Starting phenix.real_space_refine on Fri Mar 6 01:07:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x0y_32929/03_2026/7x0y_32929_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x0y_32929/03_2026/7x0y_32929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x0y_32929/03_2026/7x0y_32929_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x0y_32929/03_2026/7x0y_32929_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x0y_32929/03_2026/7x0y_32929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x0y_32929/03_2026/7x0y_32929.map" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14118 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 64 5.16 5 C 9842 2.51 5 N 2582 2.21 5 O 2746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15242 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3718 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 25, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3739 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 25, 'TRANS': 434} Chain breaks: 1 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3742 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 25, 'TRANS': 434} Chain breaks: 1 Chain: "D" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3751 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 25, 'TRANS': 436} Chain breaks: 1 Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.58, per 1000 atoms: 0.23 Number of scatterers: 15242 At special positions: 0 Unit cell: (81.75, 119.9, 131.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 8 15.00 O 2746 8.00 N 2582 7.00 C 9842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 643.1 milliseconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3506 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 5 sheets defined 55.5% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'C' and resid 23 through 28 removed outlier: 3.671A pdb=" N ALA C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 28' Processing helix chain 'C' and resid 43 through 47 removed outlier: 4.019A pdb=" N TYR C 47 " --> pdb=" O GLY C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 68 removed outlier: 3.738A pdb=" N LYS C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN C 58 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 59 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 81 through 94 removed outlier: 3.969A pdb=" N ALA C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.996A pdb=" N VAL C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ARG C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.794A pdb=" N TYR C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS C 158 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.931A pdb=" N LEU C 205 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 206 " --> pdb=" O ASN C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.616A pdb=" N ALA C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP C 218 " --> pdb=" O TRP C 214 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 257 through 275 removed outlier: 3.537A pdb=" N ASP C 275 " --> pdb=" O ILE C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 304 removed outlier: 3.549A pdb=" N GLU C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG C 298 " --> pdb=" O ARG C 294 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 303 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 325 through 332 removed outlier: 3.722A pdb=" N TRP C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 removed outlier: 4.029A pdb=" N GLY C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 369 removed outlier: 3.842A pdb=" N PHE C 365 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 4.435A pdb=" N TYR C 380 " --> pdb=" O TRP C 376 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 401 removed outlier: 4.699A pdb=" N LEU C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 401 " --> pdb=" O TRP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 Processing helix chain 'C' and resid 435 through 438 removed outlier: 4.160A pdb=" N ALA C 438 " --> pdb=" O PRO C 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 438' Processing helix chain 'C' and resid 447 through 452 Proline residue: C 452 - end of helix Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.582A pdb=" N LYS C 457 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 458' Processing helix chain 'B' and resid 20 through 28 removed outlier: 3.652A pdb=" N ALA B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 70 removed outlier: 4.192A pdb=" N ALA B 61 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 91 removed outlier: 4.001A pdb=" N ARG B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 121 removed outlier: 4.191A pdb=" N VAL B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 181 through 185 removed outlier: 4.321A pdb=" N ILE B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 213 through 226 removed outlier: 3.559A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 218 " --> pdb=" O TRP B 214 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 removed outlier: 3.565A pdb=" N TYR B 232 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA B 233 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 266 through 275 removed outlier: 4.905A pdb=" N TRP B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 273 " --> pdb=" O GLN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 285 removed outlier: 3.806A pdb=" N ASP B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 302 removed outlier: 3.596A pdb=" N GLY B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 removed outlier: 3.814A pdb=" N ARG B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 352 removed outlier: 3.809A pdb=" N GLU B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 360 through 369 removed outlier: 3.766A pdb=" N SER B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 369 " --> pdb=" O PHE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.683A pdb=" N LYS B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 380 " --> pdb=" O TRP B 376 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 399 removed