Starting phenix.real_space_refine on Sat Mar 7 02:20:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wnr_21855/03_2026/6wnr_21855.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wnr_21855/03_2026/6wnr_21855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wnr_21855/03_2026/6wnr_21855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wnr_21855/03_2026/6wnr_21855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wnr_21855/03_2026/6wnr_21855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wnr_21855/03_2026/6wnr_21855.map" } resolution = 3.3 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= -0.000 sd= 0.003 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 16 5.49 5 Mg 5 5.21 5 S 180 5.16 5 C 23468 2.51 5 N 6312 2.21 5 O 6953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 274 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36934 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1317 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "X" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1179 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 554 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1157 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} 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: 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: "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: "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: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.98, per 1000 atoms: 0.22 Number of scatterers: 36934 At special positions: 0 Unit cell: (181.272, 214.721, 131.638, 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 180 16.00 P 16 15.00 Mg 5 11.99 O 6953 8.00 N 6312 7.00 C 23468 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: 2.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8818 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 27 sheets defined 61.3% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'W' and resid 3 through 19 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 23 through 38 removed outlier: 3.661A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 49 removed outlier: 3.581A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY W 49 " --> pdb=" O GLU W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 62 Processing helix chain 'W' and resid 71 through 82 removed outlier: 4.583A pdb=" N ARG W 77 " --> pdb=" O GLN W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 86 No H-bonds generated for 'chain 'W' and resid 84 through 86' Processing helix chain 'W' and resid 87 through 103 removed outlier: 3.669A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 132 Processing helix chain 'W' and resid 144 through 147 Processing helix chain 'W' and resid 162 through 174 Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 187 removed outlier: 3.671A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.525A pdb=" N HIS C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 Proline residue: C 239 - end of helix removed outlier: 3.569A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.579A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.656A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 333 through 336 removed outlier: 3.546A pdb=" N ASP C 336 " --> pdb=" O GLN C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 377 through 382 removed outlier: 4.181A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 Processing helix chain 'C' and resid 392 through 407 Processing helix chain 'C' and resid 416 through 432 Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.991A pdb=" N ARG C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 478 removed outlier: 3.550A pdb=" N ALA C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 490 removed outlier: 3.658A pdb=" N GLU C 485 " --> pdb=" O PRO C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'B' and resid 4 through 19 removed outlier: 4.040A pdb=" N ILE B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.583A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.981A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 187 removed outlier: 3.683A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.613A pdb=" N ALA B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.772A pdb=" N ARG B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.591A pdb=" N ALA B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.930A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.592A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 408 removed outlier: 3.947A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 removed outlier: 3.590A pdb=" N GLN B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 479 through 490 Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'A' and resid 4 through 20 removed outlier: 3.529A pdb=" N ASN A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.824A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 231 through 253 Proline residue: A 239 - end of helix removed outlier: 3.651A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.664A pdb=" N ALA A 285 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.864A pdb=" N ARG A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.537A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 4.145A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.653A pdb=" N GLN A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 411 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.651A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.926A pdb=" N ASP A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.660A pdb=" N ALA A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.656A pdb=" N GLN A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'X' and resid 5 through 25 Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.652A pdb=" N LEU X 29 " --> pdb=" O VAL X 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE X 135 " --> pdb=" O GLY X 131 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE X 136 " --> pdb=" O ALA X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 153 removed outlier: 4.010A pdb=" N ILE X 148 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL X 153 " --> pdb=" O VAL X 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 103 removed outlier: 3.575A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.697A pdb=" N LEU H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.918A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 58 removed outlier: 4.147A pdb=" N ALA G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.732A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.554A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.551A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 