) REVERT: F 82 MET cc_start: 0.8861 (tpt) cc_final: 0.8437 (tpp) REVERT: F 227 MET cc_start: 0.8992 (mmm) cc_final: 0.8775 (mmm) REVERT: F 294 TYR cc_start: 0.7657 (m-80) cc_final: 0.7433 (t80) REVERT: F 355 MET cc_start: 0.9301 (mtp) cc_final: 0.8965 (ptp) REVERT: F 364 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: G 85 LEU cc_start: 0.9142 (mm) cc_final: 0.8589 (mt) REVERT: H 125 PHE cc_start: 0.8466 (m-80) cc_final: 0.8032 (m-80) outliers start: 22 outliers final: 15 residues processed: 174 average time/residue: 0.3185 time to fit residues: 94.3861 Evaluate side-chains 172 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 125 GLU 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 B residue 257 CYS 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 E residue 364 GLU Chi-restraints excluded: chain F residue 103 THR 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 158 VAL Chi-restraints excluded: chain G residue 174 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 51 optimal weight: 0.0770 chunk 240 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.9942 ------------------------------------------------------------------------------- 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** F 88 HIS F 92 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 HIS ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.060468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.045611 restraints weight = 109241.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.047136 restraints weight = 51410.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048133 restraints weight = 31072.353| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 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 = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23793 Z= 0.157 Angle : 0.606 10.855 32266 Z= 0.292 Chirality : 0.044 0.192 3539 Planarity : 0.004 0.051 4160 Dihedral : 6.453 78.893 3327 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.01 % Allowed : 10.82 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2917 helix: 0.85 (0.16), residues: 1099 sheet: 0.37 (0.20), residues: 668 loop : 0.49 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 86 HIS 0.003 0.001 HIS D 371 PHE 0.011 0.001 PHE C 31 TYR 0.018 0.001 TYR G 140 ARG 0.003 0.000 ARG E 254 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 992) hydrogen bonds : angle 4.47852 ( 2646) covalent geometry : bond 0.00363 (23793) covalent geometry : angle 0.60578 (32266) *********************** 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: 21 poor density : 158 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9312 (mtp) cc_final: 0.8909 (tpp) REVERT: A 305 MET cc_start: 0.9152 (mmm) cc_final: 0.8864 (mmt) REVERT: A 325 MET cc_start: 0.8939 (mmm) cc_final: 0.8376 (tpp) REVERT: A 355 MET cc_start: 0.8833 (mpp) cc_final: 0.8404 (mmt) REVERT: B 47 MET cc_start: 0.8202 (mmm) cc_final: 0.7928 (mmt) REVERT: B 162 ASN cc_start: 0.8557 (t0) cc_final: 0.8307 (t0) REVERT: B 337 TYR cc_start: 0.8906 (m-10) cc_final: 0.8679 (m-80) REVERT: B 355 MET cc_start: 0.8411 (mtm) cc_final: 0.8058 (mtm) REVERT: C 44 MET cc_start: 0.8761 (mmm) cc_final: 0.7924 (mmt) REVERT: C 82 MET cc_start: 0.8670 (tpp) cc_final: 0.8293 (tpp) REVERT: C 227 MET cc_start: 0.8711 (mmt) cc_final: 0.8401 (mmt) REVERT: C 283 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8437 (mpp) REVERT: D 47 MET cc_start: 0.7195 (pmm) cc_final: 0.6881 (pmm) REVERT: D 82 MET cc_start: 0.9273 (tpp) cc_final: 0.8818 (tpp) REVERT: D 217 CYS cc_start: 0.8671 (m) cc_final: 0.8260 (m) REVERT: D 276 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7758 (tm-30) REVERT: E 82 MET cc_start: 0.9203 (tpt) cc_final: 0.8734 (mmm) REVERT: E 269 MET cc_start: 0.8608 (mmm) cc_final: 0.8153 (mmm) REVERT: F 82 MET cc_start: 0.8877 (tpt) cc_final: 0.8605 (tpp) REVERT: F 227 MET cc_start: 0.8999 (mmm) cc_final: 0.8797 (mmm) REVERT: F 294 TYR cc_start: 0.7622 (m-80) cc_final: 0.7374 (t80) REVERT: F 355 MET cc_start: 0.9352 (mtp) cc_final: 0.9047 (ptp) REVERT: F 364 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: G 25 MET cc_start: 0.5220 (tmm) cc_final: 0.4995 (tmm) REVERT: G 85 LEU cc_start: 0.9146 (mm) cc_final: 0.8658 (mt) REVERT: H 25 MET cc_start: 0.6241 (mmp) cc_final: 0.6012 (tpt) REVERT: H 125 PHE cc_start: 0.8479 (m-80) cc_final: 0.8038 (m-80) outliers start: 21 outliers final: 14 residues processed: 172 average time/residue: 0.2970 time to fit residues: 86.4821 Evaluate side-chains 170 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 125 GLU 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 B residue 115 ASN Chi-restraints excluded: chain B residue 257 CYS 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 E residue 364 GLU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 185 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 282 optimal weight: 20.0000 chunk 32 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 263 GLN F 92 ASN ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.058179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.043294 restraints weight = 112261.