outlier: 3.820A pdb=" N LEU B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 removed outlier: 4.143A pdb=" N LYS B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.782A pdb=" N TRP B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 438 Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.370A pdb=" N HIS B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.761A pdb=" N ASP B 450 " --> pdb=" O HIS B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 459 removed outlier: 3.546A pdb=" N LEU B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 26 removed outlier: 3.901A pdb=" N ALA A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 49 through 69 removed outlier: 3.652A pdb=" N TRP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HIS A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 66 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.558A pdb=" N ASP A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.630A pdb=" N ARG A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.907A pdb=" N LYS A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 4.080A pdb=" N ASP A 160 " --> pdb=" O LYS A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.526A pdb=" N ASN A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 204' Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.649A pdb=" N ARG A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.583A pdb=" N LYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.881A pdb=" N GLN A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS A 268 " --> pdb=" O CYS A 264 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 304 removed outlier: 3.517A pdb=" N ALA A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 324 through 332 removed outlier: 4.227A pdb=" N PHE A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 352 removed outlier: 3.560A pdb=" N MET A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.537A pdb=" N ILE A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.555A pdb=" N GLY A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 380 " --> pdb=" O TRP A 376 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 removed outlier: 3.574A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 424 removed outlier: 3.608A pdb=" N GLN A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 434 removed outlier: 3.621A pdb=" N TRP A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.517A pdb=" N HIS A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.523A pdb=" N ASP A 450 " --> pdb=" O HIS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'D' and resid 22 through 30 removed outlier: 3.607A pdb=" N ALA D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 30' Processing helix chain 'D' and resid 51 through 68 removed outlier: 3.575A pdb=" N LEU D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'D' and resid 108 through 118 removed outlier: 3.576A pdb=" N HIS D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 123 removed outlier: 3.775A pdb=" N ARG D 122 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 160 Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.874A pdb=" N ARG D 208 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.657A pdb=" N LYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU D 226 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.718A pdb=" N LEU D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 262 through 276 removed outlier: 4.593A pdb=" N LYS D 268 " --> pdb=" O CYS D 264 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE D 271 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 273 " --> pdb=" O GLN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 304 removed outlier: 3.631A pdb=" N ASP D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.764A pdb=" N GLN D 310 " --> pdb=" O THR D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.922A pdb=" N ARG D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN D 333 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 removed outlier: 3.591A pdb=" N GLY D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET D 345 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 346 " --> pdb=" O ASP D 342 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 369 removed outlier: 4.006A pdb=" N VAL D 360 " --> pdb=" O ASN D 356 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 364 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.734A pdb=" N TYR D 380 " --> pdb=" O TRP D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 400 removed outlier: 3.705A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 424 removed outlier: 3.949A pdb=" N GLN D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 420 " --> pdb=" O PRO D 416 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 452 through 459 removed outlier: 3.750A pdb=" N LEU D 456 " --> pdb=" O PRO D 452 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 457 " --> pdb=" O LEU D 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'F' and resid 2 through 6 Processing sheet with id=AA1, first strand: chain 'C' and resid 98 through 101 removed outlier: 6.573A pdb=" N VAL C 98 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR C 129 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE C 100 " --> pdb=" O TYR C 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.057A pdb=" N PHE A 33 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 9 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 8 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 99 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 98 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N TYR A 129 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE A 100 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA5, first strand: chain 'D' and resid 75 through 78 removed outlier: 8.930A pdb=" N THR D 75 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE D 77 " --> pdb=" O PRO D 34 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE D 36 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 7 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE D 33 