196 through 203 removed outlier: 4.455A pdb=" N LYS G 199 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 283 removed outlier: 3.533A pdb=" N LEU G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 154 through 168 removed outlier: 4.085A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 212 through 233 removed outlier: 3.660A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 3.795A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.644A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 305 through 313 removed outlier: 4.393A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 377 removed outlier: 4.361A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 382 removed outlier: 3.653A pdb=" N GLU F 381 " --> pdb=" O GLY F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 419 through 432 removed outlier: 3.553A pdb=" N GLU F 432 " --> pdb=" O LYS F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.591A pdb=" N ALA F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.617A pdb=" N LEU E 119 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.572A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 212 through 233 removed outlier: 3.503A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.626A pdb=" N TYR E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.581A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 322 through 328 removed outlier: 3.596A pdb=" N ALA E 326 " --> pdb=" O SER E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 378 removed outlier: 3.890A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.708A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 419 through 432 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 169 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 197 through 200 removed outlier: 4.225A pdb=" N ASP D 200 " --> pdb=" O ASN D 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 197 through 200' Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.888A pdb=" N VAL D 219 " --> pdb=" O ASN D 215 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 removed outlier: 3.578A pdb=" N TYR D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.641A pdb=" N ASP D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 378 removed outlier: 7.409A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 385 through 400 removed outlier: 3.846A pdb=" N ALA D 391 " --> pdb=" O LYS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 432 removed outlier: 3.530A pdb=" N GLU D 432 " --> pdb=" O LYS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 8 through 42 removed outlier: 3.846A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.884A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 42 Processing helix chain 'J' and resid 45 through 77 removed outlier: 3.828A pdb=" N ILE J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 42 removed outlier: 3.922A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 77 removed outlier: 3.633A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.624A pdb=" N LEU M 8 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 3.819A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 77 Processing helix chain 'N' and resid 4 through 42 removed outlier: 3.744A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 76 removed outlier: 3.712A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 3 through 5 No H-bonds generated for 'chain 'O' and resid 3 through 5' Processing helix chain 'O' and resid 6 through 42 removed outlier: 3.526A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.807A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 77 Processing helix chain 'P' and resid 5 through 42 removed outlier: 3.724A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.820A pdb=" N GLN P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.865A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.736A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 4 through 40 Processing helix chain 'R' and resid 42 through 44 No H-bonds generated for 'chain 'R' and resid 42 through 44' Processing helix chain 'R' and resid 45 through 76 removed outlier: 3.858A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 6 through 42 removed outlier: 4.108A pdb=" N TYR S 10 " --> pdb=" O MET S 6 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.510A pdb=" N THR S 51 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 Processing helix chain 'Y' and resid 2 through 139 removed outlier: 3.623A pdb=" N TRP Y 26 " --> pdb=" O MET Y 22 " (cutoff:3.500A) Proline residue: Y 27 - end of helix removed outlier: 3.606A pdb=" N LYS Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 153 Processing helix chain 'a' and resid 7 through 17 Processing helix chain 'a' and resid 43 through 67 Processing helix chain 'a' and resid 73 through 94 Processing helix chain 'a' and resid 100 through 118 Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 3.732A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN a 181 " --> pdb=" O GLU a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 187 No H-bonds generated for 'chain 'a' and resid 185 through 187' Processing helix chain 'a' and resid 188 through 229 removed outlier: 3.594A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.713A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN a 214 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 3.922A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.779A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 105 through 106 Processing sheet with id=AA2, first strand: chain 'W' and resid 139 through 142 removed outlier: 5.628A pdb=" N ILE B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS B 42 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR B 60 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN B 27 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 59 through 66 removed outlier: 6.519A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 66 removed outlier: 4.053A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU C 66 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASP F 67 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN F 32 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 96 through 99 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 108 Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 331 removed outlier: 7.663A pdb=" N ILE C 330 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.622A pdb=" N TYR B 260 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.622A pdb=" N TYR B 260 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.358A