Starting phenix.real_space_refine on Tue Aug 26 14:52:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byk_45036/08_2025/9byk_45036.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byk_45036/08_2025/9byk_45036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byk_45036/08_2025/9byk_45036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byk_45036/08_2025/9byk_45036.map" model { file = "/net/cci-nas-00/data/ceres_data/9byk_45036/08_2025/9byk_45036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byk_45036/08_2025/9byk_45036.cif" } resolution = 3.03 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= 0.007 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 4 5.21 5 S 135 5.16 5 C 23650 2.51 5 N 6413 2.21 5 O 7048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37263 Number of models: 1 Model: "" Number of chains: 34 Chain: "8" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3828 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 485} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3541 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3522 Classifications: {'peptide': 465} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 440} Chain: "F" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3527 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 441} Chain: "G" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2106 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 945 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 353 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 45} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 335 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 44} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "S" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1430 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 177} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 317 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "a" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1638 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 202} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "b" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1430 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 3, 'TRANS': 195} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "c" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 417 Classifications: {'peptide': 69} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 63} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 1, 'PHE:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 99 Chain: "d" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 741 Classifications: {'peptide': 147} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 125} Link IDs: {'PTRANS': 8, 'TRANS': 138} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 472 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 10, 'TRP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 16, 'ASN:plan1': 6, 'GLN:plan1': 3, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 238 Chain: "e" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 259 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 38} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "i" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 277 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "k" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3678 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 504 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 6, 'GLU:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3796 Classifications: {'peptide': 499} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.27, per 1000 atoms: 0.22 Number of scatterers: 37263 At special positions: 0 Unit cell: (132.68, 145.52, 246.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 135 16.00 P 13 15.00 Mg 4 11.99 O 7048 8.00 N 6413 7.00 C 23650 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: 2.92 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.4 microseconds 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9164 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 23 sheets defined 60.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain '8' and resid 12 through 31 removed outlier: 3.933A pdb=" N ILE 8 17 " --> pdb=" O ILE 8 13 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N MET 8 18 " --> pdb=" O THR 8 14 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR 8 19 " --> pdb=" O SER 8 15 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN 8 30 " --> pdb=" O LEU 8 26 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR 8 31 " --> pdb=" O LYS 8 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.778A pdb=" N LEU A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.531A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.587A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.835A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.514A pdb=" N HIS A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.641A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 removed outlier: 3.914A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.187A pdb=" N GLN A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 490 through 509 removed outlier: 4.562A pdb=" N GLU A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.536A pdb=" N THR D 92 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 93 " --> pdb=" O PRO D 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 93' Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 260 through 275 removed outlier: 3.943A pdb=" N THR D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU D 273 " --> pdb=" O GLU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 298 removed outlier: 4.021A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE D 298 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 318 Processing helix chain 'D' and resid 321 through 329 removed outlier: 3.791A pdb=" N THR D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA D 329 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 344 Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 366 through 394 removed outlier: 3.921A pdb=" N ASP D 388 " --> pdb=" O LYS D 384 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 398 Processing helix chain 'D' and resid 399 through 417 removed outlier: 3.629A pdb=" N LEU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER D 417 " --> pdb=" O GLN D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 Processing helix chain 'D' and resid 435 through 449 Processing helix chain 'D' and resid 455 through 460 Processing helix chain 'D' and resid 464 through 478 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 227 through 249 removed outlier: 4.519A pdb=" N ALA E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 245 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 279 through 283 Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 314 through 318 Processing helix chain 'E' and resid 321 through 329 Processing helix chain 'E' and resid 338 through 344 Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 366 through 393 Processing helix chain 'E' and resid 399 through 416 Processing helix chain 'E' and resid 420 through 422 No H-bonds generated for 'chain 'E' and resid 420 through 422' Processing helix chain 'E' and resid 423 through 428 Processing helix chain 'E' and resid 435 through 448 Processing helix chain 'E' and resid 455 through 460 Processing helix chain 'E' and resid 464 through 475 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 233 through 248 Processing helix chain 'F' and resid 260 through 275 removed outlier: 4.005A pdb=" N THR F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA F 272 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.812A pdb=" N ASP F 290 " --> pdb=" O THR F 286 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 318 Processing helix chain 'F' and resid 321 through 327 removed outlier: 3.851A pdb=" N THR F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 331 Processing helix chain 'F' and resid 338 through 344 Processing helix chain 'F' and resid 361 through 366 Processing helix chain 'F' and resid 366 through 393 removed outlier: 4.492A pdb=" N ASP F 388 " --> pdb=" O LYS F 384 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE F 389 " --> pdb=" O SER F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 398 Processing helix chain 'F' and resid 399 through 417 removed outlier: 3.818A pdb=" N SER F 417 " --> pdb=" O GLN F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 428 Processing helix chain 'F' and resid 435 through 449 Processing helix chain 'F' and resid 455 through 460 Processing helix chain 'F' and resid 464 through 473 removed outlier: 3.710A pdb=" N ASP F 473 " --> pdb=" O VAL F 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 54 removed outlier: 4.095A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 4.351A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 99 removed outlier: 3.814A pdb=" N ALA G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 117 Processing helix chain 'G' and resid 137 through 151 Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 187 through 193 removed outlier: 3.748A pdb=" N SER G 191 " --> pdb=" O ALA G 187 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 272 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 119 Processing helix chain 'H' and resid 124 through 145 Processing helix chain 'I' and resid 11 through 27 Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 31 through 39 Processing helix chain 'J' and resid 13 through 19 removed outlier: 4.027A pdb=" N ASP J 17 " --> pdb=" O GLY J 13 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY J 19 " --> pdb=" O VAL J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 51 removed outlier: 3.616A pdb=" N ASN J 51 " --> pdb=" O LYS J 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 Processing helix chain 'K' and resid 17 through 39 removed outlier: 3.957A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 73 removed outlier: 4.018A pdb=" N SER K 48 " --> pdb=" O GLN K 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 Processing helix chain 'L' and resid 17 through 39 removed outlier: 4.268A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY L 22 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG L 38 " --> pdb=" O ILE L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 73 removed outlier: 3.509A pdb=" N SER L 48 " --> pdb=" O GLN L 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 16 removed outlier: 3.819A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 39 Processing helix chain 'M' and resid 44 through 73 removed outlier: 4.217A pdb=" N ALA M 50 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY M 61 " --> pdb=" O SER M 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 17 through 39 removed outlier: 4.356A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 73 removed outlier: 3.576A pdb=" N ALA N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL N 67 " --> pdb=" O PHE N 63 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA N 68 " --> pdb=" O CYS N 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 39 removed outlier: 4.199A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY O 22 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA O 23 " --> pdb=" O ALA O 19 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY O 24 " --> pdb=" O GLY O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 73 removed outlier: 4.176A pdb=" N SER O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 17 through 39 removed outlier: 3.691A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 73 removed outlier: 3.904A pdb=" N SER P 48 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 15 Processing helix chain 'Q' and resid 18 through 39 Processing helix chain 'Q' and resid 44 through 73 removed outlier: 3.538A pdb=" N SER Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 15 removed outlier: 3.916A pdb=" N PHE R 8 " --> pdb=" O THR R 4 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE R 9 " --> pdb=" O ALA R 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 39 removed outlier: 4.242A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 73 removed outlier: 3.769A pdb=" N VAL R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA R 68 " --> pdb=" O CYS R 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 28 removed outlier: 3.800A pdb=" N TYR S 18 " --> pdb=" O ILE S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 43 Processing helix chain 'S' and resid 44 through 47 removed outlier: 3.535A pdb=" N LYS S 47 " --> pdb=" O GLN S 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 44 through 47' Processing helix chain 'S' and resid 48 through 53 Processing helix chain 'S' and resid 61 through 76 Processing helix chain 'S' and resid 81 through 93 Processing helix chain 'S' and resid 94 through 96 No H-bonds generated for 'chain 'S' and resid 94 through 96' Processing helix chain 'S' and resid 97 through 114 Processing helix chain 'S' and resid 127 through 143 Processing helix chain 'S' and resid 175 through 180 Processing helix chain 'S' and resid 181 through 187 Processing helix chain 'T' and resid 45 through 63 removed outlier: 4.137A pdb=" N ALA T 49 " --> pdb=" O GLU T 45 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE T 50 " --> pdb=" O ILE T 46 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY T 63 " --> pdb=" O SER T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 68 Processing helix chain 'T' and resid 70 through 84 removed outlier: 3.587A pdb=" N VAL T 83 " --> pdb=" O VAL T 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 30 removed outlier: 4.079A pdb=" N ILE a 23 " --> pdb=" O ILE a 19 " (cutoff:3.500A) Proline residue: a 27 - end of helix removed outlier: 3.711A pdb=" N LEU a 30 " --> pdb=" O PHE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 62 removed outlier: 4.072A pdb=" N GLN a 46 " --> pdb=" O THR a 42 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE a 60 " --> pdb=" O GLN a 56 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS a 61 " --> pdb=" O MET a 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN a 62 " --> pdb=" O MET a 58 