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL D 9 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE D 37 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 97 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN D 101 " --> pdb=" O TRP D 10 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N TYR D 129 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE D 100 " --> pdb=" O TYR D 129 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1314 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: 2.12 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4793 1.34 - 1.46: 3786 1.46 - 1.58: 7031 1.58 - 1.69: 5 1.69 - 1.81: 96 Bond restraints: 15711 Sorted by residual: bond pdb=" O5B FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sigma weight residual 1.634 1.516 0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" O3P FAD A 701 " pdb=" P FAD A 701 " ideal model delta sigma weight residual 1.660 1.558 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O3P FAD D 701 " pdb=" P FAD D 701 " ideal model delta sigma weight residual 1.660 1.561 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O5B FAD B 701 " pdb=" PA FAD B 701 " ideal model delta sigma weight residual 1.634 1.543 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O5B FAD D 701 " pdb=" PA FAD D 701 " ideal model delta sigma weight residual 1.634 1.545 0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 15706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 21249 3.17 - 6.35: 133 6.35 - 9.52: 14 9.52 - 12.69: 4 12.69 - 15.87: 1 Bond angle restraints: 21401 Sorted by residual: angle pdb=" C ASN B 303 " pdb=" N PHE B 304 " pdb=" CA PHE B 304 " ideal model delta sigma weight residual 120.69 104.82 15.87 2.95e+00 1.15e-01 2.89e+01 angle pdb=" N VAL B 325 " pdb=" CA VAL B 325 " pdb=" C VAL B 325 " ideal model delta sigma weight residual 112.12 108.74 3.38 8.40e-01 1.42e+00 1.62e+01 angle pdb=" N ARG D 317 " pdb=" CA ARG D 317 " pdb=" C ARG D 317 " ideal model delta sigma weight residual 114.62 110.10 4.52 1.14e+00 7.69e-01 1.57e+01 angle pdb=" C ASN B 81 " pdb=" N THR B 82 " pdb=" CA THR B 82 " ideal model delta sigma weight residual 120.82 126.31 -5.49 1.50e+00 4.44e-01 1.34e+01 angle pdb=" C ASP A 414 " pdb=" N ASN A 415 " pdb=" CA ASN A 415 " ideal model delta sigma weight residual 121.27 132.96 -11.69 3.40e+00 8.65e-02 1.18e+01 ... (remaining 21396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 9075 34.61 - 69.22: 177 69.22 - 103.83: 21 103.83 - 138.44: 2 138.44 - 173.05: 2 Dihedral angle restraints: 9277 sinusoidal: 3864 harmonic: 5413 Sorted by residual: dihedral pdb=" CA ALA C 183 " pdb=" C ALA C 183 " pdb=" N ILE C 184 " pdb=" CA ILE C 184 " ideal model delta harmonic sigma weight residual -180.00 -138.62 -41.38 0 5.00e+00 4.00e-02 6.85e+01 dihedral pdb=" CA LEU A 312 " pdb=" C LEU A 312 " pdb=" N LEU A 313 " pdb=" CA LEU A 313 " ideal model delta harmonic sigma weight residual 180.00 -144.54 -35.46 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" O5' FAD D 701 " pdb=" O3P FAD D 701 " pdb=" P FAD D 701 " pdb=" PA FAD D 701 " ideal model delta sinusoidal sigma weight residual -61.77 111.28 -173.05 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1744 0.053 - 0.107: 454 0.107 - 0.160: 56 0.160 - 0.214: 3 0.214 - 0.267: 2 Chirality restraints: 2259 Sorted by residual: chirality pdb=" CA UNK E 1 " pdb=" N UNK E 1 " pdb=" C UNK E 1 " pdb=" CB UNK E 1 " both_signs ideal model delta sigma weight residual False 2.52 2.25 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA UNK F 1 " pdb=" N UNK F 1 " pdb=" C UNK F 1 " pdb=" CB UNK F 1 " both_signs ideal model delta sigma weight residual False 2.52 2.26 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C2B FAD A 701 " pdb=" C1B FAD A 701 " pdb=" C3B FAD A 701 " pdb=" O2B FAD A 701 " both_signs ideal model delta sigma weight residual False -2.53 -2.71 0.18 2.00e-01 2.50e+01 8.08e-01 ... (remaining 2256 not shown) Planarity restraints: 2662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 105 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.62e+00 pdb=" N PRO D 106 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 106 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 106 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 338 " 0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 339 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 138 " 0.011 2.00e-02 2.50e+03 1.03e-02 2.66e+00 pdb=" CG TRP B 138 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 138 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 138 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 138 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 138 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 138 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 138 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 138 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 138 " -0.006 2.00e-02 2.50e+03 ... (remaining 2659 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 275 2.62 - 3.19: 15570 3.19 - 3.76: 22308 3.76 - 4.33: 31504 4.33 - 4.90: 48238 Nonbonded interactions: 117895 Sorted by model distance: nonbonded pdb=" O ASN B 235 " pdb=" OG SER B 243 " model vdw 2.049 3.040 nonbonded pdb=" OG1 THR B 244 " pdb=" O2A FAD B 701 " model vdw 2.070 3.040 nonbonded pdb=" O ARG C 111 " pdb=" OG1 THR C 114 " model vdw 2.077 3.040 nonbonded pdb=" OG SER A 31 " pdb=" O MET A 175 " model vdw 2.093 3.040 nonbonded pdb=" O THR D 149 " pdb=" OH TYR D 296 " model vdw 2.093 3.040 ... (remaining 117890 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 5 through 177 or resid 181 through 401 or resid 415 throug \ h 475 or resid 701)) selection = (chain 'B' and (resid 5 through 177 or resid 181 through 475 or resid 701)) selection = (chain 'C' and (resid 5 through 401 or resid 415 through 701)) selection = (chain 'D' and (resid 5 through 177 or resid 181 through 401 or resid 415 throug \ h 475 or resid 701)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 0.118 15711 Z= 0.287 Angle : 0.751 15.867 21401 Z= 0.394 Chirality : 0.046 0.267 2259 Planarity : 0.004 0.054 2662 Dihedral : 15.126 173.047 5771 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.06 % Allowed : 5.34 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.17), residues: 1820 helix: -3.44 (0.12), residues: 767 sheet: -3.49 (0.37), residues: 122 loop : -2.79 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 266 TYR 0.018 0.002 TYR A 47 PHE 0.025 0.002 PHE C 306 TRP 0.027 0.001 TRP B 138 HIS 0.008 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00604 (15711) covalent geometry : angle 0.75082 (21401) hydrogen bonds : bond 0.32651 ( 470) hydrogen bonds : angle 11.59177 ( 1314) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 429 TYR cc_start: 0.8818 (t80) cc_final: 0.8469 (t80) REVERT: A 14 ASP cc_start: 0.7562 (p0) cc_final: 0.6822 (p0) REVERT: A 57 LYS cc_start: 0.9270 (tppp) cc_final: 0.8878 (tptm) REVERT: A 220 LEU cc_start: 0.9213 (tp) cc_final: 0.8912 (tt) REVERT: A 345 MET cc_start: 0.9263 (mmm) cc_final: 0.9063 (mmt) REVERT: D 56 MET cc_start: 0.8555 (mtt) cc_final: 0.8353 (mtm) REVERT: D 134 LEU cc_start: 0.8894 (mt) cc_final: 0.8655 (mp) REVERT: D 347 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7898 (tm-30) REVERT: D 426 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7882 (tp30) outliers start: 1 outliers final: 1 residues processed: 168 average time/residue: 0.1386 time to fit residues: 33.9593 Evaluate side-chains 112 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 196 ASN C 242 ASN C 252 HIS C 260 HIS C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS B 419 GLN B 432 GLN A 28 HIS A 252 HIS D 196 ASN D 216 ASN D 252 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.091099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.073988 restraints weight = 53329.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.076481 restraints weight = 28957.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078214 restraints weight = 19166.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079238 restraints weight = 14397.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080147 restraints weight = 11962.239| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 15711 Z= 0.242 Angle : 0.723 8.303 21401 Z= 0.367 Chirality : 0.047 0.156 2259 Planarity : 0.005 0.052 2662 Dihedral : 11.678 163.168 2193 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 1.19 % Allowed : 11.93 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.18), residues: 1820 helix: -1.83 (0.16), residues: 849 sheet: -3.03 (0.37), residues: 129 loop : -2.44 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 346 TYR 0.022 0.002 TYR C 154 PHE 0.036 0.002 PHE C 306 TRP 0.016 0.002 TRP A 138 HIS 0.005 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00538 (15711) covalent geometry : angle 0.72308 (21401) hydrogen bonds : bond 0.05715 ( 470) hydrogen bonds : angle 6.53021 ( 1314) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7942 (mtp-110) REVERT: C 161 MET cc_start: 0.9224 (tpp) cc_final: 0.8930 (tpp) REVERT: C 227 LYS cc_start: 0.9493 (mmmm) cc_final: 0.9023 (mmmm) REVERT: C 256 ILE cc_start: 0.9266 (tp) cc_final: 0.9045 (tt) REVERT: C 267 MET cc_start: 0.8806 (tpp) cc_final: 0.8435 (ttp) REVERT: C 345 MET cc_start: 0.8330 (mmp) cc_final: 0.8117 (mmp) REVERT: C 397 TRP cc_start: 0.8369 (m100) cc_final: 0.8143 (m100) REVERT: C 429 TYR cc_start: 0.8679 (t80) cc_final: 0.8425 (t80) REVERT: B 129 TYR cc_start: 0.8765 (m-80) cc_final: 0.8500 (m-80) REVERT: B 132 ASP cc_start: 0.7763 (t0) cc_final: 0.7541 (t0) REVERT: B 133 LEU cc_start: 0.9402 (mp) cc_final: 0.9031 (mt) REVERT: B 172 TRP cc_start: 0.7229 (t60) cc_final: 0.6779 (t60) REVERT: B 175 MET cc_start: 0.8520 (mtm) cc_final: 0.8136 (ptt) REVERT: B 354 MET cc_start: 0.9086 (mtp) cc_final: 0.8809 (mtp) REVERT: A 14 ASP cc_start: 0.7926 (p0) cc_final: 0.7077 (p0) REVERT: A 220 LEU cc_start: 0.9384 (tp) cc_final: 0.9108 (tt) REVERT: A 345 MET cc_start: 0.9075 (mmm) cc_final: 0.8835 (mmt) REVERT: A 445 ILE cc_start: 0.9130 (tt) cc_final: 0.8815 (tp) REVERT: D 56 MET cc_start: 0.8628 (mtt) cc_final: 0.8428 (mtm) REVERT: D 223 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8637 (tm-30) REVERT: D 312 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8121 (mm) REVERT: D 346 ARG cc_start: 0.8892 (mtp85) cc_final: 0.8634 (tpp80) REVERT: D 347 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 357 ARG cc_start: 0.8437 (mtt90) cc_final: 0.8095 (mtt90) REVERT: D 426 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8196 (tp30) REVERT: D 429 TYR cc_start: 0.9278 (t80) cc_final: 0.8996 (t80) outliers start: 19 outliers final: 9 residues processed: 157 average time/residue: 0.1278 time to fit residues: 30.1453 Evaluate side-chains 131 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 361 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 79 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN D 260 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.095295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.078697 restraints weight = 51320.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.081427 restraints weight = 26720.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083301 restraints weight = 17298.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.084692 restraints weight = 12724.