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044776 restraints weight = 54232.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045748 restraints weight = 33174.264| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 23793 Z= 0.322 Angle : 0.747 12.368 32266 Z= 0.368 Chirality : 0.048 0.202 3539 Planarity : 0.004 0.051 4160 Dihedral : 6.856 77.855 3327 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.80 % Allowed : 11.55 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2917 helix: 0.55 (0.16), residues: 1096 sheet: 0.21 (0.20), residues: 642 loop : 0.24 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 44 HIS 0.006 0.001 HIS B 40 PHE 0.013 0.002 PHE G 125 TYR 0.027 0.002 TYR F 143 ARG 0.004 0.001 ARG E 254 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 992) hydrogen bonds : angle 4.92630 ( 2646) covalent geometry : bond 0.00721 (23793) covalent geometry : angle 0.74683 (32266) ********************** 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 161 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9380 (mtp) cc_final: 0.8966 (tpp) REVERT: A 305 MET cc_start: 0.9132 (mmm) cc_final: 0.8817 (mmt) REVERT: A 355 MET cc_start: 0.8857 (mpp) cc_final: 0.8381 (mmt) REVERT: B 162 ASN cc_start: 0.8575 (t0) cc_final: 0.8372 (t0) REVERT: B 227 MET cc_start: 0.9215 (tpp) cc_final: 0.8878 (tpt) REVERT: B 325 MET cc_start: 0.9084 (mmm) cc_final: 0.8484 (tpp) REVERT: B 337 TYR cc_start: 0.8973 (m-10) cc_final: 0.8754 (m-80) REVERT: B 355 MET cc_start: 0.8467 (mtm) cc_final: 0.8028 (mtm) REVERT: C 44 MET cc_start: 0.8789 (mmm) cc_final: 0.7969 (mmt) REVERT: C 82 MET cc_start: 0.8843 (tpp) cc_final: 0.8501 (tpp) REVERT: C 227 MET cc_start: 0.8707 (mmt) cc_final: 0.8443 (mmt) REVERT: C 283 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8512 (mpp) REVERT: D 82 MET cc_start: 0.9304 (tpp) cc_final: 0.8855 (tpp) REVERT: D 217 CYS cc_start: 0.8659 (m) cc_final: 0.8374 (m) REVERT: D 276 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7775 (tm-30) REVERT: E 82 MET cc_start: 0.9250 (tpt) cc_final: 0.8856 (mmm) REVERT: E 269 MET cc_start: 0.8725 (mmm) cc_final: 0.8342 (mmm) REVERT: F 294 TYR cc_start: 0.7460 (m-80) cc_final: 0.7192 (t80) REVERT: F 364 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: H 25 MET cc_start: 0.6180 (mmp) cc_final: 0.5752 (tmm) REVERT: H 125 PHE cc_start: 0.8590 (m-80) cc_final: 0.8170 (m-10) outliers start: 16 outliers final: 10 residues processed: 158 average time/residue: 0.3086 time to fit residues: 82.8784 Evaluate side-chains 155 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 2.798 ------------------------------------------------------------------------------- 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 B residue 257 CYS Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 84 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 137 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.045208 restraints weight = 109355.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046694 restraints weight = 52954.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.047669 restraints weight = 32379.904| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 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 = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3705 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= 0.103 Angle : 0.598 11.869 32266 Z= 0.289 Chirality : 0.044 0.202 3539 Planarity : 0.004 0.051 4160 Dihedral : 6.432 79.389 3327 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.80 % Allowed : 11.35 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.16), residues: 2917 helix: 0.75 (0.16), residues: 1108 sheet: 0.44 (0.20), residues: 646 loop : 0.43 (0.20), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 86 HIS 0.003 0.001 HIS D 371 PHE 0.016 0.001 PHE G 125 TYR 0.019 0.001 TYR G 140 ARG 0.002 0.000 ARG E 254 Details of bonding type rmsd hydrogen bonds : bond 0.02973 ( 992) hydrogen bonds : angle 4.56489 ( 2646) covalent geometry : bond 0.00243 (23793) covalent geometry : angle 0.59848 (32266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7894.74 seconds wall clock time: 137 minutes 46.26 seconds (8266.26 seconds total)