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 67 removed outlier: 3.610A pdb=" N THR a 67 " --> pdb=" O LYS a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 86 removed outlier: 4.056A pdb=" N SER a 74 " --> pdb=" O LEU a 70 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY a 86 " --> pdb=" O THR a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 97 through 119 removed outlier: 4.193A pdb=" N ASN a 101 " --> pdb=" O GLN a 97 " (cutoff:3.500A) Proline residue: a 107 - end of helix Processing helix chain 'a' and resid 120 through 127 Processing helix chain 'a' and resid 134 through 136 No H-bonds generated for 'chain 'a' and resid 134 through 136' Processing helix chain 'a' and resid 137 through 181 Proline residue: a 153 - end of helix removed outlier: 3.709A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN a 163 " --> pdb=" O ARG a 159 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS a 168 " --> pdb=" O ILE a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 203 Processing helix chain 'a' and resid 204 through 224 removed outlier: 3.531A pdb=" N LEU a 208 " --> pdb=" O PHE a 204 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 30 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 37 through 51 Processing helix chain 'b' and resid 57 through 62 removed outlier: 3.833A pdb=" N ILE b 61 " --> pdb=" O THR b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 63 through 75 Processing helix chain 'b' and resid 75 through 136 removed outlier: 4.459A pdb=" N GLY b 79 " --> pdb=" O GLY b 75 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU b 87 " --> pdb=" O ASP b 83 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE b 90 " --> pdb=" O ASN b 86 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN b 92 " --> pdb=" O GLN b 88 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN b 119 " --> pdb=" O GLN b 115 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG b 121 " --> pdb=" O LEU b 117 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N HIS b 122 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL b 127 " --> pdb=" O TYR b 123 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU b 136 " --> pdb=" O ILE b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 138 through 187 removed outlier: 4.000A pdb=" N GLU b 142 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG b 143 " --> pdb=" O THR b 139 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS b 149 " --> pdb=" O HIS b 145 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL b 182 " --> pdb=" O GLU b 178 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLN b 183 " --> pdb=" O LYS b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 196 removed outlier: 4.017A pdb=" N ILE b 194 " --> pdb=" O GLU b 190 " (cutoff:3.500A) Processing helix chain 'b' and resid 199 through 211 Processing helix chain 'c' and resid 9 through 23 Processing helix chain 'c' and resid 32 through 51 removed outlier: 4.319A pdb=" N GLN c 36 " --> pdb=" O GLY c 32 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN c 37 " --> pdb=" O PRO c 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 17 removed outlier: 4.040A pdb=" N GLY d 16 " --> pdb=" O TRP d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 44 removed outlier: 3.701A pdb=" N LEU d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 66 through 76 Processing helix chain 'd' and resid 83 through 125 removed outlier: 3.512A pdb=" N ILE d 125 " --> pdb=" O MET d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 138 Processing helix chain 'e' and resid 5 through 17 removed outlier: 3.566A pdb=" N LEU e 9 " --> pdb=" O GLN e 5 " (cutoff:3.500A) Processing helix chain 'e' and resid 18 through 21 Processing helix chain 'e' and resid 24 through 44 Proline residue: e 34 - end of helix Processing helix chain 'i' and resid 14 through 26 removed outlier: 4.215A pdb=" N LEU i 23 " --> pdb=" O ASN i 19 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR i 24 " --> pdb=" O SER i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 46 removed outlier: 4.034A pdb=" N LEU i 31 " --> pdb=" O MET i 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 13 through 18 Processing helix chain 'k' and resid 18 through 29 removed outlier: 4.187A pdb=" N UNK k 22 " --> pdb=" O UNK k 18 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N UNK k 23 " --> pdb=" O UNK k 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.238A pdb=" N LEU C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.669A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 259 Proline residue: C 247 - end of helix removed outlier: 3.730A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.952A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.635A pdb=" N ALA C 378 " --> pdb=" O GLY C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 4.034A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 429 Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 460 through 475 Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 509 Processing helix chain 'f' and resid 2 through 16 Processing helix chain 'f' and resid 24 through 35 removed outlier: 3.798A pdb=" N PHE f 28 " --> pdb=" O LEU f 24 " (cutoff:3.500A) Proline residue: f 30 - end of helix Processing helix chain 'f' and resid 35 through 40 Processing helix chain 'f' and resid 56 through 75 Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.522A pdb=" N LEU B 81 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.540A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.582A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.611A pdb=" N GLY B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 239 through 260 Proline residue: B 247 - end of helix removed outlier: 3.767A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.860A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 380 through 401 removed outlier: 4.062A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 475 removed outlier: 3.622A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.753A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 509 removed outlier: 3.597A pdb=" N GLU B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.581A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 91 " --> pdb=" O MET A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.990A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.303A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR A 200 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE A 267 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASP A 269 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 204 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.634A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 12 through 17 removed outlier: 6.437A pdb=" N ASP D 24 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR D 59 " --> pdb=" O HIS D 54 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS D 54 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG D 61 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 85 through 88 removed outlier: 3.928A pdb=" N GLN D 114 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 96 through 97 removed outlier: 6.205A pdb=" N MET D 97 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 253 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL D 309 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 255 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA D 311 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE D 257 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TYR D 313 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 312 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 13 through 17 removed outlier: 6.316A pdb=" N ASP E 24 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR E 59 " --> pdb=" O HIS E 54 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N HIS E 54 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG E 61 " --> pdb=" O ALA E 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 88 removed outlier: 4.233A pdb=" N GLN E 114 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 97 removed outlier: 7.184A pdb=" N SER E 183 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL E 220 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE E 185 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLY E 222 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY E 187 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 257 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.253A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 12 through 19 removed outlier: 6.520A pdb=" N ASP F 24 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL F 18 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 22 through 27 current: chain 'F' and resid 48 through 56 removed outlier: 6.637A pdb=" N ARG F 61 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N HIS F 54 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR F 59 " --> pdb=" O HIS F 54 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 59 through 64 current: chain 'C' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 60 through 66 removed outlier: 5.723A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 75 current: chain 'B' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 5.824A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 85 through 88 removed outlier: 3.578A pdb=" N VAL F 88 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN F 114 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 96 through 97 removed outlier: 6.078A pdb=" N MET F 97 " --> pdb=" O TYR F 221 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL F 253 " --> pdb=" O THR F 307 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL F 309 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU F 255 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA F 311 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE F 257 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N TYR F 313 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE F 154 " --> pdb=" O GLN F 310 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE F 312 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU F 156 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY F 155 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 171 through 178 removed outlier: 6.479A pdb=" N LYS G 65 " --> pdb=" O GLU G 157 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N SER G 159 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU G 67 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE G 161 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE G 69 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN G 163 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N HIS G 66 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU G 125 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE G 105 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR G 127 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY G 107 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS G 129 " --> pdb=" O GLY G 107 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS G 129 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS I 44 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 26 through 31 removed outlier: 4.398A pdb=" N PHE H 18 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA H 94 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 44 through 47 removed outlier: 3.538A pdb=" N PHE H 45 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY H 61 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 148 through 153 removed outlier: 6.316A pdb=" N VAL S 116 " --> pdb=" O LYS S 149 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLU S 151 " --> pdb=" O VAL S 116 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N CYS S 118 " --> pdb=" O GLU S 151 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE S 163 " --> pdb=" O THR S 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.993A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.460A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 327 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.208A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.514A pdb=" N VAL B 108 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 206 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 326 through 328 removed outlier: 7.107A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) 2227 hydrogen bonds defined for protein. 