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085467 restraints weight = 10159.889| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15711 Z= 0.109 Angle : 0.591 12.551 21401 Z= 0.294 Chirality : 0.043 0.173 2259 Planarity : 0.004 0.046 2662 Dihedral : 10.738 157.492 2191 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.57 % Allowed : 14.06 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.19), residues: 1820 helix: -1.05 (0.17), residues: 849 sheet: -2.35 (0.40), residues: 125 loop : -2.19 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 13 TYR 0.018 0.001 TYR C 154 PHE 0.028 0.001 PHE C 306 TRP 0.029 0.001 TRP A 172 HIS 0.004 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00241 (15711) covalent geometry : angle 0.59065 (21401) hydrogen bonds : bond 0.03978 ( 470) hydrogen bonds : angle 5.36343 ( 1314) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9279 (tpp) cc_final: 0.9001 (tpp) REVERT: C 227 LYS cc_start: 0.9539 (mmmm) cc_final: 0.8820 (mmmm) REVERT: C 267 MET cc_start: 0.8869 (tpp) cc_final: 0.8474 (ttp) REVERT: C 345 MET cc_start: 0.8381 (mmp) cc_final: 0.8113 (mmm) REVERT: C 397 TRP cc_start: 0.8367 (m100) cc_final: 0.7970 (m100) REVERT: C 426 GLU cc_start: 0.8016 (tp30) cc_final: 0.7363 (tm-30) REVERT: C 429 TYR cc_start: 0.8537 (t80) cc_final: 0.8062 (t80) REVERT: B 129 TYR cc_start: 0.8859 (m-80) cc_final: 0.8536 (m-80) REVERT: B 133 LEU cc_start: 0.9337 (mp) cc_final: 0.8731 (mt) REVERT: B 172 TRP cc_start: 0.7425 (t60) cc_final: 0.6632 (t60) REVERT: B 175 MET cc_start: 0.8512 (mtm) cc_final: 0.7954 (ptt) REVERT: B 354 MET cc_start: 0.8999 (mtp) cc_final: 0.8559 (mtp) REVERT: B 389 ASP cc_start: 0.8177 (t0) cc_final: 0.7968 (t0) REVERT: A 14 ASP cc_start: 0.7884 (p0) cc_final: 0.7070 (p0) REVERT: A 175 MET cc_start: 0.8411 (mtm) cc_final: 0.7913 (mtp) REVERT: A 242 ASN cc_start: 0.8578 (p0) cc_final: 0.8296 (p0) REVERT: D 223 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8579 (tm-30) REVERT: D 312 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8168 (mm) REVERT: D 346 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8568 (mtp85) REVERT: D 347 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 357 ARG cc_start: 0.8435 (mtt90) cc_final: 0.8080 (mtt90) REVERT: D 426 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8135 (tp30) REVERT: D 429 TYR cc_start: 0.9200 (t80) cc_final: 0.8966 (t80) outliers start: 25 outliers final: 16 residues processed: 170 average time/residue: 0.1178 time to fit residues: 30.8787 Evaluate side-chains 140 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 312 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 162 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 HIS A 260 HIS D 260 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.090630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074221 restraints weight = 53057.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076778 restraints weight = 28425.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078201 restraints weight = 18604.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079556 restraints weight = 14437.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.080561 restraints weight = 11384.909| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15711 Z= 0.246 Angle : 0.673 9.409 21401 Z= 0.338 Chirality : 0.046 0.162 2259 Planarity : 0.004 0.041 2662 Dihedral : 10.740 154.772 2191 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 3.20 % Allowed : 15.63 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.19), residues: 1820 helix: -0.85 (0.17), residues: 840 sheet: -2.40 (0.40), residues: 129 loop : -2.09 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 91 TYR 0.021 0.002 TYR A 47 PHE 0.030 0.002 PHE C 306 TRP 0.022 0.001 TRP A 321 HIS 0.005 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00545 (15711) covalent geometry : angle 0.67275 (21401) hydrogen bonds : bond 0.04618 ( 470) hydrogen bonds : angle 5.69764 ( 1314) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 113 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 MET cc_start: 0.8656 (mmt) cc_final: 0.8398 (mmt) REVERT: C 267 MET cc_start: 0.8781 (tpp) cc_final: 0.8363 (ttp) REVERT: C 321 TRP cc_start: 0.5800 (OUTLIER) cc_final: 0.3713 (m-90) REVERT: C 345 MET cc_start: 0.8437 (mmp) cc_final: 0.8196 (mmp) REVERT: C 397 TRP cc_start: 0.8387 (m100) cc_final: 0.8165 (m100) REVERT: C 426 GLU cc_start: 0.8098 (tp30) cc_final: 0.7318 (tm-30) REVERT: C 429 TYR cc_start: 0.8668 (t80) cc_final: 0.8380 (t80) REVERT: B 129 TYR cc_start: 0.8792 (m-80) cc_final: 0.8545 (m-80) REVERT: B 132 ASP cc_start: 0.8149 (t0) cc_final: 0.7936 (t0) REVERT: B 172 TRP cc_start: 0.7436 (t60) cc_final: 0.6819 (t60) REVERT: B 175 MET cc_start: 0.8530 (mtm) cc_final: 0.7983 (ptt) REVERT: B 347 GLU cc_start: 0.8459 (tt0) cc_final: 0.7872 (tm-30) REVERT: A 14 ASP cc_start: 0.7925 (p0) cc_final: 0.7087 (p0) REVERT: A 242 ASN cc_start: 0.8451 (p0) cc_final: 0.8229 (p0) REVERT: D 167 MET cc_start: 0.7398 (ttt) cc_final: 0.7185 (tpp) REVERT: D 223 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8596 (tm-30) REVERT: D 312 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8172 (mm) REVERT: D 346 ARG cc_start: 0.8870 (mtp85) cc_final: 0.8557 (tpp80) REVERT: D 347 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8248 (tm-30) REVERT: D 354 MET cc_start: 0.9214 (mtp) cc_final: 0.8898 (mtp) REVERT: D 357 ARG cc_start: 0.8368 (mtt90) cc_final: 0.8010 (mtt90) REVERT: D 426 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8094 (tp30) REVERT: D 429 TYR cc_start: 0.9262 (t80) cc_final: 0.9013 (t80) outliers start: 51 outliers final: 25 residues processed: 159 average time/residue: 0.1006 time to fit residues: 25.4883 Evaluate side-chains 135 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 0.0770 chunk 155 optimal weight: 0.0570 chunk 2 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** 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 = 0.3634 r_free = 0.3634 target = 0.093363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.076932 restraints weight = 51430.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079548 restraints weight = 27249.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081346 restraints weight = 17719.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.082591 restraints weight = 13097.