6465 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: 7.33 Time building geometry restraints manager: 3.67 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: 12383 1.34 - 1.46: 4944 1.46 - 1.57: 20194 1.57 - 1.69: 21 1.69 - 1.81: 250 Bond restraints: 37792 Sorted by residual: bond pdb=" C GLU B 27 " pdb=" N THR B 28 " ideal model delta sigma weight residual 1.331 1.277 0.053 1.38e-02 5.25e+03 1.48e+01 bond pdb=" C TYR i 21 " pdb=" N THR i 22 " ideal model delta sigma weight residual 1.332 1.285 0.046 1.53e-02 4.27e+03 9.22e+00 bond pdb=" N VAL R 28 " pdb=" CA VAL R 28 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.30e+00 bond pdb=" N ILE R 34 " pdb=" CA ILE R 34 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.48e+00 bond pdb=" N VAL S 66 " pdb=" CA VAL S 66 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.48e+00 ... (remaining 37787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 50402 1.51 - 3.03: 624 3.03 - 4.54: 119 4.54 - 6.06: 33 6.06 - 7.57: 7 Bond angle restraints: 51185 Sorted by residual: angle pdb=" N VAL d 138 " pdb=" CA VAL d 138 " pdb=" C VAL d 138 " ideal model delta sigma weight residual 113.47 110.00 3.47 1.01e+00 9.80e-01 1.18e+01 angle pdb=" CA ILE Q 33 " pdb=" C ILE Q 33 " pdb=" O ILE Q 33 " ideal model delta sigma weight residual 121.29 118.07 3.22 1.07e+00 8.73e-01 9.08e+00 angle pdb=" N LEU R 32 " pdb=" CA LEU R 32 " pdb=" C LEU R 32 " ideal model delta sigma weight residual 111.28 108.03 3.25 1.09e+00 8.42e-01 8.91e+00 angle pdb=" CA VAL R 28 " pdb=" C VAL R 28 " pdb=" O VAL R 28 " ideal model delta sigma weight residual 121.17 118.01 3.16 1.06e+00 8.90e-01 8.86e+00 angle pdb=" CA ILE R 33 " pdb=" C ILE R 33 " pdb=" O ILE R 33 " ideal model delta sigma weight residual 121.17 118.02 3.15 1.06e+00 8.90e-01 8.84e+00 ... (remaining 51180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.99: 22489 31.99 - 63.98: 346 63.98 - 95.97: 18 95.97 - 127.95: 0 127.95 - 159.94: 2 Dihedral angle restraints: 22855 sinusoidal: 8557 harmonic: 14298 Sorted by residual: dihedral pdb=" C2' ADP D 501 " pdb=" C1' ADP D 501 " pdb=" N9 ADP D 501 " pdb=" C4 ADP D 501 " ideal model delta sinusoidal sigma weight residual 91.55 -108.51 -159.94 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 81.02 -141.02 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" CA GLU b 137 " pdb=" C GLU b 137 " pdb=" N VAL b 138 " pdb=" CA VAL b 138 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 22852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4679 0.042 - 0.084: 1054 0.084 - 0.126: 346 0.126 - 0.168: 7 0.168 - 0.210: 4 Chirality restraints: 6090 Sorted by residual: chirality pdb=" CA ILE S 64 " pdb=" N ILE S 64 " pdb=" C ILE S 64 " pdb=" CB ILE S 64 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE R 33 " pdb=" N ILE R 33 " pdb=" C ILE R 33 " pdb=" CB ILE R 33 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CA VAL S 66 " pdb=" N VAL S 66 " pdb=" C VAL S 66 " pdb=" CB VAL S 66 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 6087 not shown) Planarity restraints: 6564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG S 62 " -0.218 9.50e-02 1.11e+02 9.77e-02 5.86e+00 pdb=" NE ARG S 62 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG S 62 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG S 62 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG S 62 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER S 79 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO S 80 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO S 80 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 80 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 59 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO H 60 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 60 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 60 " -0.030 5.00e-02 4.00e+02 ... (remaining 6561 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 321 2.54 - 3.13: 30586 3.13 - 3.72: 61508 3.72 - 4.31: 84193 4.31 - 4.90: 140274 Nonbonded interactions: 316882 Sorted by model distance: nonbonded pdb=" O3G ATP C 601 " pdb="MG MG C 602 " model vdw 1.952 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 1.962 2.170 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 1.974 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 2.004 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.034 2.170 ... (remaining 316877 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 23 through 401 or resid 410 through 601)) selection = (chain 'B' and (resid 23 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 601)) selection = (chain 'C' and (resid 23 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 401 or resid 410 through 601)) } ncs_group { reference = (chain 'D' and resid 12 through 476) selection = chain 'E' selection = (chain 'F' and resid 12 through 476) } ncs_group { reference = (chain 'K' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'L' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'M' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = chain 'N' selection = (chain 'O' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'P' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'Q' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'R' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 12.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 31.990 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.003 0.060 37792 Z= 0.139 Angle : 0.479 7.572 51185 Z= 0.271 Chirality : 0.039 0.210 6090 Planarity : 0.003 0.098 6564 Dihedral : 11.138 159.942 13691 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.02 % Rotamer: Outliers : 3.97 % Allowed : 6.76 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.12), residues: 4940 helix: 2.22 (0.10), residues: 2602 sheet: -0.43 (0.24), residues: 521 loop : -0.40 (0.15), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.015 0.001 TYR i 21 PHE 0.016 0.001 PHE N 63 TRP 0.012 0.001 TRP 8 9 HIS 0.004 0.001 HIS b 122 Details of bonding type rmsd covalent geometry : bond 0.00261 (37792) covalent geometry : angle 0.47868 (51185) hydrogen bonds : bond 0.14726 ( 2227) hydrogen bonds : angle 5.74773 ( 6465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 959 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 MET cc_start: 0.8537 (tpp) cc_final: 0.8305 (tpt) REVERT: A 406 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: D 99 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8452 (p) REVERT: D 395 MET cc_start: 0.7001 (tpt) cc_final: 0.6647 (tpt) REVERT: F 28 ASP cc_start: 0.7588 (p0) cc_final: 0.7290 (p0) REVERT: G 44 TYR cc_start: 0.7481 (t80) cc_final: 0.6869 (t80) REVERT: G 205 GLN cc_start: 0.7394 (tp-100) cc_final: 0.6817 (tp-100) REVERT: G 272 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7718 (mt) REVERT: J 26 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7229 (tm-30) REVERT: K 38 ARG cc_start: 0.6030 (ttm-80) cc_final: 0.5648 (ttm-80) REVERT: M 58 GLU cc_start: 0.6466 (tp30) cc_final: 0.5872 (tp30) REVERT: M 65 LEU cc_start: 0.8054 (mp) cc_final: 0.7777 (mp) REVERT: M 71 ILE cc_start: 0.8189 (mm) cc_final: 0.7974 (mm) REVERT: N 9 ILE cc_start: 0.8661 (pt) cc_final: 0.8385 (tt) REVERT: O 36 TYR cc_start: 0.7185 (t80) cc_final: 0.6784 (t80) REVERT: P 67 VAL cc_start: 0.9039 (t) cc_final: 0.8731 (t) REVERT: Q 16 VAL cc_start: 0.8566 (t) cc_final: 0.8236 (m) REVERT: Q 25 ILE cc_start: 0.7254 (pt) cc_final: 0.6755 (pt) REVERT: Q 65 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8302 (tt) REVERT: R 32 LEU cc_start: 0.7970 (tp) cc_final: 0.7748 (tp) REVERT: R 62 LEU cc_start: 0.8313 (mm) cc_final: 0.8067 (mt) REVERT: R 65 LEU cc_start: 0.8245 (tp) cc_final: 0.7354 (tt) REVERT: S 29 GLN cc_start: 0.7517 (mt0) cc_final: 0.7186 (mm-40) REVERT: S 172 ASP cc_start: 0.7755 (t70) cc_final: 0.7493 (t0) REVERT: b 171 GLU cc_start: 0.7733 (pp20) cc_final: 0.6784 (pp20) REVERT: b 172 HIS cc_start: 0.7251 (t70) cc_final: 0.6985 (t70) REVERT: b 182 VAL cc_start: 0.7729 (m) cc_final: 0.7434 (p) REVERT: C 95 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8842 (m) REVERT: C 403 PHE cc_start: 0.7054 (m-80) cc_final: 0.6822 (t80) REVERT: f 83 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5788 (pp) REVERT: B 334 VAL cc_start: 0.8721 (t) cc_final: 0.8377 (m) REVERT: B 351 PHE cc_start: 0.7245 (m-80) cc_final: 0.7043 (m-80) outliers start: 148 outliers final: 49 residues processed: 1062 average time/residue: 0.2240 time to fit residues: 376.7710 Evaluate side-chains 737 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 682 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 63 PHE Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain a residue 138 ILE Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 454 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 30 ASN A 208 GLN A 476 HIS A 477 GLN D 41 GLN D 179 HIS D 330 HIS E 225 ASN E 248 GLN F 36 ASN F 41 GLN F 330 HIS G 117 HIS G 120 HIS G 163 ASN G 205 GLN G 255 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN H 111 ASN I 17 GLN L 39 ASN L 44 GLN N 39 ASN N 44 GLN S 57 ASN a 39 ASN a 47 GLN a 61 HIS a 63 GLN a 168 HIS b 122 HIS b 163 ASN b 167 GLN C 147 GLN C 330 GLN C 341 ASN C 441 GLN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 70 ASN B 70 ASN B 190 ASN B 330 GLN B 341 ASN B 441 GLN B 466 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.073512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053769 restraints weight = 126967.136| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.40 r_work: 0.2950 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37792 Z= 0.160 Angle : 0.603 10.555 51185 Z= 0.309 Chirality : 0.043 0.358 6090 Planarity : 0.004 0.064 6564 Dihedral : 7.345 159.936 5564 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 3.78 % Allowed : 11.84 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.12), residues: 4940 helix: 1.92 (0.10), residues: 2652 sheet: -0.45 (0.24), residues: 503 loop : -0.45 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 381 TYR 0.023 0.002 TYR I 15 PHE 0.034 0.002 PHE a 193 TRP 0.020 0.002 TRP 8 9 HIS 0.010 0.001 HIS a 127 Details of bonding type rmsd covalent geometry : bond 0.00356 (37792) covalent geometry : angle 0.60335 (51185) hydrogen bonds : bond 0.04606 ( 2227) hydrogen bonds : angle 4.82761 ( 6465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 724 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 15 SER cc_start: 0.9395 (t) cc_final: 0.9052 (p) REVERT: A 52 MET cc_start: 0.8722 (tpp) cc_final: 0.8421 (tpp) REVERT: A 406 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: A 463 LYS cc_start: 0.9295 (ptmt) cc_final: 0.9063 (ptmm) REVERT: D 421 GLN cc_start: 0.8267 (mp10) cc_final: 0.7713 (mp10) REVERT: E 88 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8467 (m) REVERT: E 110 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8777 (mt) REVERT: E 374 ARG cc_start: 0.9114 (mmm160) cc_final: 0.8845 (mmm160) REVERT: E 400 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7587 (tm-30) REVERT: E 438 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8452 (tm-30) REVERT: F 88 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.9042 (m) REVERT: F 395 MET cc_start: 0.8724 (mmm) cc_final: 0.8342 (tmm) REVERT: G 44 TYR cc_start: 0.7886 (t80) cc_final: 0.7580 (t80) REVERT: G 162 PHE cc_start: 0.8981 (p90) cc_final: 0.8437 (p90) REVERT: G 175 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: G 193 TYR cc_start: 0.7245 (m-80) cc_final: 0.6555 (t80) REVERT: G 211 ASN cc_start: 0.8732 (m-40) cc_final: 0.8449 (m110) REVERT: G 272 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8331 (mt) REVERT: H 35 GLN cc_start: 0.7873 (tp-100) cc_final: 0.7595 (tp40) REVERT: H 131 ILE cc_start: 0.7477 (mm) cc_final: 0.7246 (mm) REVERT: H 135 ILE cc_start: 0.8503 (pt) cc_final: 0.8238 (tp) REVERT: J 26 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7997 (tm-30) REVERT: J 40 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7858 (mt-10) REVERT: K 8 PHE cc_start: 0.8253 (m-80) cc_final: 0.7707 (m-80) REVERT: K 18 VAL cc_start: 0.9404 (m) cc_final: 0.9016 (t) REVERT: K 29 PHE cc_start: 0.9101 (m-80) cc_final: 0.8779 (m-10) REVERT: K 54 PHE cc_start: 0.8630 (t80) cc_final: 0.8272 (t80) REVERT: K 64 CYS cc_start: 0.9019 (p) cc_final: 0.8766 (p) REVERT: L 36 TYR cc_start: 0.8331 (t80) cc_final: 0.7639 (t80) REVERT: L 47 PHE cc_start: 0.9088 (t80) cc_final: 0.8738 (t80) REVERT: L 49 TYR cc_start: 0.8594 (m-80) cc_final: 0.8338 (m-80) REVERT: L 51 ILE cc_start: 0.8982 (mm) cc_final: 0.8738 (mm) REVERT: L 54 PHE cc_start: 0.8815 (t80) cc_final: 0.8548 (t80) REVERT: L 69 PHE cc_start: 0.8889 (t80) cc_final: 0.8325 (t80) REVERT: L 73 PHE cc_start: 0.6914 (m-10) cc_final: 0.6690 (m-10) REVERT: M 7 LYS cc_start: 0.7866 (mttm) cc_final: 0.7398 (mttt) REVERT: M 36 TYR cc_start: 0.7952 (t80) cc_final: 0.7739 (t80) REVERT: M 58 GLU cc_start: 0.7672 (tp30) cc_final: 0.7434 (tp30) REVERT: M 71 ILE cc_start: 0.8758 (mm) cc_final: 0.8449 (mm) REVERT: O 7 LYS cc_start: 0.8844 (mttt) cc_final: 0.8332 (tmmt) REVERT: O 45 GLN cc_start: 0.7536 (tp40) cc_final: 0.7296 (tp40) REVERT: P 15 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7292 (p) REVERT: P 38 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8213 (tpp-160) REVERT: P 62 LEU cc_start: 0.9399 (mt) cc_final: 0.8861 (mt) REVERT: Q 15 THR cc_start: 0.9023 (p) cc_final: 0.8765 (t) REVERT: Q 16 VAL cc_start: 0.8925 (t) cc_final: 0.8691 (m) REVERT: Q 29 PHE cc_start: 0.8815 (m-80) cc_final: 0.8545 (m-80) REVERT: Q 54 PHE cc_start: 0.8950 (t80) cc_final: 0.8676 (t80) REVERT: Q 58 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8174 (mm-30) REVERT: Q 63 PHE cc_start: 0.8822 (t80) cc_final: 0.8226 (t80) REVERT: R 7 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7158 (ttpp) REVERT: R 8 PHE cc_start: 0.8694 (m-80) cc_final: 0.8307 (m-80) REVERT: R 15 THR cc_start: 0.8805 (m) cc_final: 0.8504 (p) REVERT: R 56 LEU cc_start: 0.8705 (mt) cc_final: 0.8363 (mt) REVERT: R 58 GLU cc_start: 0.8207 (pp20) cc_final: 0.7930 (pp20) REVERT: R 62 LEU cc_start: 0.9134 (mm) cc_final: 0.8731 (mt) REVERT: R 65 LEU cc_start: 0.8475 (tp) cc_final: 0.8186 (tt) REVERT: S 62 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8560 (ttm-80) REVERT: S 165 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.8020 (ttm-80) REVERT: S 186 MET cc_start: 0.8158 (ptm) cc_final: 0.7737 (ppp) REVERT: a 97 GLN cc_start: 0.8577 (mm110) cc_final: 0.8363 (mm-40) REVERT: a 140 MET cc_start: 0.8699 (tmm) cc_final: 0.8432 (tmm) REVERT: a 218 VAL cc_start: 0.9355 (t) cc_final: 0.9099 (m) REVERT: a 221 TYR cc_start: 0.9266 (t80) cc_final: 0.9032 (t80) REVERT: a 223 HIS cc_start: 0.8149 (t-170) cc_final: 0.7766 (t-170) REVERT: b 129 ARG cc_start: 0.9098 (mtp85) cc_final: 0.8825 (mtt180) REVERT: b 140 TYR cc_start: 0.8634 (t80) cc_final: 0.8212 (t80) REVERT: b 143 ARG cc_start: 0.8617 (ptp-170) cc_final: 0.8020 (ptt-90) REVERT: b 145 HIS cc_start: 0.8524 (p-80) cc_final: 0.8148 (m-70) REVERT: i 24 THR cc_start: 0.7153 (p) cc_final: 0.6896 (p) REVERT: C 50 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8623 (mp0) REVERT: C 140 ILE cc_start: 0.9230 (tp) cc_final: 0.8988 (tt) REVERT: C 415 GLN cc_start: 0.7851 (mt0) cc_final: 0.7527 (mt0) REVERT: f 66 TYR cc_start: 0.8958 (t80) cc_final: 0.8641 (t80) REVERT: f 83 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5855 (pp) REVERT: B 333 ASP cc_start: 0.8008 (t0) cc_final: 0.7253 (p0) REVERT: B 334 VAL cc_start: 0.8837 (t) cc_final: 0.8571 (m) REVERT: B 465 GLU cc_start: 0.8472 (tt0) cc_final: 0.8136 (tm-30) outliers start: 141 outliers final: 73 residues processed: 816 average time/residue: 0.2092 time to fit residues: 276.5807 Evaluate side-chains 733 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 651 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 47 GLN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 217 LEU Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain b residue 130 ASN Chi-restraints excluded: chain b residue 136 LEU Chi-restraints excluded: chain b residue 169 GLU Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 497 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 456 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 331 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 343 optimal weight: 8.9990 chunk 344 optimal weight: 7.9990 chunk 351 optimal weight: 8.9990 chunk 339 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 30 ASN A 471 HIS E 41 GLN F 132 GLN G 15 ASN G 117 HIS ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 GLN O 39 ASN S 87 ASN T 51 GLN a 39 ASN a 47 GLN ** b 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 GLN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN B 366 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.072692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052877 restraints weight = 127419.175| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.41 r_work: 0.2926 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 37792 Z= 0.198 Angle : 0.604 14.175 51185 Z= 0.308 Chirality : 0.044 0.341 6090 Planarity : 0.004 0.065 6564 Dihedral : 7.132 160.586 5540 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 4.16 % Allowed : 12.91 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.12), residues: 4940 helix: 1.76 (0.10), residues: 2657 sheet: -0.48 (0.23), residues: 525 loop : -0.48 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 381 TYR 0.020 0.002 TYR E 383 PHE 0.032 0.002 PHE M 47 TRP 0.017 0.002 TRP 8 9 HIS 0.011 0.001 HIS a 127 Details of bonding type rmsd covalent geometry : bond 0.00452 (37792) covalent geometry : angle 0.60401 (51185) hydrogen bonds : bond 0.04394 ( 2227) hydrogen bonds : angle 4.71202 ( 6465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 682 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 15 SER cc_start: 0.9245 (t) cc_final: 0.8975 (p) REVERT: A 406 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: D 29 GLU cc_start: 0.8348 (pt0) cc_final: 0.8107 (pt0) REVERT: D 270 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8827 (p) REVERT: D 395 MET cc_start: 0.7505 (tpt) cc_final: 0.7070 (tpt) REVERT: D 421 GLN cc_start: 0.8335 (mp10) cc_final: 0.7728 (mp10) REVERT: D 461 MET cc_start: 0.9049 (mmp) cc_final: 0.8749 (mmm) REVERT: D 477 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7591 (mm-30) REVERT: E 92 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9162 (t) REVERT: E 110 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8756 (mt) REVERT: E 354 ASP cc_start: 0.8994 (m-30) cc_final: 0.8517 (t0) REVERT: E 374 ARG cc_start: 0.9150 (mmm160) cc_final: 0.8867 (mmm160) REVERT: E 387 GLN cc_start: 0.8295 (mp10) cc_final: 0.7546 (mp10) REVERT: E 438 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8468 (tm-30) REVERT: F 28 ASP cc_start: 0.8614 (p0) cc_final: 0.8388 (p0) REVERT: F 396 ASP cc_start: 0.8750 (p0) cc_final: 0.8472 (p0) REVERT: G 44 TYR cc_start: 0.7928 (t80) cc_final: 0.7600 (t80) REVERT: G 108 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7333 (p) REVERT: G 175 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6914 (tp30) REVERT: G 193 TYR cc_start: 0.7445 (m-80) cc_final: 0.6684 (t80) REVERT: G 272 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8276 (tp) REVERT: H 96 GLU cc_start: 0.8060 (tp30) cc_final: 0.7803 (tm-30) REVERT: H 132 GLN cc_start: 0.9533 (mt0) cc_final: 0.9088 (mt0) REVERT: H 133 ILE cc_start: 0.8663 (mt) cc_final: 0.8157 (mt) REVERT: I 17 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: J 26 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8037 (tm-30) REVERT: J 33 TYR cc_start: 0.8875 (t80) cc_final: 0.8577 (t80) REVERT: J 37 ARG cc_start: 0.8298 (mmp80) cc_final: 0.7624 (mmp80) REVERT: J 40 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7914 (mt-10) REVERT: K 8 PHE cc_start: 0.8385 (m-80) cc_final: 0.7785 (m-80) REVERT: K 18 VAL cc_start: 0.9389 (m) cc_final: 0.9042 (t) REVERT: K 29 PHE cc_start: 0.9041 (m-80) cc_final: 0.8741 (m-10) REVERT: K 36 TYR cc_start: 0.8537 (t80) cc_final: 0.8255 (t80) REVERT: K 54 PHE cc_start: 0.8564 (t80) cc_final: 0.8214 (t80) REVERT: L 36 TYR cc_start: 0.8385 (t80) cc_final: 0.7794 (t80) REVERT: L 49 TYR cc_start: 0.8690 (m-80) cc_final: 0.8278 (m-80) REVERT: L 60 MET cc_start: 0.9412 (tpp) cc_final: 0.9208 (mmm) REVERT: L 73 PHE cc_start: 0.7117 (m-10) cc_final: 0.6854 (m-10) REVERT: M 7 LYS cc_start: 0.8081 (mttm) cc_final: 0.7694 (mttt) REVERT: M 27 THR cc_start: 0.8997 (t) cc_final: 0.8741 (p) REVERT: M 36 TYR cc_start: 0.8012 (t80) cc_final: 0.7704 (t80) REVERT: M 71 ILE cc_start: 0.8744 (mm) cc_final: 0.8402 (mm) REVERT: N 38 ARG cc_start: 0.8891 (tpt-90) cc_final: 0.8613 (tpp80) REVERT: O 7 LYS cc_start: 0.8835 (mttt) cc_final: 0.8353 (tmmt) REVERT: P 42 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7986 (tt) REVERT: P 65 LEU cc_start: 0.9495 (tt) cc_final: 0.9257 (mm) REVERT: Q 16 VAL cc_start: 0.8964 (t) cc_final: 0.8597 (p) REVERT: Q 58 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7857 (mm-30) REVERT: Q 63 PHE cc_start: 0.8978 (t80) cc_final: 0.8770 (t80) REVERT: Q 66 MET cc_start: 0.8873 (ppp) cc_final: 0.8609 (ppp) REVERT: R 7 LYS cc_start: 0.7843 (mmtt) cc_final: 0.7112 (ttpp) REVERT: R 15 THR cc_start: 0.8786 (m) cc_final: 0.8529 (p) REVERT: R 56 LEU cc_start: 0.8817 (mt) cc_final: 0.8570 (mt) REVERT: R 62 LEU cc_start: 0.9135 (mm) cc_final: 0.8725 (mt) REVERT: R 65 LEU cc_start: 0.8529 (tp) cc_final: 0.8328 (tt) REVERT: S 121 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.8030 (t) REVERT: S 186 MET cc_start: 0.8165 (ptm) cc_final: 0.7872 (ppp) REVERT: a 47 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8262 (mm-40) REVERT: a 97 GLN cc_start: 0.8451 (mm110) cc_final: 0.8167 (mm110) REVERT: a 140 MET cc_start: 0.8737 (tmm) cc_final: 0.8412 (tmm) REVERT: a 212 TYR cc_start: 0.8846 (t80) cc_final: 0.8445 (t80) REVERT: a 214 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8861 (m-80) REVERT: a 218 VAL cc_start: 0.9344 (t) cc_final: 0.9117 (m) REVERT: a 221 TYR cc_start: 0.9320 (t80) cc_final: 0.9031 (t80) REVERT: a 223 HIS cc_start: 0.7979 (t-170) cc_final: 0.7717 (t-90) REVERT: b 131 ASN cc_start: 0.8808 (t0) cc_final: 0.8382 (p0) REVERT: b 140 TYR cc_start: 0.8539 (t80) cc_final: 0.8206 (t80) REVERT: b 143 ARG cc_start: 0.8653 (ptp-170) cc_final: 0.8126 (ptt-90) REVERT: b 150 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: b 158 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.8316 (m-70) REVERT: b 164 MET cc_start: 0.8298 (tmm) cc_final: 0.7896 (tmm) REVERT: b 173 MET cc_start: 0.8996 (mmp) cc_final: 0.8793 (mmp) REVERT: b 197 CYS cc_start: 0.9012 (m) cc_final: 0.8702 (t) REVERT: i 24 THR cc_start: 0.7233 (p) cc_final: 0.6699 (t) REVERT: C 50 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8628 (mp0) REVERT: C 140 ILE cc_start: 0.9254 (tp) cc_final: 0.9004 (tt) REVERT: C 266 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8817 (tp) REVERT: C 415 GLN cc_start: 0.7797 (mt0) cc_final: 0.7380 (mt0) REVERT: C 426 GLU cc_start: 0.8244 (tp30) cc_final: 0.7948 (tp30) REVERT: f 66 TYR cc_start: 0.9025 (t80) cc_final: 0.8661 (t80) REVERT: f 71 TYR cc_start: 0.9046 (t80) cc_final: 0.8769 (t80) REVERT: f 80 HIS cc_start: 0.6067 (OUTLIER) cc_final: 0.5474 (m-70) REVERT: f 83 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5875 (pp) REVERT: B 333 ASP cc_start: 0.7892 (t0) cc_final: 0.7239 (p0) REVERT: B 334 VAL cc_start: 0.8749 (t) cc_final: 0.8449 (m) REVERT: B 353 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: B 465 GLU cc_start: 0.8465 (tt0) cc_final: 0.8204 (tm-30) outliers start: 155 outliers final: 92 residues processed: 785 average time/residue: 0.2100 time to fit residues: 267.3937 Evaluate side-chains 748 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 637 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 81 THR Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 47 GLN Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 138 ILE Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 214 PHE Chi-restraints excluded: chain a residue 217 LEU Chi-restraints excluded: chain b residue 130 ASN Chi-restraints excluded: chain b residue 150 GLU Chi-restraints excluded: chain b residue 158 HIS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain i residue 18 PHE Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 80 HIS Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 410 optimal weight: 0.5980 chunk 462 optimal weight: 0.9980 chunk 340 optimal weight: 9.9990 chunk 321 optimal weight: 2.9990 chunk 351 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 433 optimal weight: 20.0000 chunk 251 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 30 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 GLN M 44 GLN a 39 ASN ** a 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 GLN c 23 GLN C 385 GLN B 302 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.072833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.053055 restraints weight = 127089.956| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.41 r_work: 0.2934 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37792 Z= 0.166 Angle : 0.595 11.191 51185 Z= 0.301 Chirality : 0.043 0.194 6090 Planarity : 0.004 0.066 6564 Dihedral : 7.045 160.179 5539 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 3.97 % Allowed : 14.28 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.12), residues: 4940 helix: 1.73 (0.10), residues: 2645 sheet: -0.53 (0.23), residues: 526 loop : -0.42 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 166 TYR 0.026 0.001 TYR c 18 PHE 0.029 0.002 PHE O 63 TRP 0.014 0.002 TRP 8 9 HIS 0.005 0.001 HIS C 471 Details of bonding type rmsd covalent geometry : bond 0.00377 (37792) covalent geometry : angle 0.59493 (51185) hydrogen bonds : bond 0.04187 ( 2227) hydrogen bonds : angle 4.61672 ( 6465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 660 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 15 SER cc_start: 0.9228 (t) cc_final: 0.8894 (p) REVERT: A 406 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: D 270 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8837 (p) REVERT: D 421 GLN cc_start: 0.8327 (mp10) cc_final: 0.7709 (mp10) REVERT: D 461 MET cc_start: 0.8968 (mmp) cc_final: 0.8649 (mmm) REVERT: E 110 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8782 (mt) REVERT: E 234 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8808 (p) REVERT: E 354 ASP cc_start: 0.8954 (m-30) cc_final: 0.8525 (t0) REVERT: E 374 ARG cc_start: 0.9155 (mmm160) cc_final: 0.8854 (mmm160) REVERT: E 438 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: F 396 ASP cc_start: 0.8737 (p0) cc_final: 0.8482 (p0) REVERT: G 108 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7355 (p) REVERT: G 162 PHE cc_start: 0.8897 (p90) cc_final: 0.8378 (p90) REVERT: G 175 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7001 (tp30) REVERT: G 193 TYR cc_start: 0.7547 (m-80) cc_final: 0.6740 (t80) REVERT: G 272 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8261 (tp) REVERT: H 96 GLU cc_start: 0.8062 (tp30) cc_final: 0.7777 (tm-30) REVERT: J 26 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8058 (tm-30) REVERT: J 33 TYR cc_start: 0.8836 (t80) cc_final: 0.8516 (t80) REVERT: J 37 ARG cc_start: 0.8268 (mmp80) cc_final: 0.7643 (mmp80) REVERT: J 40 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8004 (mt-10) REVERT: K 8 PHE cc_start: 0.8408 (m-80) cc_final: 0.7914 (m-80) REVERT: K 18 VAL cc_start: 0.9387 (m) cc_final: 0.8984 (t) REVERT: K 29 PHE cc_start: 0.9020 (m-80) cc_final: 0.8597 (m-10) REVERT: K 36 TYR cc_start: 0.8580 (t80) cc_final: 0.8357 (t80) REVERT: K 54 PHE cc_start: 0.8583 (t80) cc_final: 0.8209 (t80) REVERT: L 36 TYR cc_start: 0.8386 (t80) cc_final: 0.7908 (t80) REVERT: L 49 TYR cc_start: 0.8770 (m-80) cc_final: 0.8528 (m-80) REVERT: L 51 ILE cc_start: 0.9024 (mm) cc_final: 0.8741 (mt) REVERT: L 69 PHE cc_start: 0.8907 (t80) cc_final: 0.8197 (t80) REVERT: L 73 PHE cc_start: 0.6960 (m-10) cc_final: 0.6678 (m-10) REVERT: M 7 LYS cc_start: 0.8065 (mttm) cc_final: 0.7719 (mttt) REVERT: M 36 TYR cc_start: 0.8048 (t80) cc_final: 0.7770 (t80) REVERT: M 38 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7661 (ttp-110) REVERT: M 49 TYR cc_start: 0.8054 (m-10) cc_final: 0.7648 (m-10) REVERT: M 52 LEU cc_start: 0.8817 (mm) cc_final: 0.8589 (mm) REVERT: M 58 GLU cc_start: 0.7735 (tp30) cc_final: 0.7495 (tp30) REVERT: M 71 ILE cc_start: 0.8739 (mm) cc_final: 0.8367 (mm) REVERT: M 72 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8905 (tt) REVERT: N 38 ARG cc_start: 0.8852 (tpt-90) cc_final: 0.8457 (tpp80) REVERT: O 7 LYS cc_start: 0.8829 (mttt) cc_final: 0.8368 (tmmt) REVERT: O 45 GLN cc_start: 0.7542 (tp40) cc_final: 0.7049 (tp40) REVERT: O 71 ILE cc_start: 0.8760 (mm) cc_final: 0.8464 (mm) REVERT: P 38 ARG cc_start: 0.8646 (tpp-160) cc_final: 0.8028 (mmt90) REVERT: P 42 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8095 (tt) REVERT: P 46 LEU cc_start: 0.8819 (mt) cc_final: 0.8594 (mm) REVERT: P 60 MET cc_start: 0.8713 (ttm) cc_final: 0.8434 (ttm) REVERT: P 65 LEU cc_start: 0.9492 (tt) cc_final: 0.9049 (mt) REVERT: Q 15 THR cc_start: 0.9036 (p) cc_final: 0.8781 (t) REVERT: Q 16 VAL cc_start: 0.8936 (t) cc_final: 0.8526 (p) REVERT: Q 58 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8063 (mp0) REVERT: Q 66 MET cc_start: 0.8826 (ppp) cc_final: 0.8548 (ppp) REVERT: R 7 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7087 (ttpp) REVERT: R 8 PHE cc_start: 0.8799 (m-80) cc_final: 0.8409 (m-80) REVERT: R 27 THR cc_start: 0.9020 (m) cc_final: 0.8768 (t) REVERT: R 56 LEU cc_start: 0.8763 (mt) cc_final: 0.8527 (mt) REVERT: R 58 GLU cc_start: 0.8196 (pp20) cc_final: 0.7939 (pp20) REVERT: R 62 LEU cc_start: 0.9131 (mm) cc_final: 0.8727 (mt) REVERT: S 69 LEU cc_start: 0.9285 (mm) cc_final: 0.8940 (mm) REVERT: S 72 MET cc_start: 0.8416 (ppp) cc_final: 0.8177 (ppp) REVERT: S 165 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8222 (ttm-80) REVERT: S 186 MET cc_start: 0.8092 (ptm) cc_final: 0.7818 (ppp) REVERT: a 55 LYS cc_start: 0.9246 (pttt) cc_final: 0.8752 (mptt) REVERT: a 56 GLN cc_start: 0.9482 (mm-40) cc_final: 0.9124 (tp-100) REVERT: a 97 GLN cc_start: 0.8460 (mm110) cc_final: 