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.083590 restraints weight = 10615.537| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15711 Z= 0.128 Angle : 0.592 11.249 21401 Z= 0.291 Chirality : 0.043 0.142 2259 Planarity : 0.004 0.045 2662 Dihedral : 10.303 149.067 2191 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.33 % Allowed : 16.20 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.20), residues: 1820 helix: -0.48 (0.18), residues: 854 sheet: -2.12 (0.41), residues: 125 loop : -1.94 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 274 TYR 0.015 0.001 TYR C 154 PHE 0.026 0.001 PHE C 306 TRP 0.022 0.001 TRP A 321 HIS 0.003 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00288 (15711) covalent geometry : angle 0.59189 (21401) hydrogen bonds : bond 0.03756 ( 470) hydrogen bonds : angle 5.10704 ( 1314) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 MET cc_start: 0.8528 (mmt) cc_final: 0.8321 (mmt) REVERT: C 161 MET cc_start: 0.9244 (tpp) cc_final: 0.8957 (tpp) REVERT: C 244 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8832 (m) REVERT: C 267 MET cc_start: 0.8756 (tpp) cc_final: 0.8130 (ptm) REVERT: C 321 TRP cc_start: 0.5600 (OUTLIER) cc_final: 0.3471 (m-90) REVERT: C 345 MET cc_start: 0.8400 (mmp) cc_final: 0.8017 (mmm) REVERT: C 426 GLU cc_start: 0.7872 (tp30) cc_final: 0.7575 (tm-30) REVERT: C 429 TYR cc_start: 0.8459 (t80) cc_final: 0.8133 (t80) REVERT: B 129 TYR cc_start: 0.8791 (m-80) cc_final: 0.8548 (m-80) REVERT: B 132 ASP cc_start: 0.8106 (t0) cc_final: 0.7854 (t0) REVERT: B 133 LEU cc_start: 0.9421 (mp) cc_final: 0.8718 (mt) REVERT: B 172 TRP cc_start: 0.7429 (t60) cc_final: 0.6836 (t60) REVERT: B 175 MET cc_start: 0.8487 (mtm) cc_final: 0.8007 (ptt) REVERT: A 14 ASP cc_start: 0.7881 (p0) cc_final: 0.7063 (p0) REVERT: A 242 ASN cc_start: 0.8434 (p0) cc_final: 0.8223 (p0) REVERT: D 14 ASP cc_start: 0.8334 (p0) cc_final: 0.8124 (p0) REVERT: D 223 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8607 (tm-30) REVERT: D 312 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8269 (mm) REVERT: D 357 ARG cc_start: 0.8378 (mtt90) cc_final: 0.8018 (mtt90) REVERT: D 426 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8085 (tp30) REVERT: D 429 TYR cc_start: 0.9212 (t80) cc_final: 0.8952 (t80) outliers start: 53 outliers final: 31 residues processed: 173 average time/residue: 0.1209 time to fit residues: 32.0072 Evaluate side-chains 149 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 157 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 118 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 154 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 466 ASN ** B 252 HIS ** 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 = 0.3566 r_free = 0.3566 target = 0.089321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073046 restraints weight = 53368.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.075466 restraints weight = 29007.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.077084 restraints weight = 19344.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.078319 restraints weight = 14611.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079221 restraints weight = 11824.691| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 15711 Z= 0.281 Angle : 0.718 9.708 21401 Z= 0.358 Chirality : 0.047 0.175 2259 Planarity : 0.005 0.047 2662 Dihedral : 10.613 150.362 2191 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 3.20 % Allowed : 17.64 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.20), residues: 1820 helix: -0.61 (0.17), residues: 862 sheet: -2.32 (0.41), residues: 128 loop : -2.02 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 16 TYR 0.023 0.002 TYR A 47 PHE 0.026 0.002 PHE C 306 TRP 0.034 0.002 TRP C 397 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00620 (15711) covalent geometry : angle 0.71829 (21401) hydrogen bonds : bond 0.04648 ( 470) hydrogen bonds : angle 5.72100 ( 1314) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 MET cc_start: 0.8637 (mmt) cc_final: 0.8428 (mmt) REVERT: C 221 LEU cc_start: 0.9763 (tp) cc_final: 0.9509 (tt) REVERT: C 244 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8988 (m) REVERT: C 267 MET cc_start: 0.8756 (tpp) cc_final: 0.8328 (ptm) REVERT: C 321 TRP cc_start: 0.5711 (OUTLIER) cc_final: 0.3683 (m-90) REVERT: C 426 GLU cc_start: 0.8103 (tp30) cc_final: 0.7596 (tm-30) REVERT: B 129 TYR cc_start: 0.8796 (m-80) cc_final: 0.8564 (m-80) REVERT: B 132 ASP cc_start: 0.8081 (t0) cc_final: 0.7839 (t0) REVERT: B 172 TRP cc_start: 0.7428 (t60) cc_final: 0.6849 (t60) REVERT: B 175 MET cc_start: 0.8519 (mtm) cc_final: 0.7987 (ptt) REVERT: A 14 ASP cc_start: 0.7937 (p0) cc_final: 0.7161 (p0) REVERT: A 242 ASN cc_start: 0.8461 (p0) cc_final: 0.8222 (p0) REVERT: A 321 TRP cc_start: 0.6295 (m-90) cc_final: 0.6077 (m-90) REVERT: D 167 MET cc_start: 0.8054 (tpp) cc_final: 0.6981 (tpp) REVERT: D 223 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8697 (tm-30) REVERT: D 312 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8230 (mm) REVERT: D 354 MET cc_start: 0.9170 (mtp) cc_final: 0.8910 (mtp) REVERT: D 357 ARG cc_start: 0.8367 (mtt90) cc_final: 0.8120 (mtt90) REVERT: D 426 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8094 (tp30) REVERT: D 429 TYR cc_start: 0.9266 (t80) cc_final: 0.9010 (t80) outliers start: 51 outliers final: 39 residues processed: 158 average time/residue: 0.1195 time to fit residues: 28.9447 Evaluate side-chains 151 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 28 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.091853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.075473 restraints weight = 52208.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078022 restraints weight = 27978.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.079764 restraints weight = 18439.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.080987 restraints weight = 13668.