0.8214 (mm110) REVERT: a 114 PHE cc_start: 0.9104 (m-10) cc_final: 0.8857 (m-10) REVERT: a 140 MET cc_start: 0.8751 (tmm) cc_final: 0.8376 (tmm) REVERT: a 212 TYR cc_start: 0.8826 (t80) cc_final: 0.8461 (t80) REVERT: a 214 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8825 (m-80) REVERT: a 217 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9143 (mm) REVERT: a 218 VAL cc_start: 0.9341 (t) cc_final: 0.9101 (m) REVERT: a 223 HIS cc_start: 0.7989 (t-170) cc_final: 0.7744 (t-90) REVERT: b 129 ARG cc_start: 0.9182 (mtt180) cc_final: 0.8967 (mtt180) REVERT: b 145 HIS cc_start: 0.8463 (p90) cc_final: 0.8135 (m-70) REVERT: b 158 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.8350 (m-70) REVERT: b 164 MET cc_start: 0.8276 (tmm) cc_final: 0.7716 (tmm) REVERT: b 173 MET cc_start: 0.9079 (mmp) cc_final: 0.8527 (mmm) REVERT: b 197 CYS cc_start: 0.8977 (m) cc_final: 0.8648 (t) REVERT: i 24 THR cc_start: 0.7180 (p) cc_final: 0.6713 (t) REVERT: C 50 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8597 (mp0) REVERT: C 140 ILE cc_start: 0.9265 (tp) cc_final: 0.9015 (tt) REVERT: C 266 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8797 (tp) REVERT: C 415 GLN cc_start: 0.7918 (mt0) cc_final: 0.7406 (mt0) REVERT: C 426 GLU cc_start: 0.8272 (tp30) cc_final: 0.7843 (tp30) REVERT: f 66 TYR cc_start: 0.9028 (t80) cc_final: 0.8674 (t80) REVERT: f 71 TYR cc_start: 0.9019 (t80) cc_final: 0.8748 (t80) REVERT: f 80 HIS cc_start: 0.5945 (OUTLIER) cc_final: 0.5538 (m-70) REVERT: f 83 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5877 (pp) REVERT: B 333 ASP cc_start: 0.7990 (t0) cc_final: 0.7304 (p0) REVERT: B 334 VAL cc_start: 0.8723 (t) cc_final: 0.8416 (m) REVERT: B 353 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: B 465 GLU cc_start: 0.8485 (tt0) cc_final: 0.8184 (tm-30) outliers start: 148 outliers final: 97 residues processed: 757 average time/residue: 0.2118 time to fit residues: 261.1008 Evaluate side-chains 751 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 637 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 29 SER Chi-restraints excluded: chain 8 residue 31 TYR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 179 PHE Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 172 ASP Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 81 THR Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 61 HIS Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 138 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 214 PHE Chi-restraints excluded: chain a residue 217 LEU Chi-restraints excluded: chain b residue 130 ASN Chi-restraints excluded: chain b residue 158 HIS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain i residue 18 PHE Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 80 HIS Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 143 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 483 optimal weight: 0.8980 chunk 437 optimal weight: 2.9990 chunk 255 optimal weight: 0.0980 chunk 289 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 400 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 26 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN a 47 GLN c 23 GLN f 70 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.073367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053636 restraints weight = 126347.499| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.41 r_work: 0.2949 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37792 Z= 0.132 Angle : 0.579 10.508 51185 Z= 0.292 Chirality : 0.042 0.219 6090 Planarity : 0.004 0.070 6564 Dihedral : 6.872 159.388 5537 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 4.00 % Allowed : 14.87 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.12), residues: 4940 helix: 1.76 (0.10), residues: 2634 sheet: -0.56 (0.23), residues: 535 loop : -0.33 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 381 TYR 0.023 0.001 TYR E 383 PHE 0.031 0.002 PHE N 47 TRP 0.018 0.002 TRP 8 9 HIS 0.008 0.001 HIS b 172 Details of bonding type rmsd covalent geometry : bond 0.00291 (37792) covalent geometry : angle 0.57894 (51185) hydrogen bonds : bond 0.03984 ( 2227) hydrogen bonds : angle 4.52256 ( 6465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 654 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 15 SER cc_start: 0.9097 (t) cc_final: 0.8831 (p) REVERT: 8 16 MET cc_start: 0.8047 (ptp) cc_final: 0.7830 (ptp) REVERT: A 301 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8801 (tp) REVERT: D 209 ASN cc_start: 0.8926 (t0) cc_final: 0.8631 (t0) REVERT: D 270 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8822 (p) REVERT: D 421 GLN cc_start: 0.8316 (mp10) cc_final: 0.7736 (mp10) REVERT: E 88 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8330 (m) REVERT: E 110 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8769 (mt) REVERT: E 354 ASP cc_start: 0.8963 (m-30) cc_final: 0.8447 (t0) REVERT: E 374 ARG cc_start: 0.9173 (mmm160) cc_final: 0.8859 (mmm160) REVERT: E 387 GLN cc_start: 0.8517 (mp10) cc_final: 0.7800 (mp10) REVERT: F 396 ASP cc_start: 0.8702 (p0) cc_final: 0.8466 (p0) REVERT: G 108 VAL cc_start: 0.7714 (OUTLIER) cc_final: 0.7343 (p) REVERT: G 162 PHE cc_start: 0.8928 (p90) cc_final: 0.8469 (p90) REVERT: G 175 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.7029 (tp30) REVERT: G 193 TYR cc_start: 0.7513 (m-80) cc_final: 0.6695 (t80) REVERT: G 272 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8270 (tp) REVERT: H 91 GLN cc_start: 0.7583 (mp10) cc_final: 0.6887 (mp10) REVERT: H 96 GLU cc_start: 0.8046 (tp30) cc_final: 0.7769 (tm-30) REVERT: J 24 LYS cc_start: 0.8822 (mmmt) cc_final: 0.8622 (mmmt) REVERT: J 26 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8078 (tm-30) REVERT: J 33 TYR cc_start: 0.8841 (t80) cc_final: 0.8559 (t80) REVERT: J 37 ARG cc_start: 0.8301 (mmp80) cc_final: 0.7759 (mmp80) REVERT: J 40 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8065 (mt-10) REVERT: K 8 PHE cc_start: 0.8397 (m-80) cc_final: 0.7935 (m-80) REVERT: K 18 VAL cc_start: 0.9279 (m) cc_final: 0.8926 (t) REVERT: K 29 PHE cc_start: 0.9020 (m-80) cc_final: 0.8590 (m-10) REVERT: K 36 TYR cc_start: 0.8625 (t80) cc_final: 0.8265 (t80) REVERT: K 49 TYR cc_start: 0.8818 (m-80) cc_final: 0.8378 (m-80) REVERT: K 54 PHE cc_start: 0.8537 (t80) cc_final: 0.8109 (t80) REVERT: L 36 TYR cc_start: 0.8380 (t80) cc_final: 0.7789 (t80) REVERT: L 38 ARG cc_start: 0.9218 (ttm110) cc_final: 0.9003 (ttm170) REVERT: L 49 TYR cc_start: 0.8847 (m-80) cc_final: 0.8614 (m-80) REVERT: L 51 ILE cc_start: 0.9075 (mm) cc_final: 0.8782 (mm) REVERT: L 69 PHE cc_start: 0.8921 (t80) cc_final: 0.8387 (t80) REVERT: M 7 LYS cc_start: 0.8015 (mttm) cc_final: 0.7540 (mttm) REVERT: M 36 TYR cc_start: 0.7912 (t80) cc_final: 0.7608 (t80) REVERT: M 38 ARG cc_start: 0.8256 (mtp-110) cc_final: 0.7713 (ttp-110) REVERT: M 45 GLN cc_start: 0.8286 (mp10) cc_final: 0.7168 (mp10) REVERT: M 49 TYR cc_start: 0.7943 (m-10) cc_final: 0.7532 (m-10) REVERT: M 52 LEU cc_start: 0.8770 (mm) cc_final: 0.8483 (mm) REVERT: M 66 MET cc_start: 0.8834 (ppp) cc_final: 0.8626 (ppp) REVERT: M 71 ILE cc_start: 0.8747 (mm) cc_final: 0.8321 (mm) REVERT: M 72 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8834 (tt) REVERT: N 25 ILE cc_start: 0.7956 (mm) cc_final: 0.7620 (mm) REVERT: N 38 ARG cc_start: 0.8808 (tpt-90) cc_final: 0.8584 (tpp80) REVERT: N 72 LEU cc_start: 0.9260 (tp) cc_final: 0.9037 (tp) REVERT: O 7 LYS cc_start: 0.8820 (mttt) cc_final: 0.8364 (tmmt) REVERT: O 38 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8323 (ttt-90) REVERT: O 71 ILE cc_start: 0.8793 (mm) cc_final: 0.8457 (mm) REVERT: P 38 ARG cc_start: 0.8642 (tpp-160) cc_final: 0.8049 (mmt90) REVERT: P 46 LEU cc_start: 0.8851 (mt) cc_final: 0.8517 (mm) REVERT: P 60 MET cc_start: 0.8718 (ttm) cc_final: 0.8428 (ttm) REVERT: P 66 MET cc_start: 0.8844 (ptt) cc_final: 0.8245 (ppp) REVERT: Q 15 THR cc_start: 0.9069 (p) cc_final: 0.8794 (t) REVERT: Q 16 VAL cc_start: 0.8888 (t) cc_final: 0.8480 (p) REVERT: Q 58 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8057 (mm-30) REVERT: Q 63 PHE cc_start: 0.8863 (t80) cc_final: 0.8617 (t80) REVERT: Q 66 MET cc_start: 0.8789 (ppp) cc_final: 0.8449 (ppp) REVERT: R 7 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7077 (ttpp) REVERT: R 8 PHE cc_start: 0.8762 (m-80) cc_final: 0.8369 (m-80) REVERT: R 27 THR cc_start: 0.9054 (m) cc_final: 0.8794 (t) REVERT: R 56 LEU cc_start: 0.8702 (mt) cc_final: 0.8482 (mt) REVERT: R 58 GLU cc_start: 0.8168 (pp20) cc_final: 0.7889 (pp20) REVERT: R 62 LEU cc_start: 0.9101 (mm) cc_final: 0.8744 (mt) REVERT: S 69 LEU cc_start: 0.9260 (mm) cc_final: 0.8898 (mm) REVERT: S 165 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8155 (ttm-80) REVERT: a 24 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8905 (tp) REVERT: a 55 LYS cc_start: 0.9232 (pttt) cc_final: 0.8729 (mptt) REVERT: a 56 GLN cc_start: 0.9482 (mm-40) cc_final: 0.9130 (tp-100) REVERT: a 97 GLN cc_start: 0.8370 (mm110) cc_final: 0.8091 (mm110) REVERT: a 114 PHE cc_start: 0.9131 (m-10) cc_final: 0.8841 (m-10) REVERT: a 140 MET cc_start: 0.8769 (tmm) cc_final: 0.8226 (tmm) REVERT: a 144 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9110 (mm) REVERT: a 187 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7931 (tpt) REVERT: a 199 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8878 (tt) REVERT: a 212 TYR cc_start: 0.8825 (t80) cc_final: 0.8621 (t80) REVERT: a 214 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8730 (m-80) REVERT: a 217 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9053 (tt) REVERT: a 218 VAL cc_start: 0.9320 (t) cc_final: 0.9075 (m) REVERT: a 223 HIS cc_start: 0.8116 (t-170) cc_final: 0.7804 (t-90) REVERT: b 77 SER cc_start: 0.8238 (t) cc_final: 0.7830 (m) REVERT: b 129 ARG cc_start: 0.9208 (mtt180) cc_final: 0.8889 (mtt180) REVERT: b 140 TYR cc_start: 0.8385 (t80) cc_final: 0.8163 (t80) REVERT: b 143 ARG cc_start: 0.8719 (ptp-170) cc_final: 0.8157 (ptp-170) REVERT: b 145 HIS cc_start: 0.8484 (p90) cc_final: 0.7931 (m170) REVERT: b 158 HIS cc_start: 0.8841 (OUTLIER) cc_final: 0.8378 (m-70) REVERT: b 164 MET cc_start: 0.8383 (tmm) cc_final: 0.7965 (tmm) REVERT: b 173 MET cc_start: 0.8972 (mmp) cc_final: 0.8761 (mmm) REVERT: b 197 CYS cc_start: 0.8957 (m) cc_final: 0.8659 (t) REVERT: e 5 GLN cc_start: 0.8378 (tp-100) cc_final: 0.8115 (pt0) REVERT: i 24 THR cc_start: 0.7114 (p) cc_final: 0.6611 (t) REVERT: C 50 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8591 (mp0) REVERT: C 140 ILE cc_start: 0.9267 (tp) cc_final: 0.9020 (tt) REVERT: C 266 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8790 (tp) REVERT: C 415 GLN cc_start: 0.7925 (mt0) cc_final: 0.7646 (mt0) REVERT: C 426 GLU cc_start: 0.8276 (tp30) cc_final: 0.7866 (tp30) REVERT: f 66 TYR cc_start: 0.9075 (t80) cc_final: 0.8708 (t80) REVERT: f 71 TYR cc_start: 0.9017 (t80) cc_final: 0.8782 (t80) REVERT: f 80 HIS cc_start: 0.5893 (OUTLIER) cc_final: 0.5581 (m-70) REVERT: f 83 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5850 (pp) REVERT: B 333 ASP cc_start: 0.7961 (t0) cc_final: 0.7335 (p0) REVERT: B 334 VAL cc_start: 0.8777 (t) cc_final: 0.8424 (m) REVERT: B 353 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8598 (mp0) outliers start: 149 outliers final: 90 residues processed: 762 average time/residue: 0.2110 time to fit residues: 262.7554 Evaluate side-chains 733 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 623 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 179 PHE Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 61 HIS Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 138 ILE Chi-restraints excluded: chain a residue 144 ILE Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 187 MET Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 214 PHE Chi-restraints excluded: chain a residue 217 LEU Chi-restraints excluded: chain b residue 150 GLU Chi-restraints excluded: chain b residue 158 HIS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain i residue 18 PHE Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 80 HIS Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 424 optimal weight: 1.9990 chunk 365 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 420 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 199 optimal weight: 0.3980 chunk 293 optimal weight: 2.9990 chunk 447 optimal weight: 0.5980 chunk 167 optimal weight: 0.3980 chunk 405 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 30 ASN D 200 HIS ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 146 GLN a 39 ASN a 90 HIS ** c 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.074052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054439 restraints weight = 125003.951| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.33 r_work: 0.2977 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37792 Z= 0.122 Angle : 0.577 11.188 51185 Z= 0.291 Chirality : 0.042 0.245 6090 Planarity : 0.004 0.072 6564 Dihedral : 6.584 158.802 5528 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 3.68 % Allowed : 15.73 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.12), residues: 4940 helix: 1.76 (0.10), residues: 2635 sheet: -0.45 (0.23), residues: 521 loop : -0.28 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 134 TYR 0.024 0.001 TYR E 383 PHE 0.029 0.001 PHE M 47 TRP 0.019 0.002 TRP 8 9 HIS 0.005 0.001 HIS b 172 Details of bonding type rmsd covalent geometry : bond 0.00268 (37792) covalent geometry : angle 0.57743 (51185) hydrogen bonds : bond 0.03859 ( 2227) hydrogen bonds : angle 4.45575 ( 6465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 653 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 15 SER cc_start: 0.9062 (t) cc_final: 0.8815 (p) REVERT: 8 16 MET cc_start: 0.7944 (ptp) cc_final: 0.7741 (ptp) REVERT: A 301 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8792 (tp) REVERT: D 209 ASN cc_start: 0.8790 (t0) cc_final: 0.8542 (t0) REVERT: D 421 GLN cc_start: 0.8291 (mp10) cc_final: 0.7734 (mp10) REVERT: E 88 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8279 (m) REVERT: E 294 MET cc_start: 0.8991 (tmm) cc_final: 0.8517 (tmm) REVERT: E 336 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8911 (m) REVERT: E 354 ASP cc_start: 0.8871 (m-30) cc_final: 0.8443 (t0) REVERT: E 