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.081899 restraints weight = 11022.654| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15711 Z= 0.156 Angle : 0.614 12.094 21401 Z= 0.303 Chirality : 0.044 0.154 2259 Planarity : 0.004 0.050 2662 Dihedral : 10.259 149.680 2191 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.33 % Allowed : 17.95 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1820 helix: -0.29 (0.18), residues: 850 sheet: -2.05 (0.43), residues: 124 loop : -1.90 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 13 TYR 0.018 0.001 TYR C 154 PHE 0.026 0.001 PHE C 306 TRP 0.022 0.001 TRP C 397 HIS 0.003 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00352 (15711) covalent geometry : angle 0.61421 (21401) hydrogen bonds : bond 0.03835 ( 470) hydrogen bonds : angle 5.19296 ( 1314) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9189 (tpp) cc_final: 0.8861 (tpp) REVERT: C 244 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8848 (m) REVERT: C 267 MET cc_start: 0.8694 (tpp) cc_final: 0.8251 (ptm) REVERT: C 321 TRP cc_start: 0.5473 (OUTLIER) cc_final: 0.3426 (m-90) REVERT: C 426 GLU cc_start: 0.8076 (tp30) cc_final: 0.7626 (tm-30) REVERT: B 129 TYR cc_start: 0.8827 (m-80) cc_final: 0.8542 (m-80) REVERT: B 172 TRP cc_start: 0.7378 (t60) cc_final: 0.6651 (t60) REVERT: B 175 MET cc_start: 0.8515 (mtm) cc_final: 0.7983 (ptt) REVERT: A 14 ASP cc_start: 0.7814 (p0) cc_final: 0.6952 (p0) REVERT: A 47 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.7759 (t80) REVERT: A 242 ASN cc_start: 0.8442 (p0) cc_final: 0.8207 (p0) REVERT: A 376 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.7691 (m-10) REVERT: D 14 ASP cc_start: 0.8252 (p0) cc_final: 0.7891 (p0) REVERT: D 223 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8709 (tm-30) REVERT: D 312 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8287 (mm) REVERT: D 354 MET cc_start: 0.9116 (mtp) cc_final: 0.8868 (mtp) REVERT: D 357 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7980 (mtt90) REVERT: D 426 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8169 (tp30) REVERT: D 429 TYR cc_start: 0.9246 (t80) cc_final: 0.8988 (t80) outliers start: 53 outliers final: 41 residues processed: 168 average time/residue: 0.1148 time to fit residues: 30.3595 Evaluate side-chains 160 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 376 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 120 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 166 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 466 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** 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 = 0.3623 r_free = 0.3623 target = 0.092641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076328 restraints weight = 51942.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078944 restraints weight = 27538.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.080646 restraints weight = 17959.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081966 restraints weight = 13358.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082738 restraints weight = 10716.487| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15711 Z= 0.138 Angle : 0.605 11.271 21401 Z= 0.296 Chirality : 0.043 0.159 2259 Planarity : 0.004 0.048 2662 Dihedral : 10.079 149.086 2191 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.39 % Allowed : 18.46 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1820 helix: -0.13 (0.18), residues: 863 sheet: -1.89 (0.44), residues: 124 loop : -1.78 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 274 TYR 0.018 0.001 TYR C 154 PHE 0.026 0.001 PHE C 306 TRP 0.022 0.001 TRP A 172 HIS 0.012 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00312 (15711) covalent geometry : angle 0.60480 (21401) hydrogen bonds : bond 0.03676 ( 470) hydrogen bonds : angle 5.00794 ( 1314) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 120 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9168 (tpp) cc_final: 0.8899 (tpp) REVERT: C 244 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8814 (m) REVERT: C 267 MET cc_start: 0.8688 (tpp) cc_final: 0.8235 (ptm) REVERT: C 321 TRP cc_start: 0.5445 (OUTLIER) cc_final: 0.3381 (m-90) REVERT: C 426 GLU cc_start: 0.8098 (tp30) cc_final: 0.7622 (tm-30) REVERT: C 429 TYR cc_start: 0.8514 (t80) cc_final: 0.8075 (t80) REVERT: B 172 TRP cc_start: 0.7451 (t60) cc_final: 0.6840 (t60) REVERT: B 175 MET cc_start: 0.8498 (mtm) cc_final: 0.7971 (ptt) REVERT: A 14 ASP cc_start: 0.7847 (p0) cc_final: 0.7022 (p0) REVERT: A 47 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.7739 (t80) REVERT: A 321 TRP cc_start: 0.6131 (m-90) cc_final: 0.5757 (m-90) REVERT: A 376 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.7784 (m-10) REVERT: D 14 ASP cc_start: 0.8255 (p0) cc_final: 0.7821 (p0) REVERT: D 167 MET cc_start: 0.8074 (tpp) cc_final: 0.7790 (tpp) REVERT: D 223 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8692 (tm-30) REVERT: D 312 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8287 (mm) REVERT: D 354 MET cc_start: 0.9092 (mtp) cc_final: 0.8811 (mtp) REVERT: D 357 ARG cc_start: 0.8378 (mtt90) cc_final: 0.8015 (mtt90) REVERT: D 426 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8104 (tp30) REVERT: D 429 TYR cc_start: 0.9225 (t80) cc_final: 0.8975 (t80) outliers start: 54 outliers final: 40 residues processed: 165 average time/residue: 0.1070 time to fit residues: 28.2989 Evaluate side-chains 158 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 376 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 86 optimal weight: 0.0570 chunk 3 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 152 optimal weight: 0.0980 chunk 169 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 466 ASN B 102 HIS ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.094736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078411 restraints weight = 51032.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081067 restraints weight = 27091.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.082785 restraints weight = 17620.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.084201 restraints weight = 13101.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.084942 restraints weight = 10438.020| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15711 Z= 0.099 Angle : 0.598 12.756 21401 Z= 0.289 Chirality : 0.042 0.167 2259 Planarity : 0.004 0.048 2662 Dihedral : 9.914 148.405 2191 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.57 % Allowed : 19.59 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.20), residues: 1820 helix: 0.06 (0.18), residues: 861 sheet: -1.73 (0.42), residues: 138 loop : -1.74 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 274 TYR 0.016 0.001 TYR C 154 PHE 0.026 0.001 PHE C 306 TRP 0.021 0.001 TRP A 172 HIS 0.013 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00223 (15711) covalent geometry : angle 0.59815 (21401) hydrogen bonds : bond 0.03235 ( 470) hydrogen bonds : angle 4.76660 ( 1314) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9130 (tpp) cc_final: 0.8887 (tpp) REVERT: C 244 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8797 (m) REVERT: C 321 TRP cc_start: 0.5392 (OUTLIER) cc_final: 0.3289 (m-90) REVERT: C 345 MET cc_start: 0.7965 (mmp) cc_final: 0.7578 (mmm) REVERT: C 361 ILE cc_start: 0.8630 (tt) cc_final: 0.8426 (tt) REVERT: C 426 GLU cc_start: 0.8055 (tp30) cc_final: 0.7549 (tm-30) REVERT: C 429 TYR cc_start: 0.8371 (t80) cc_final: 0.8157 (t80) REVERT: B 172 TRP cc_start: 0.7414 (t60) cc_final: 0.6348 (t60) REVERT: B 175 MET cc_start: 0.8500 (mtm) cc_final: 0.8015 (ptt) REVERT: B 437 LEU cc_start: 0.9222 (mt) cc_final: 0.8482 (pp) REVERT: A 14 ASP cc_start: 0.7758 (p0) cc_final: 0.7016 (p0) REVERT: A 321 TRP cc_start: 0.6060 (m-90) cc_final: 0.5723 (m-90) REVERT: A 376 TRP cc_start: 0.8294 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: D 14 ASP cc_start: 0.8192 (p0) cc_final: 0.7674 (p0) REVERT: D 167 MET cc_start: 0.8121 (tpp) cc_final: 0.7480 (tpp) REVERT: D 223 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8684 (tm-30) REVERT: D 312 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8292 (mm) REVERT: D 354 MET cc_start: 0.9045 (mtp) cc_final: 0.8786 (mtp) REVERT: D 357 ARG cc_start: 0.8383 (mtt90) cc_final: 0.8038 (mtt90) REVERT: D 426 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8096 (tp30) REVERT: D 429 TYR cc_start: 0.9188 (t80) cc_final: 0.8965 (t80) outliers start: 41 outliers final: 31 residues processed: 163 average time/residue: 0.1069 time to fit residues: 27.7867 Evaluate side-chains 157 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 376 TRP Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 107 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 101 ASN C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073037 restraints weight = 53864.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.075486 restraints weight = 29464.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077139 restraints weight = 19505.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.078248 restraints weight = 14655.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079201 restraints weight = 12044.056| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 15711 Z= 0.288 Angle : 0.747 11.138 21401 Z= 0.369 Chirality : 0.048 0.192 2259 Planarity : 0.005 0.044 2662 Dihedral : 10.378 149.671 2191 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.89 % Allowed : 19.52 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.20), residues: 1820 helix: -0.30 (0.18), residues: 856 sheet: -2.12 (0.42), residues: 126 loop : -1.76 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 274 TYR 0.022 0.002 TYR A 47 PHE 0.028 0.002 PHE C 306 TRP 0.024 0.002 TRP A 172 HIS 0.012 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00635 (15711) covalent geometry : angle 0.74663 (21401) hydrogen bonds : bond 0.04414 ( 470) hydrogen bonds : angle 5.49760 ( 1314) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 244 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.8972 (m) REVERT: C 267 MET cc_start: 0.8728 (tpp) cc_final: 0.8342 (ptt) REVERT: C 345 MET cc_start: 0.8296 (mmp) cc_final: 0.7780 (mmm) REVERT: C 426 GLU cc_start: 0.8172 (tp30) cc_final: 0.7692 (tm-30) REVERT: C 429 TYR cc_start: 0.8664 (t80) cc_final: 0.8419 (t80) REVERT: B 172 TRP cc_start: 0.7439 (t60) cc_final: 0.6761 (t60) REVERT: B 175 MET cc_start: 0.8488 (mtm) cc_final: 0.7915 (ptt) REVERT: B 426 GLU cc_start: 0.7750 (pm20) cc_final: 0.7439 (pm20) REVERT: B 437 LEU cc_start: 0.9138 (mt) cc_final: 0.8340 (pp) REVERT: A 14 ASP cc_start: 0.7939 (p0) cc_final: 0.7150 (p0) REVERT: A 321 TRP cc_start: 0.6161 (m-90) cc_final: 0.5808 (m-90) REVERT: A 376 TRP cc_start: 0.8412 (OUTLIER) cc_final: 0.7878 (m-10) REVERT: D 223 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8731 (tm-30) REVERT: D 312 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8311 (mm) REVERT: D 354 MET cc_start: 0.9206 (mtp) cc_final: 0.8852 (mtp) REVERT: D 357 ARG cc_start: 0.8352 (mtt90) cc_final: 0.8099 (mtt90) REVERT: D 426 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8120 (tp30) REVERT: D 429 TYR cc_start: 0.9271 (t80) cc_final: 0.9025 (t80) outliers start: 46 outliers final: 38 residues processed: 152 average time/residue: 0.1075 time to fit residues: 25.9207 Evaluate side-chains 150 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 376 TRP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 108 optimal weight: 0.0470 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 466 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 HIS A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.094774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078430 restraints weight = 51225.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.081057 restraints weight = 27325.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.082975 restraints weight = 17838.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.084186 restraints weight = 13076.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085122 restraints weight = 10600.556| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15711 Z= 0.099 Angle : 0.618 12.502 21401 Z= 0.296 Chirality : 0.042 0.171 2259 Planarity : 0.004 0.050 2662 Dihedral : 9.949 148.871 2191 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.39 % Allowed : 20.34 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1820 helix: 0.18 (0.19), residues: 856 sheet: -1.71 (0.45), residues: 124 loop : -1.62 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 173 TYR 0.017 0.001 TYR C 154 PHE 0.026 0.001 PHE C 306 TRP 0.033 0.001 TRP A 172 HIS 0.003 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00224 (15711) covalent geometry : angle 0.61759 (21401) hydrogen bonds : bond 0.03208 ( 470) hydrogen bonds : angle 4.73920 ( 1314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.38 seconds wall clock time: 36 minutes 58.30 seconds (2218.30 seconds total)