363 ASN cc_start: 0.9266 (m110) cc_final: 0.9056 (m110) REVERT: E 374 ARG cc_start: 0.9137 (mmm160) cc_final: 0.8811 (mmm160) REVERT: F 28 ASP cc_start: 0.8378 (p0) cc_final: 0.8125 (p0) REVERT: F 396 ASP cc_start: 0.8662 (p0) cc_final: 0.8384 (p0) REVERT: G 108 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7481 (p) REVERT: G 162 PHE cc_start: 0.8882 (p90) cc_final: 0.8570 (p90) REVERT: G 193 TYR cc_start: 0.7494 (m-80) cc_final: 0.6725 (t80) REVERT: H 91 GLN cc_start: 0.7688 (mp10) cc_final: 0.6965 (mp10) REVERT: H 96 GLU cc_start: 0.8009 (tp30) cc_final: 0.7763 (tm-30) REVERT: J 26 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8109 (tm-30) REVERT: J 33 TYR cc_start: 0.8872 (t80) cc_final: 0.8614 (t80) REVERT: J 37 ARG cc_start: 0.8269 (mmp80) cc_final: 0.7741 (mmp80) REVERT: J 40 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8097 (mt-10) REVERT: K 8 PHE cc_start: 0.8407 (m-80) cc_final: 0.7974 (m-80) REVERT: K 18 VAL cc_start: 0.9294 (m) cc_final: 0.8857 (t) REVERT: K 29 PHE cc_start: 0.8934 (m-80) cc_final: 0.8490 (m-10) REVERT: K 36 TYR cc_start: 0.8574 (t80) cc_final: 0.8282 (t80) REVERT: K 49 TYR cc_start: 0.8684 (m-80) cc_final: 0.8063 (m-80) REVERT: K 54 PHE cc_start: 0.8584 (t80) cc_final: 0.8219 (t80) REVERT: L 36 TYR cc_start: 0.8396 (t80) cc_final: 0.7930 (t80) REVERT: L 49 TYR cc_start: 0.8784 (m-80) cc_final: 0.8416 (m-80) REVERT: L 63 PHE cc_start: 0.8627 (t80) cc_final: 0.8383 (t80) REVERT: L 69 PHE cc_start: 0.8818 (t80) cc_final: 0.8338 (t80) REVERT: M 7 LYS cc_start: 0.8006 (mttm) cc_final: 0.7514 (mttm) REVERT: M 18 VAL cc_start: 0.8546 (p) cc_final: 0.8282 (m) REVERT: M 36 TYR cc_start: 0.7949 (t80) cc_final: 0.7662 (t80) REVERT: M 45 GLN cc_start: 0.8209 (mp10) cc_final: 0.7210 (mp10) REVERT: M 49 TYR cc_start: 0.7875 (m-10) cc_final: 0.7478 (m-10) REVERT: M 58 GLU cc_start: 0.7740 (tp30) cc_final: 0.7499 (tp30) REVERT: M 66 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8600 (ppp) REVERT: M 71 ILE cc_start: 0.8720 (mm) cc_final: 0.8279 (mm) REVERT: N 25 ILE cc_start: 0.7974 (mm) cc_final: 0.7714 (mm) REVERT: N 72 LEU cc_start: 0.9250 (tp) cc_final: 0.9028 (tp) REVERT: O 7 LYS cc_start: 0.8816 (mttt) cc_final: 0.8354 (tmmt) REVERT: O 45 GLN cc_start: 0.8000 (mt0) cc_final: 0.7759 (mt0) REVERT: O 71 ILE cc_start: 0.8815 (mm) cc_final: 0.8460 (mm) REVERT: P 60 MET cc_start: 0.8694 (ttm) cc_final: 0.8384 (ttm) REVERT: P 65 LEU cc_start: 0.9436 (tt) cc_final: 0.8942 (mt) REVERT: P 66 MET cc_start: 0.8791 (ptt) cc_final: 0.8153 (ppp) REVERT: Q 15 THR cc_start: 0.9071 (p) cc_final: 0.8766 (t) REVERT: Q 16 VAL cc_start: 0.8870 (t) cc_final: 0.8454 (p) REVERT: Q 58 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8014 (mm-30) REVERT: Q 66 MET cc_start: 0.8751 (ppp) cc_final: 0.8386 (ppp) REVERT: R 7 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7055 (ttpp) REVERT: R 8 PHE cc_start: 0.8761 (m-80) cc_final: 0.8338 (m-80) REVERT: R 27 THR cc_start: 0.9042 (m) cc_final: 0.8777 (t) REVERT: R 56 LEU cc_start: 0.8643 (mt) cc_final: 0.8439 (mt) REVERT: R 58 GLU cc_start: 0.8094 (pp20) cc_final: 0.7720 (pp20) REVERT: R 62 LEU cc_start: 0.9032 (mm) cc_final: 0.8617 (mt) REVERT: R 65 LEU cc_start: 0.8160 (tp) cc_final: 0.7859 (tt) REVERT: S 165 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8177 (ttm-80) REVERT: a 24 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8883 (tp) REVERT: a 40 ASN cc_start: 0.8180 (m110) cc_final: 0.7934 (m110) REVERT: a 43 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8753 (tt) REVERT: a 47 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8585 (mm-40) REVERT: a 55 LYS cc_start: 0.9211 (pttt) cc_final: 0.8709 (mptt) REVERT: a 56 GLN cc_start: 0.9481 (mm-40) cc_final: 0.9108 (tp-100) REVERT: a 97 GLN cc_start: 0.8351 (mm110) cc_final: 0.8017 (mm-40) REVERT: a 100 MET cc_start: 0.8913 (ttp) cc_final: 0.8527 (ptp) REVERT: a 114 PHE cc_start: 0.9118 (m-10) cc_final: 0.8843 (m-10) REVERT: a 140 MET cc_start: 0.8765 (tmm) cc_final: 0.8508 (tmm) REVERT: a 172 HIS cc_start: 0.7496 (m90) cc_final: 0.7273 (t-170) REVERT: a 187 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7862 (tpt) REVERT: a 212 TYR cc_start: 0.8709 (t80) cc_final: 0.8440 (t80) REVERT: a 217 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9036 (tt) REVERT: a 218 VAL cc_start: 0.9304 (t) cc_final: 0.9027 (m) REVERT: a 223 HIS cc_start: 0.8089 (t-170) cc_final: 0.7783 (t-90) REVERT: b 77 SER cc_start: 0.8097 (t) cc_final: 0.7719 (m) REVERT: b 129 ARG cc_start: 0.9303 (mtt180) cc_final: 0.9018 (mtt180) REVERT: b 140 TYR cc_start: 0.8328 (t80) cc_final: 0.8086 (t80) REVERT: b 143 ARG cc_start: 0.8711 (ptp-170) cc_final: 0.8213 (ptt180) REVERT: b 145 HIS cc_start: 0.8475 (p90) cc_final: 0.7966 (m170) REVERT: b 158 HIS cc_start: 0.8857 (OUTLIER) cc_final: 0.8417 (m-70) REVERT: b 164 MET cc_start: 0.8377 (tmm) cc_final: 0.8015 (tmm) REVERT: b 173 MET cc_start: 0.9088 (mmp) cc_final: 0.8627 (mmm) REVERT: e 18 LEU cc_start: 0.9159 (pp) cc_final: 0.8877 (tp) REVERT: i 24 THR cc_start: 0.7148 (p) cc_final: 0.6947 (p) REVERT: C 95 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9055 (m) REVERT: C 140 ILE cc_start: 0.9271 (tp) cc_final: 0.9029 (tt) REVERT: C 266 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8756 (tp) REVERT: C 415 GLN cc_start: 0.8002 (mt0) cc_final: 0.7710 (mt0) REVERT: C 426 GLU cc_start: 0.8247 (tp30) cc_final: 0.7995 (tp30) REVERT: C 477 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8729 (mm-40) REVERT: f 66 TYR cc_start: 0.9080 (t80) cc_final: 0.8677 (t80) REVERT: f 80 HIS cc_start: 0.5957 (OUTLIER) cc_final: 0.5636 (m-70) REVERT: f 83 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5712 (pp) REVERT: B 333 ASP cc_start: 0.7905 (t0) cc_final: 0.7329 (p0) REVERT: B 334 VAL cc_start: 0.8721 (t) cc_final: 0.8369 (m) REVERT: B 353 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8520 (mp0) outliers start: 137 outliers final: 96 residues processed: 754 average time/residue: 0.2122 time to fit residues: 260.6538 Evaluate side-chains 718 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 607 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 395 MET Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 179 PHE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 61 HIS Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 138 ILE Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 187 MET Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 217 LEU Chi-restraints excluded: chain b residue 130 ASN Chi-restraints excluded: chain b residue 150 GLU Chi-restraints excluded: chain b residue 158 HIS Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain i residue 18 PHE Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 80 HIS Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 187 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 316 optimal weight: 0.9980 chunk 396 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 488 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 284 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 26 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 131 GLN ** c 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 GLN B 415 GLN B 432 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054212 restraints weight = 125707.392| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.34 r_work: 0.2973 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37792 Z= 0.136 Angle : 0.600 12.323 51185 Z= 0.301 Chirality : 0.043 0.208 6090 Planarity : 0.004 0.075 6564 Dihedral : 6.510 158.956 5526 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 3.70 % Allowed : 16.26 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.12), residues: 4940 helix: 1.75 (0.10), residues: 2648 sheet: -0.48 (0.23), residues: 541 loop : -0.30 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 381 TYR 0.026 0.001 TYR K 36 PHE 0.034 0.001 PHE N 47 TRP 0.032 0.002 TRP 8 9 HIS 0.005 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00305 (37792) covalent geometry : angle 0.59977 (51185) hydrogen bonds : bond 0.03874 ( 2227) hydrogen bonds : angle 4.44259 ( 6465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 628 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 15 SER cc_start: 0.9053 (t) cc_final: 0.8794 (p) REVERT: 8 16 MET cc_start: 0.7895 (ptp) cc_final: 0.7686 (ptp) REVERT: A 301 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 209 ASN cc_start: 0.8803 (t0) cc_final: 0.8522 (t0) REVERT: D 421 GLN cc_start: 0.8373 (mp10) cc_final: 0.7766 (mp10) REVERT: E 88 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8341 (m) REVERT: E 110 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8742 (mt) REVERT: E 294 MET cc_start: 0.9004 (tmm) cc_final: 0.8533 (tmm) REVERT: E 336 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8927 (m) REVERT: E 354 ASP cc_start: 0.8868 (m-30) cc_final: 0.8443 (t0) REVERT: E 374 ARG cc_start: 0.9169 (mmm160) cc_final: 0.8849 (mmm160) REVERT: F 28 ASP cc_start: 0.8432 (p0) cc_final: 0.8165 (p0) REVERT: F 396 ASP cc_start: 0.8662 (p0) cc_final: 0.8389 (p0) REVERT: G 108 VAL cc_start: 0.7903 (OUTLIER) cc_final: 0.7546 (p) REVERT: G 193 TYR cc_start: 0.7544 (m-80) cc_final: 0.6747 (t80) REVERT: H 56 GLN cc_start: 0.7365 (mm-40) cc_final: 0.7129 (mm-40) REVERT: H 91 GLN cc_start: 0.7695 (mp10) cc_final: 0.6892 (mp10) REVERT: H 96 GLU cc_start: 0.8009 (tp30) cc_final: 0.7796 (tm-30) REVERT: H 134 ARG cc_start: 0.9216 (mtp85) cc_final: 0.8991 (ttp-110) REVERT: J 24 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8681 (mmmt) REVERT: J 26 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8155 (tm-30) REVERT: J 33 TYR cc_start: 0.8903 (t80) cc_final: 0.8639 (t80) REVERT: J 37 ARG cc_start: 0.8250 (mmp80) cc_final: 0.7728 (mmp80) REVERT: J 40 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8162 (mt-10) REVERT: K 8 PHE cc_start: 0.8418 (m-80) cc_final: 0.7900 (m-80) REVERT: K 18 VAL cc_start: 0.9258 (m) cc_final: 0.8896 (t) REVERT: K 29 PHE cc_start: 0.8923 (m-80) cc_final: 0.8530 (m-10) REVERT: K 36 TYR cc_start: 0.8603 (t80) cc_final: 0.8311 (t80) REVERT: K 49 TYR cc_start: 0.8611 (m-80) cc_final: 0.7896 (m-80) REVERT: K 54 PHE cc_start: 0.8552 (t80) cc_final: 0.8311 (t80) REVERT: L 7 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6596 (mmtt) REVERT: L 45 GLN cc_start: 0.8678 (pm20) cc_final: 0.8455 (pm20) REVERT: L 49 TYR cc_start: 0.8818 (m-80) cc_final: 0.8512 (m-80) REVERT: L 58 GLU cc_start: 0.8925 (tp30) cc_final: 0.8366 (tp30) REVERT: L 69 PHE cc_start: 0.8783 (t80) cc_final: 0.8302 (t80) REVERT: M 7 LYS cc_start: 0.8034 (mttm) cc_final: 0.7535 (mttm) REVERT: M 18 VAL cc_start: 0.8482 (p) cc_final: 0.8240 (m) REVERT: M 36 TYR cc_start: 0.7961 (t80) cc_final: 0.7700 (t80) REVERT: M 38 ARG cc_start: 0.8071 (mtp-110) cc_final: 0.7809 (ttp-110) REVERT: M 45 GLN cc_start: 0.8161 (mp10) cc_final: 0.7169 (mp10) REVERT: M 49 TYR cc_start: 0.8123 (m-10) cc_final: 0.7584 (m-10) REVERT: M 66 MET cc_start: 0.8876 (ppp) cc_final: 0.8593 (ppp) REVERT: M 71 ILE cc_start: 0.8743 (mm) cc_final: 0.8262 (mm) REVERT: M 72 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8782 (tt) REVERT: N 25 ILE cc_start: 0.7977 (mm) cc_final: 0.7757 (mm) REVERT: N 38 ARG cc_start: 0.8842 (tpp80) cc_final: 0.8608 (tpp80) REVERT: N 72 LEU cc_start: 0.9228 (tp) cc_final: 0.9003 (tp) REVERT: O 7 LYS cc_start: 0.8790 (mttt) cc_final: 0.8339 (tmmt) REVERT: O 38 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8665 (ttt-90) REVERT: O 71 ILE cc_start: 0.8816 (mm) cc_final: 0.8458 (mm) REVERT: P 60 MET cc_start: 0.8703 (ttm) cc_final: 0.8425 (ttm) REVERT: Q 7 LYS cc_start: 0.8526 (mttp) cc_final: 0.8268 (mmmt) REVERT: Q 15 THR cc_start: 0.9080 (p) cc_final: 0.8772 (t) REVERT: Q 16 VAL cc_start: 0.8880 (t) cc_final: 0.8461 (p) REVERT: Q 45 GLN cc_start: 0.8199 (mp10) cc_final: 0.7882 (mp10) REVERT: Q 58 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8097 (mm-30) REVERT: Q 63 PHE cc_start: 0.8798 (t80) cc_final: 0.8572 (t80) REVERT: Q 66 MET cc_start: 0.8711 (ppp) cc_final: 0.8347 (ppp) REVERT: R 7 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7082 (ttpp) REVERT: R 8 PHE cc_start: 0.8763 (m-80) cc_final: 0.8251 (m-80) REVERT: R 15 THR cc_start: 0.8497 (m) cc_final: 0.8214 (p) REVERT: R 27 THR cc_start: 0.9041 (m) cc_final: 0.8762 (t) REVERT: R 56 LEU cc_start: 0.8568 (mt) cc_final: 0.8355 (mt) REVERT: R 58 GLU cc_start: 0.8104 (pp20) cc_final: 0.7743 (pp20) REVERT: R 62 LEU cc_start: 0.8997 (mm) cc_final: 0.8586 (mt) REVERT: R 65 LEU cc_start: 0.8137 (tp) cc_final: 0.7865 (tt) REVERT: S 150 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8296 (mp) REVERT: a 24 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8864 (tp) REVERT: a 40 ASN cc_start: 0.8216 (m110) cc_final: 0.7997 (m110) REVERT: a 47 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8694 (mm-40) REVERT: a 55 LYS cc_start: 0.9204 (pttt) cc_final: 0.8710 (mptt) REVERT: a 56 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9256 (mm-40) REVERT: a 97 GLN cc_start: 0.8375 (mm110) cc_final: 0.7974 (mm-40) REVERT: a 100 MET cc_start: 0.9017 (ttp) cc_final: 0.8671 (ptp) REVERT: a 140 MET cc_start: 0.8766 (tmm) cc_final: 0.8511 (tmm) REVERT: a 159 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8417 (ttm-80) REVERT: a 187 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7874 (tpt) REVERT: a 212 TYR cc_start: 0.8713 (t80) cc_final: 0.8490 (t80) REVERT: a 217 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9019 (tt) REVERT: a 218 VAL cc_start: 0.9242 (t) cc_final: 0.8997 (m) REVERT: a 223 HIS cc_start: 0.8062 (t-170) cc_final: 0.7767 (t-90) REVERT: b 77 SER cc_start: 0.8109 (t) cc_final: 0.7713 (m) REVERT: b 129 ARG cc_start: 0.9324 (mtt180) cc_final: 0.9031 (mtt180) REVERT: b 143 ARG cc_start: 0.8750 (ptp-170) cc_final: 0.8008 (ptm160) REVERT: b 145 HIS cc_start: 0.8467 (p90) cc_final: 0.7989 (m170) REVERT: b 148 TYR cc_start: 0.9081 (t80) cc_final: 0.8705 (t80) REVERT: b 158 HIS cc_start: 0.8867 (OUTLIER) cc_final: 0.8385 (m-70) REVERT: b 164 MET cc_start: 0.8538 (tmm) cc_final: 0.8060 (tmm) REVERT: b 173 MET cc_start: 0.9068 (mmp) cc_final: 0.8594 (mmm) REVERT: i 18 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8693 (t80) REVERT: C 140 ILE cc_start: 0.9276 (tp) cc_final: 0.9061 (tt) REVERT: C 266 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8764 (tp) REVERT: C 415 GLN cc_start: 0.7990 (mt0) cc_final: 0.7685 (mt0) REVERT: C 426 GLU cc_start: 0.8256 (tp30) cc_final: 0.7743 (tp30) REVERT: C 477 GLN cc_start: 0.8943 (mm110) cc_final: 0.8700 (mm-40) REVERT: f 66 TYR cc_start: 0.9057 (t80) cc_final: 0.8706 (t80) REVERT: f 80 HIS cc_start: 0.6085 (OUTLIER) cc_final: 0.5709 (m-70) REVERT: f 83 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5709 (pp) REVERT: B 333 ASP cc_start: 0.7894 (t0) cc_final: 0.7314 (p0) REVERT: B 334 VAL cc_start: 0.8734 (t) cc_final: 0.8383 (m) REVERT: B 353 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8495 (mp0) REVERT: B 355 GLU cc_start: 0.8839 (tp30) cc_final: 0.8513 (tp30) REVERT: B 410 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7624 (mp) outliers start: 138 outliers final: 97 residues processed: 730 average time/residue: 0.2018 time to fit residues: 240.7428 Evaluate side-chains 713 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 598 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 395 MET Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 179 PHE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 172 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 61 HIS Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 138 ILE Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 187 MET Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 217 LEU Chi-restraints excluded: chain b residue 130 ASN Chi-restraints excluded: chain b residue 150 GLU Chi-restraints excluded: chain b residue 158 HIS Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 18 PHE Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 80 HIS Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 379 optimal weight: 7.9990 chunk 339 optimal weight: 8.9990 chunk 26 optimal weight: 0.4980 chunk 201 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 464 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 478 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 30 ASN E 330 HIS ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN O 45 GLN a 168 HIS b 170 GLN ** c 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 70 ASN B 415 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.074221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054537 restraints weight = 125615.421| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.34 r_work: 0.2979 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37792 Z= 0.127 Angle : 0.596 11.452 51185 Z= 0.299 Chirality : 0.042 0.214 6090 Planarity : 0.004 0.076 6564 Dihedral : 6.442 158.491 5524 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.84 % Rotamer: Outliers : 3.65 % Allowed : 16.80 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.12), residues: 4940 helix: 1.76 (0.10), residues: 2647 sheet: -0.46 (0.23), residues: 540 loop : -0.25 (0.16), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 381 TYR 0.022 0.001 TYR E 383 PHE 0.028 0.001 PHE N 54 TRP 0.027 0.002 TRP 8 9 HIS 0.008 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00281 (37792) covalent geometry : angle 0.59625 (51185) hydrogen bonds : bond 0.03802 ( 2227) hydrogen bonds : angle 4.41638 ( 6465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 616 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 15 SER cc_start: 0.9029 (t) cc_final: 0.8781 (p) REVERT: A 301 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8786 (tp) REVERT: D 209 ASN cc_start: 0.8799 (t0) cc_final: 0.8511 (t0) REVERT: D 395 MET cc_start: 0.7697 (tpt) cc_final: 0.7243 (tpt) REVERT: D 421 GLN cc_start: 0.8404 (mp10) cc_final: 0.7789 (mp10) REVERT: E 88 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8327 (m) REVERT: E 294 MET cc_start: 0.8978 (tmm) cc_final: 0.8512 (tmm) REVERT: E 336 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8928 (m) REVERT: E 354 ASP cc_start: 0.8854 (m-30) cc_final: 0.8442 (t0) REVERT: E 374 ARG cc_start: 0.9147 (mmm160) cc_final: 0.8940 (mmm160) REVERT: F 28 ASP cc_start: 0.8373 (p0) cc_final: 0.8068 (p0) REVERT: F 396 ASP cc_start: 0.8662 (p0) cc_final: 0.8409 (p0) REVERT: G 108 VAL cc_start: 0.7910 (OUTLIER) cc_final: 0.7547 (p) REVERT: G 193 TYR cc_start: 0.7540 (m-80) cc_final: 0.6694 (t80) REVERT: H 25 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7852 (pp30) REVERT: H 91 GLN cc_start: 0.7704 (mp10) cc_final: 0.6897 (mp10) REVERT: J 24 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8655 (mmmt) REVERT: J 26 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8107 (tm-30) REVERT: J 33 TYR cc_start: 0.8902 (t80) cc_final: 0.8683 (t80) REVERT: J 37 ARG cc_start: 0.8243 (mmp80) cc_final: 0.7774 (mmp80) REVERT: J 40 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8152 (mt-10) REVERT: K 7 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7673 (mmtm) REVERT: K 8 PHE cc_start: 0.8433 (m-80) cc_final: 0.7935 (m-80) REVERT: K 18 VAL cc_start: 0.9261 (m) cc_final: 0.8886 (t) REVERT: K 29 PHE cc_start: 0.8927 (m-80) cc_final: 0.8580 (m-10) REVERT: K 49 TYR cc_start: 0.8497 (m-80) cc_final: 0.7646 (m-80) REVERT: L 7 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6490 (mmtt) REVERT: L 49 TYR cc_start: 0.8751 (m-80) cc_final: 0.8425 (m-80) REVERT: L 51 ILE cc_start: 0.9080 (tt) cc_final: 0.8876 (pt) REVERT: L 58 GLU cc_start: 0.8903 (tp30) cc_final: 0.8201 (tp30) REVERT: L 69 PHE cc_start: 0.8803 (t80) cc_final: 0.8315 (t80) REVERT: M 7 LYS cc_start: 0.8014 (mttm) cc_final: 0.7511 (mttm) REVERT: M 18 VAL cc_start: 0.8493 (p) cc_final: 0.8245 (m) REVERT: M 36 TYR cc_start: 0.7996 (t80) cc_final: 0.7678 (t80) REVERT: M 45 GLN cc_start: 0.8073 (mp10) cc_final: 0.7347 (mp10) REVERT: M 49 TYR cc_start: 0.8155 (m-10) cc_final: 0.7763 (m-10) REVERT: M 66 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8611 (ppp) REVERT: M 71 ILE cc_start: 0.8739 (mm) cc_final: 0.8247 (mm) REVERT: M 72 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8763 (tt) REVERT: N 25 ILE cc_start: 0.7914 (mm) cc_final: 0.7673 (mm) REVERT: N 38 ARG cc_start: 0.8847 (tpp80) cc_final: 0.8477 (tpp80) REVERT: O 7 LYS cc_start: 0.8788 (mttt) cc_final: 0.8352 (tmmt) REVERT: P 45 GLN cc_start: 0.8476 (mt0) cc_final: 0.7847 (tp40) REVERT: P 60 MET cc_start: 0.8694 (ttm) cc_final: 0.8419 (ttm) REVERT: Q 3 ASP cc_start: 0.9339 (m-30) cc_final: 0.8868 (p0) REVERT: Q 15 THR cc_start: 0.9087 (p) cc_final: 0.8792 (t) REVERT: Q 16 VAL cc_start: 0.8876 (t) cc_final: 0.8458 (p) REVERT: Q 49 TYR cc_start: 0.7903 (m-10) cc_final: 0.7660 (m-10) REVERT: Q 58 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8055 (mm-30) REVERT: Q 66 MET cc_start: 0.8705 (ppp) cc_final: 0.8372 (ppp) REVERT: R 7 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7187 (ptmt) REVERT: R 15 THR cc_start: 0.8513 (m) cc_final: 0.8224 (p) REVERT: R 27 THR cc_start: 0.9037 (m) cc_final: 0.8743 (t) REVERT: R 62 LEU cc_start: 0.8952 (mm) cc_final: 0.8555 (mt) REVERT: R 65 LEU cc_start: 0.8153 (tp) cc_final: 0.7916 (tt) REVERT: S 150 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8314 (mp) REVERT: S 165 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8157 (ttm-80) REVERT: a 24 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8894 (tp) REVERT: a 40 ASN cc_start: 0.8204 (m110) cc_final: 0.7966 (m110) REVERT: a 47 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8647 (mm-40) REVERT: a 55 LYS cc_start: 0.9172 (pttt) cc_final: 0.8692 (mptt) REVERT: a 100 MET cc_start: 0.8970 (ttp) cc_final: 0.8513 (ptp) REVERT: a 140 MET cc_start: 0.8784 (tmm) cc_final: 0.8381 (tmm) REVERT: a 159 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8399 (ttm-80) REVERT: a 187 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7880 (tpt) REVERT: a 212 TYR cc_start: 0.8745 (t80) cc_final: 0.8464 (t80) REVERT: a 218 VAL cc_start: 0.9237 (t) cc_final: 0.9004 (m) REVERT: a 223 HIS cc_start: 0.8068 (t-170) cc_final: 0.7768 (t-90) REVERT: b 77 SER cc_start: 0.8087 (t) cc_final: 0.7701 (m) REVERT: b 129 ARG cc_start: 0.9340 (mtt180) cc_final: 0.9096 (mtt180) REVERT: b 140 TYR cc_start: 0.8597 (t80) cc_final: 0.8334 (t80) REVERT: b 143 ARG cc_start: 0.8629 (ptp-170) cc_final: 0.8052 (ptt-90) REVERT: b 145 HIS cc_start: 0.8478 (p90) cc_final: 0.8027 (m170) REVERT: b 148 TYR cc_start: 0.9099 (t80) cc_final: 0.8727 (t80) REVERT: b 158 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.8366 (m-70) REVERT: b 164 MET cc_start: 0.8532 (tmm) cc_final: 0.8056 (tmm) REVERT: b 173 MET cc_start: 0.9104 (mmp) cc_final: 0.8629 (mmm) REVERT: b 176 TRP cc_start: 0.7402 (t60) cc_final: 0.7096 (t60) REVERT: i 18 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8747 (t80) REVERT: C 266 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8763 (tp) REVERT: C 415 GLN cc_start: 0.8095 (mt0) cc_final: 0.7821 (mt0) REVERT: C 426 GLU cc_start: 0.8226 (tp30) cc_final: 0.7901 (tp30) REVERT: C 477 GLN cc_start: 0.8932 (mm110) cc_final: 0.8694 (mm-40) REVERT: f 66 TYR cc_start: 0.9170 (t80) cc_final: 0.8584 (t80) REVERT: f 80 HIS cc_start: 0.6014 (OUTLIER) cc_final: 0.5627 (m-70) REVERT: f 83 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5712 (pp) REVERT: B 333 ASP cc_start: 0.7896 (t0) cc_final: 0.7313 (p0) REVERT: B 334 VAL cc_start: 0.8705 (t) cc_final: 0.8349 (m) REVERT: B 353 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8495 (mp0) REVERT: B 410 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7640 (mp) outliers start: 136 outliers final: 100 residues processed: 711 average time/residue: 0.1983 time to fit residues: 230.1070 Evaluate side-chains 707 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 591 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 377 GLN Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 395 MET Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 179 PHE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 61 HIS Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 138 ILE Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 187 MET Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain b residue 130 ASN Chi-restraints excluded: chain b residue 150 GLU Chi-restraints excluded: chain b residue 158 HIS Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 18 PHE Chi-restraints excluded: chain i residue 21 TYR Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 80 HIS Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 471 optimal weight: 0.8980 chunk 447 optimal weight: 0.5980 chunk 345 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 307 optimal weight: 0.7980 chunk 253 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054305 restraints weight = 125731.572| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.33 r_work: 0.2972 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37792 Z= 0.145 Angle : 0.619 11.714 51185 Z= 0.311 Chirality : 0.043 0.279 6090 Planarity : 0.004 0.093 6564 Dihedral : 6.434 158.550 5523 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 3.60 % Allowed : 17.10 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.12), residues: 4940 helix: 1.73 (0.10), residues: 2652 sheet: -0.45 (0.23), residues: 552 loop : -0.28 (0.16), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG b 175 TYR 0.022 0.001 TYR E 383 PHE 0.033 0.001 PHE N 54 TRP 0.029 0.003 TRP 8 9 HIS 0.007 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00330 (37792) covalent geometry : angle 0.61945 (51185) hydrogen bonds : bond 0.03870 ( 2227) hydrogen bonds : angle 4.45435 ( 6465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 598 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 15 SER cc_start: 0.8834 (t) cc_final: 0.8624 (p) REVERT: A 301 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8789 (tp) REVERT: D 209 ASN cc_start: 0.8807 (t0) cc_final: 0.8515 (t0) REVERT: D 421 GLN cc_start: 0.8375 (mp10) cc_final: 0.7738 (mp10) REVERT: E 294 MET cc_start: 0.8997 (tmm) cc_final: 0.8521 (tmm) REVERT: E 336 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8929 (m) REVERT: E 354 ASP cc_start: 0.8870 (m-30) cc_final: 0.8439 (t0) REVERT: E 374 ARG cc_start: 0.9153 (mmm160) cc_final: 0.8929 (mmm160) REVERT: F 28 ASP cc_start: 0.8388 (p0) cc_final: 0.8084 (p0) REVERT: F 396 ASP cc_start: 0.8652 (p0) cc_final: 0.8398 (p0) REVERT: G 108 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7568 (p) REVERT: G 193 TYR cc_start: 0.7609 (m-80) cc_final: 0.6722 (t80) REVERT: H 25 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7971 (pp30) REVERT: H 91 GLN cc_start: 0.7691 (mp10) cc_final: 0.6934 (mp10) REVERT: H 96 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7923 (pp20) REVERT: J 24 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8622 (mmmt) REVERT: J 26 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8098 (tm-30) REVERT: J 33 TYR cc_start: 0.8929 (t80) cc_final: 0.8676 (t80) REVERT: J 37 ARG cc_start: 0.8244 (mmp80) cc_final: 0.7800 (mmp80) REVERT: J 40 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8165 (mt-10) REVERT: K 7 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7664 (mmtm) REVERT: K 8 PHE cc_start: 0.8408 (m-80) cc_final: 0.7911 (m-80) REVERT: K 18 VAL cc_start: 0.9248 (m) cc_final: 0.8801 (t) REVERT: K 49 TYR cc_start: 0.8437 (m-80) cc_final: 0.7624 (m-80) REVERT: L 7 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6567 (mmtt) REVERT: L 49 TYR cc_start: 0.8759 (m-80) cc_final: 0.8365 (m-80) REVERT: L 52 LEU cc_start: 0.9191 (mp) cc_final: 0.8980 (mp) REVERT: L 58 GLU cc_start: 0.8907 (tp30) cc_final: 0.8375 (tp30) REVERT: L 60 MET cc_start: 0.9469 (mmt) cc_final: 0.9106 (mmm) REVERT: L 69 PHE cc_start: 0.8806 (t80) cc_final: 0.8298 (t80) REVERT: M 7 LYS cc_start: 0.8038 (mttm) cc_final: 0.7528 (mttm) REVERT: M 18 VAL cc_start: 0.8412 (p) cc_final: 0.8163 (m) REVERT: M 36 TYR cc_start: 0.8114 (t80) cc_final: 0.7773 (t80) REVERT: M 38 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8152 (ttp-110) REVERT: M 49 TYR cc_start: 0.8209 (m-10) cc_final: 0.7744 (m-10) REVERT: M 66 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8624 (ppp) REVERT: M 71 ILE cc_start: 0.8768 (mm) cc_final: 0.8274 (mm) REVERT: M 72 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8754 (tt) REVERT: N 25 ILE cc_start: 0.7922 (mm) cc_final: 0.7622 (mm) REVERT: N 38 ARG cc_start: 0.8820 (tpp80) cc_final: 0.8431 (tpp80) REVERT: O 7 LYS cc_start: 0.8738 (mttt) cc_final: 0.8341 (tmmt) REVERT: P 29 PHE cc_start: 0.8887 (m-10) cc_final: 0.8678 (m-10) REVERT: P 45 GLN cc_start: 0.8442 (mt0) cc_final: 0.7762 (tp40) REVERT: P 49 TYR cc_start: 0.8405 (m-10) cc_final: 0.8190 (m-10) REVERT: P 60 MET cc_start: 0.8709 (ttm) cc_final: 0.8457 (ttm) REVERT: Q 3 ASP cc_start: 0.9313 (m-30) cc_final: 0.8846 (p0) REVERT: Q 7 LYS cc_start: 0.8513 (mttp) cc_final: 0.8237 (mmmt) REVERT: Q 15 THR cc_start: 0.9096 (p) cc_final: 0.8817 (t) REVERT: Q 16 VAL cc_start: 0.8905 (t) cc_final: 0.8642 (m) REVERT: Q 58 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8070 (mm-30) REVERT: Q 63 PHE cc_start: 0.8808 (t80) cc_final: 0.8606 (t80) REVERT: Q 66 MET cc_start: 0.8661 (ppp) cc_final: 0.8307 (ppp) REVERT: R 7 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7156 (ptmt) REVERT: R 15 THR cc_start: 0.8482 (m) cc_final: 0.8192 (p) REVERT: R 27 THR cc_start: 0.9026 (m) cc_final: 0.8751 (t) REVERT: R 62 LEU cc_start: 0.8979 (mm) cc_final: 0.8578 (mt) REVERT: R 65 LEU cc_start: 0.8148 (tp) cc_final: 0.7913 (tt) REVERT: S 159 MET cc_start: 0.8420 (mmm) cc_final: 0.8061 (mmm) REVERT: a 40 ASN cc_start: 0.8204 (m110) cc_final: 0.7966 (m110) REVERT: a 47 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8595 (mm-40) REVERT: a 55 LYS cc_start: 0.9190 (pttt) cc_final: 0.8699 (mptt) REVERT: a 100 MET cc_start: 0.8994 (ttp) cc_final: 0.8659 (ptp) REVERT: a 140 MET cc_start: 0.8779 (tmm) cc_final: 0.8495 (tmm) REVERT: a 159 ARG cc_start: 0.8704 (ttm-80) cc_final: 0.8423 (ttm-80) REVERT: a 187 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7862 (tpt) REVERT: a 212 TYR cc_start: 0.8803 (t80) cc_final: 0.8560 (t80) REVERT: a 218 VAL cc_start: 0.9186 (t) cc_final: 0.8959 (m) REVERT: b 77 SER cc_start: 0.8109 (t) cc_final: 0.7742 (m) REVERT: b 129 ARG cc_start: 0.9323 (mtt180) cc_final: 0.9064 (mtt180) REVERT: b 140 TYR cc_start: 0.8605 (t80) cc_final: 0.8283 (t80) REVERT: b 143 ARG cc_start: 0.8664 (ptp-170) cc_final: 0.8091 (ptt-90) REVERT: b 145 HIS cc_start: 0.8476 (p90) cc_final: 0.8018 (m170) REVERT: b 148 TYR cc_start: 0.9097 (t80) cc_final: 0.8724 (t80) REVERT: b 158 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.8363 (m-70) REVERT: b 164 MET cc_start: 0.8526 (tmm) cc_final: 0.8059 (tmm) REVERT: b 173 MET cc_start: 0.9033 (mmp) cc_final: 0.8509 (mmm) REVERT: i 18 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8714 (t80) REVERT: C 266 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8770 (tp) REVERT: C 415 GLN cc_start: 0.8109 (mt0) cc_final: 0.7811 (mt0) REVERT: C 426 GLU cc_start: 0.8194 (tp30) cc_final: 0.7824 (tp30) REVERT: C 477 GLN cc_start: 0.8936 (mm110) cc_final: 0.8699 (mm-40) REVERT: f 66 TYR cc_start: 0.9051 (t80) cc_final: 0.8637 (t80) REVERT: f 80 HIS cc_start: 0.6069 (OUTLIER) cc_final: 0.5676 (m-70) REVERT: f 83 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5723 (pp) REVERT: B 333 ASP cc_start: 0.7889 (t0) cc_final: 0.7296 (p0) REVERT: B 334 VAL cc_start: 0.8722 (t) cc_final: 0.8365 (m) REVERT: B 353 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: B 355 GLU cc_start: 0.8799 (tp30) cc_final: 0.8460 (tp30) REVERT: B 410 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7622 (mp) outliers start: 134 outliers final: 107 residues processed: 689 average time/residue: 0.2056 time to fit residues: 232.1888 Evaluate side-chains 707 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 586 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 377 GLN Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 395 MET Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 179 PHE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 172 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 61 HIS Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 123 THR Chi-restraints excluded: chain a residue 138 ILE Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 187 MET Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain b residue 130 ASN Chi-restraints excluded: chain b residue 150 GLU Chi-restraints excluded: chain b residue 158 HIS Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain c residue 11 PHE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 18 PHE Chi-restraints excluded: chain i residue 21 TYR Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 80 HIS Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 174 optimal weight: 0.4980 chunk 257 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 109 optimal weight: 0.0050 chunk 16 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 442 optimal weight: 2.9990 chunk 425 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 30 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.074495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054703 restraints weight = 125754.976| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.35 r_work: 0.2987 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 37792 Z= 0.131 Angle : 0.627 13.464 51185 Z= 0.315 Chirality : 0.043 0.257 6090 Planarity : 0.004 0.077 6564 Dihedral : 6.396 158.010 5523 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.08 % Favored : 96.88 % Rotamer: Outliers : 3.30 % Allowed : 17.61 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.12), residues: 4940 helix: 1.69 (0.10), residues: 2647 sheet: -0.39 (0.23), residues: 542 loop : -0.27 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 175 TYR 0.037 0.001 TYR K 36 PHE 0.028 0.001 PHE M 54 TRP 0.041 0.003 TRP 8 9 HIS 0.007 0.001 HIS a 223 Details of bonding type rmsd covalent geometry : bond 0.00293 (37792) covalent geometry : angle 0.62714 (51185) hydrogen bonds : bond 0.03863 ( 2227) hydrogen bonds : angle 4.47630 ( 6465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9880 Ramachandran restraints generated. 4940 Oldfield, 0 Emsley, 4940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 600 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 15 SER cc_start: 0.8723 (t) cc_final: 0.8479 (p) REVERT: A 301 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8790 (tp) REVERT: A 406 PHE cc_start: 0.8592 (m-80) cc_final: 0.8230 (m-80) REVERT: D 209 ASN cc_start: 0.8802 (t0) cc_final: 0.8517 (t0) REVERT: D 395 MET cc_start: 0.7687 (tpt) cc_final: 0.7222 (tpt) REVERT: D 421 GLN cc_start: 0.8348 (mp10) cc_final: 0.7737 (mp10) REVERT: E 88 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8355 (m) REVERT: E 294 MET cc_start: 0.8969 (tmm) cc_final: 0.8507 (tmm) REVERT: E 336 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8927 (m) REVERT: E 354 ASP cc_start: 0.8859 (m-30) cc_final: 0.8439 (t0) REVERT: E 374 ARG cc_start: 0.9131 (mmm160) cc_final: 0.8900 (mmm160) REVERT: F 28 ASP cc_start: 0.8341 (p0) cc_final: 0.8030 (p0) REVERT: F 396 ASP cc_start: 0.8656 (p0) cc_final: 0.8400 (p0) REVERT: G 108 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7511 (p) REVERT: G 193 TYR cc_start: 0.7553 (m-80) cc_final: 0.6657 (t80) REVERT: H 25 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7980 (pp30) REVERT: H 91 GLN cc_start: 0.7717 (mp10) cc_final: 0.6936 (mp10) REVERT: J 26 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8087 (tm-30) REVERT: J 33 TYR cc_start: 0.8907 (t80) cc_final: 0.8703 (t80) REVERT: J 37 ARG cc_start: 0.8233 (mmp80) cc_final: 0.7802 (mmp80) REVERT: J 40 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8179 (mt-10) REVERT: K 7 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7641 (mmtm) REVERT: K 8 PHE cc_start: 0.8416 (m-80) cc_final: 0.7875 (m-80) REVERT: K 18 VAL cc_start: 0.9275 (m) cc_final: 0.8856 (t) REVERT: K 49 TYR cc_start: 0.8376 (m-80) cc_final: 0.7505 (m-80) REVERT: L 7 LYS cc_start: 0.7007 (mmtt) cc_final: 0.6467 (mmtt) REVERT: L 49 TYR cc_start: 0.8810 (m-80) cc_final: 0.8352 (m-80) REVERT: L 58 GLU cc_start: 0.8946 (tp30) cc_final: 0.8264 (tp30) REVERT: L 60 MET cc_start: 0.9471 (mmt) cc_final: 0.9112 (mmm) REVERT: L 66 MET cc_start: 0.8793 (ttp) cc_final: 0.8453 (ppp) REVERT: L 69 PHE cc_start: 0.8828 (t80) cc_final: 0.8325 (t80) REVERT: M 7 LYS cc_start: 0.7948 (mttm) cc_final: 0.7483 (mttm) REVERT: M 18 VAL cc_start: 0.8409 (p) cc_final: 0.8156 (m) REVERT: M 36 TYR cc_start: 0.8168 (t80) cc_final: 0.7908 (t80) REVERT: M 38 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8287 (ttp-110) REVERT: M 49 TYR cc_start: 0.8198 (m-10) cc_final: 0.7900 (m-10) REVERT: M 66 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8644 (ppp) REVERT: M 71 ILE cc_start: 0.8741 (mm) cc_final: 0.8237 (mm) REVERT: M 72 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8740 (tt) REVERT: N 7 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8180 (mmtt) REVERT: N 38 ARG cc_start: 0.8847 (tpp80) cc_final: 0.8451 (tpp80) REVERT: N 73 PHE cc_start: 0.8627 (m-80) cc_final: 0.8374 (m-80) REVERT: O 7 LYS cc_start: 0.8727 (mttt) cc_final: 0.8322 (tmmt) REVERT: O 36 TYR cc_start: 0.8991 (t80) cc_final: 0.8113 (t80) REVERT: O 45 GLN cc_start: 0.7837 (mt0) cc_final: 0.7283 (pt0) REVERT: O 71 ILE cc_start: 0.8854 (mm) cc_final: 0.8635 (mm) REVERT: P 45 GLN cc_start: 0.8433 (mt0) cc_final: 0.7745 (tp40) REVERT: P 60 MET cc_start: 0.8674 (ttm) cc_final: 0.8429 (ttm) REVERT: Q 3 ASP cc_start: 0.9285 (m-30) cc_final: 0.8821 (p0) REVERT: Q 7 LYS cc_start: 0.8490 (mttp) cc_final: 0.8216 (mmmt) REVERT: Q 15 THR cc_start: 0.9100 (p) cc_final: 0.8834 (t) REVERT: Q 16 VAL cc_start: 0.8905 (t) cc_final: 0.8674 (m) REVERT: Q 58 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8173 (mm-30) REVERT: Q 63 PHE cc_start: 0.8753 (t80) cc_final: 0.8520 (t80) REVERT: Q 66 MET cc_start: 0.8661 (ppp) cc_final: 0.8326 (ppp) REVERT: R 7 LYS cc_start: 0.7756 (mmtt) cc_final: 0.7091 (ptmt) REVERT: R 15 THR cc_start: 0.8482 (m) cc_final: 0.8187 (p) REVERT: R 27 THR cc_start: 0.9047 (m) cc_final: 0.8834 (t) REVERT: R 62 LEU cc_start: 0.8826 (mm) cc_final: 0.8412 (mt) REVERT: R 65 LEU cc_start: 0.8093 (tp) cc_final: 0.7857 (tt) REVERT: S 150 LEU cc_start: 0.8828 (tt) cc_final: 0.8257 (mp) REVERT: S 159 MET cc_start: 0.8293 (mmm) cc_final: 0.7822 (mmm) REVERT: a 40 ASN cc_start: 0.8161 (m110) cc_final: 0.7881 (m110) REVERT: a 43 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8763 (tt) REVERT: a 55 LYS cc_start: 0.9204 (pttt) cc_final: 0.8730 (mptt) REVERT: a 140 MET cc_start: 0.8761 (tmm) cc_final: 0.8388 (tmm) REVERT: a 159 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8471 (ttm-80) REVERT: a 187 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7885 (tpt) REVERT: a 212 TYR cc_start: 0.8858 (t80) cc_final: 0.8604 (t80) REVERT: a 218 VAL cc_start: 0.9142 (t) cc_final: 0.8910 (m) REVERT: b 69 TYR cc_start: 0.8001 (m-10) cc_final: 0.7676 (m-10) REVERT: b 77 SER cc_start: 0.8070 (t) cc_final: 0.7721 (m) REVERT: b 129 ARG cc_start: 0.9324 (mtt180) cc_final: 0.9061 (mmt180) REVERT: b 143 ARG cc_start: 0.8640 (ptp-170) cc_final: 0.8122 (ptt-90) REVERT: b 145 HIS cc_start: 0.8468 (p90) cc_final: 0.8017 (m170) REVERT: b 148 TYR cc_start: 0.9131 (t80) cc_final: 0.8760 (t80) REVERT: b 158 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8397 (m-70) REVERT: b 164 MET cc_start: 0.8538 (tmm) cc_final: 0.8066 (tmm) REVERT: i 31 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8468 (tt) REVERT: C 266 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8763 (tp) REVERT: C 415 GLN cc_start: 0.8125 (mt0) cc_final: 0.7823 (mt0) REVERT: C 426 GLU cc_start: 0.8183 (tp30) cc_final: 0.7835 (tp30) REVERT: C 477 GLN cc_start: 0.8933 (mm110) cc_final: 0.8694 (mm-40) REVERT: f 66 TYR cc_start: 0.9121 (t80) cc_final: 0.8665 (t80) REVERT: f 80 HIS cc_start: 0.5785 (OUTLIER) cc_final: 0.5498 (m-70) REVERT: f 83 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5720 (pp) REVERT: B 253 MET cc_start: 0.8861 (mtt) cc_final: 0.8661 (mtt) REVERT: B 333 ASP cc_start: 0.7861 (t0) cc_final: 0.7268 (p0) REVERT: B 353 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: B 355 GLU cc_start: 0.8755 (tp30) cc_final: 0.8347 (tp30) outliers start: 123 outliers final: 97 residues processed: 684 average time/residue: 0.2048 time to fit residues: 228.3815 Evaluate side-chains 693 residues out of total 4035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 581 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 377 GLN Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 395 MET Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 179 PHE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 172 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 61 HIS Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 123 THR Chi-restraints excluded: chain a residue 138 ILE Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 187 MET Chi-restraints excluded: chain b residue 130 ASN Chi-restraints excluded: chain b residue 150 GLU Chi-restraints excluded: chain b residue 158 HIS Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 21 TYR Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 80 HIS Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 279 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 361 optimal weight: 30.0000 chunk 430 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 353 optimal weight: 7.9990 chunk 341 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.073877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054078 restraints weight = 125463.272| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.32 r_work: 0.2969 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37792 Z= 0.164 Angle : 0.643 12.805 51185 Z= 0.323 Chirality : 0.044 0.414 6090 Planarity : 0.004 0.079 6564 Dihedral : 6.442 158.550 5523 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 3.41 % Allowed : 17.63 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.12), residues: 4940 helix: 1.69 (0.10), residues: 2648 sheet: -0.43 (0.23), residues: 557 loop : -0.28 (0.16), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 175 TYR 0.023 0.001 TYR N 49 PHE 0.032 0.002 PHE N 69 TRP 0.039 0.003 TRP 8 9 HIS 0.007 0.001 HIS a 127 Details of bonding type rmsd covalent geometry : bond 0.00377 (37792) covalent geometry : angle 0.64262 (51185) hydrogen bonds : bond 0.03973 ( 2227) hydrogen bonds : angle 4.51467 ( 6465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11968.09 seconds wall clock time: 204 minutes 37.08 seconds (12277.08 seconds total)