pdb=" N ILE B 159 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.556A pdb=" N LYS A 89 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 28 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 36 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AB5, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.228A pdb=" N LYS A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 259 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 194 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP A 261 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 196 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.228A pdb=" N LYS A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 259 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 194 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP A 261 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 196 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 14 through 16 removed outlier: 6.073A pdb=" N VAL H 8 " --> pdb=" O MET H 15 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 30 through 34 removed outlier: 6.268A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA H 80 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL H 9 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 132 through 136 removed outlier: 7.870A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 11.682A pdb=" N PHE G 174 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE G 169 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLN G 186 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER G 171 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE G 184 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS G 173 " --> pdb=" O PRO G 182 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE G 175 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLN G 180 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AC2, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.446A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N TYR F 297 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.880A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.404A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR E 173 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.404A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR E 173 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.356A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AC8, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.380A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 175 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS D 144 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL D 319 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY D 146 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 20 through 22 2385 hydrogen bonds defined for protein. 6906 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: 8.96 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7576 1.33 - 1.45: 7761 1.45 - 1.57: 21772 1.57 - 1.69: 25 1.69 - 1.81: 360 Bond restraints: 37494 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.48e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.13e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.68e+01 ... (remaining 37489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 50416 4.03 - 8.06: 329 8.06 - 12.09: 9 12.09 - 16.12: 3 16.12 - 20.15: 3 Bond angle restraints: 50760 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 119.72 20.15 1.00e+00 1.00e+00 4.06e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 122.80 17.07 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 122.94 16.93 1.00e+00 1.00e+00 2.86e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 122.66 14.17 1.00e+00 1.00e+00 2.01e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 122.72 14.11 1.00e+00 1.00e+00 1.99e+02 ... (remaining 50755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 22280 35.31 - 70.61: 419 70.61 - 105.92: 51 105.92 - 141.23: 3 141.23 - 176.53: 1 Dihedral angle restraints: 22754 sinusoidal: 8970 harmonic: 13784 Sorted by residual: dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 116.53 -176.53 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 71.63 -131.63 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O2A ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PA ADP F 500 " pdb=" PB ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 63.82 -123.82 1 2.00e+01 2.50e-03 3.74e+01 ... (remaining 22751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5261 0.087 - 0.173: 603 0.173 - 0.260: 45 0.260 - 0.346: 4 0.346 - 0.433: 6 Chirality restraints: 5919 Sorted by residual: chirality pdb=" CB ILE P 63 " pdb=" CA ILE P 63 " pdb=" CG1 ILE P 63 " pdb=" CG2 ILE P 63 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA TYR X 24 " pdb=" N TYR X 24 " pdb=" C TYR X 24 " pdb=" CB TYR X 24 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA PHE S 76 " pdb=" N PHE S 76 " pdb=" C PHE S 76 " pdb=" CB PHE S 76 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 5916 not shown) Planarity restraints: 6543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 41 " -0.146 9.50e-02 1.11e+02 8.11e-02 3.12e+01 pdb=" NE ARG P 41 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG P 41 " -0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG P 41 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG P 41 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 46 " -0.024 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C ILE J 46 " 0.080 2.00e-02 2.50e+03 pdb=" O ILE J 46 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO J 47 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 139 " -0.122 9.50e-02 1.11e+02 6.68e-02 2.01e+01 pdb=" NE ARG C 139 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 139 " -0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG C 139 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG C 139 " 0.020 2.00e-02 2.50e+03 ... (remaining 6540 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 53 2.48 - 3.08: 25947 3.08 - 3.69: 55040 3.69 - 4.29: 81435 4.29 - 4.90: 137864 Nonbonded interactions: 300339 Sorted by model distance: nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.869 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.883 2.170 nonbonded pdb=" O3G ATP B 600 " pdb="MG MG B 601 " model vdw 1.884 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.896 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.943 2.170 ... (remaining 300334 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 0 through 500) selection = chain 'E' selection = (chain 'F' and resid 0 through 500) } ncs_group { reference = (chain 'I' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'J' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'L' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'M' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'N' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = chain 'O' selection = (chain 'P' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'Q' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'R' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'S' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) } ncs_group { reference = (chain 'X' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 57 or (resid 58 through 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resi \ d 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throug \ h 65 or (resid 66 through 70 and (name N or name CA or name C or name O or name \ CB )) or resid 71 through 72 or (resid 73 and (name N or name CA or name C or na \ me O or name CB )) or resid 74 through 76 or (resid 77 and (name N or name CA or \ name C or name O or name CB )) or resid 78 through 153)) selection = (chain 'Y' and (resid 1 through 90 or (resid 91 through 92 and (name N or name C \ A or name C or name O or name CB )) or resid 93 through 153)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.290 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 37494 Z= 0.301 Angle : 0.960 20.147 50760 Z= 0.614 Chirality : 0.056 0.433 5919 Planarity : 0.008 0.123 6543 Dihedral : 14.569 176.532 13936 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.81 % Favored : 97.17 % Rotamer: Outliers : 1.44 % Allowed : 5.86 % Favored : 92.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.11), residues: 4807 helix: -0.48 (0.09), residues: 2611 sheet: -0.65 (0.21), residues: 502 loop : -1.30 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.007 ARG P 41 TYR 0.040 0.005 TYR N 10 PHE 0.039 0.003 PHE A 19 TRP 0.053 0.003 TRP a 186 HIS 0.009 0.002 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00499 (37494) covalent geometry : angle 0.95985 (50760) hydrogen bonds : bond 0.13738 ( 2342) hydrogen bonds : angle 6.52016 ( 6906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 906 time to evaluate : 1.329 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: W 76 ILE cc_start: 0.9216 (mm) cc_final: 0.9003 (mm) REVERT: W 151 ILE cc_start: 0.9163 (mm) cc_final: 0.8920 (mm) REVERT: C 484 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8069 (mp10) REVERT: B 236 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.7717 (t80) REVERT: B 386 MET cc_start: 0.8736 (mmm) cc_final: 0.8388 (mmt) REVERT: B 422 ASP cc_start: 0.8466 (t0) cc_final: 0.8055 (t0) REVERT: X 17 PHE cc_start: 0.7935 (m-10) cc_final: 0.7480 (m-80) REVERT: X 22 MET cc_start: 0.8284 (ttm) cc_final: 0.7937 (ttp) REVERT: X 42 ASP cc_start: 0.8344 (m-30) cc_final: 0.8079 (m-30) REVERT: X 83 ARG cc_start: 0.8916 (ttt-90) cc_final: 0.8630 (ttm-80) REVERT: X 145 ASN cc_start: 0.7287 (m110) cc_final: 0.6794 (p0) REVERT: H 13 GLN cc_start: 0.8956 (pm20) cc_final: 0.8662 (pp30) REVERT: H 31 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7483 (tt0) REVERT: H 118 SER cc_start: 0.9241 (t) cc_final: 0.8905 (p) REVERT: G 177 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8952 (t) REVERT: G 200 HIS cc_start: 0.6964 (m170) cc_final: 0.6744 (m170) REVERT: G 206 LEU cc_start: 0.8813 (mt) cc_final: 0.8609 (mp) REVERT: F 228 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7649 (mt-10) REVERT: E 325 ILE cc_start: 0.8989 (mm) cc_final: 0.8444 (mm) REVERT: D 428 LYS cc_start: 0.8415 (tttt) cc_final: 0.7276 (ttpp) REVERT: D 445 MET cc_start: 0.8445 (mmt) cc_final: 0.8184 (mmm) REVERT: D 457 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7654 (ttpp) REVERT: I 6 MET cc_start: 0.5741 (mtm) cc_final: 0.5249 (mmm) REVERT: I 73 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7571 (t80) REVERT: I 75 MET cc_start: 0.8429 (ttp) cc_final: 0.8149 (tmm) REVERT: J 11 MET cc_start: 0.7451 (tpp) cc_final: 0.6693 (tmm) REVERT: J 51 THR cc_start: 0.8794 (m) cc_final: 0.8454 (p) REVERT: L 10 TYR cc_start: 0.8106 (m-80) cc_final: 0.7658 (m-10) REVERT: L 11 MET cc_start: 0.8074 (tpt) cc_final: 0.7575 (mmt) REVERT: M 42 GLN cc_start: 0.7952 (pt0) cc_final: 0.7659 (pt0) REVERT: M 55 ILE cc_start: 0.8553 (mm) cc_final: 0.8302 (mt) REVERT: N 42 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7162 (mt0) REVERT: N 68 VAL cc_start: 0.8975 (p) cc_final: 0.8554 (m) REVERT: N 76 PHE cc_start: 0.7856 (m-80) cc_final: 0.7590 (t80) REVERT: O 46 ILE cc_start: 0.9075 (pt) cc_final: 0.8726 (mt) REVERT: P 6 MET cc_start: 0.6316 (mmt) cc_final: 0.5666 (ptp) REVERT: P 73 TYR cc_start: 0.8578 (t80) cc_final: 0.8346 (t80) REVERT: P 78 VAL cc_start: 0.6734 (t) cc_final: 0.6139 (t) REVERT: Q 6 MET cc_start: 0.6491 (mtp) cc_final: 0.5437 (ppp) REVERT: Q 7 ASP cc_start: 0.6286 (t70) cc_final: 0.5743 (t0) REVERT: Q 17 MET cc_start: 0.7032 (mtm) cc_final: 0.6787 (mtt) REVERT: R 10 TYR cc_start: 0.8669 (m-80) cc_final: 0.8318 (m-10) REVERT: R 26 ILE cc_start: 0.9437 (mm) cc_final: 0.9108 (mt) REVERT: R 37 GLU cc_start: 0.8129 (pp20) cc_final: 0.7088 (tm-30) REVERT: S 11 MET cc_start: 0.8670 (tpp) cc_final: 0.8360 (tpt) REVERT: S 76 PHE cc_start: 0.7681 (m-80) cc_final: 0.7043 (m-80) REVERT: Y 22 MET cc_start: 0.5786 (mmt) cc_final: 0.5175 (mmt) REVERT: Y 35 LYS cc_start: 0.8693 (tttt) cc_final: 0.8343 (ttmm) REVERT: Y 51 HIS cc_start: 0.7395 (m170) cc_final: 0.7126 (m90) REVERT: a 63 VAL cc_start: 0.6445 (t) cc_final: 0.6194 (p) REVERT: a 168 MET cc_start: 0.8479 (mmt) cc_final: 0.8224 (mmm) outliers start: 55 outliers final: 22 residues processed: 949 average time/residue: 0.2386 time to fit residues: 357.9682 Evaluate side-chains 589 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 564 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain I residue 73 TYR Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain a residue 149 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 40.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 82 ASN W 86 ASN W 94 GLN W 139 ASN ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 435 GLN B 493 ASN A 58 ASN A 294 HIS A 333 GLN A 344 ASN A 425 GLN H 14 GLN H 127 GLN G 91 ASN G 252 ASN G 265 ASN G 269 GLN F 365 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN D 19 GLN D 170 HIS D 279 GLN J 42 GLN R 52 GLN a 15 HIS a 116 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.072912 restraints weight = 83985.621| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.30 r_work: 0.2929 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37494 Z= 0.160 Angle : 0.651 14.675 50760 Z= 0.339 Chirality : 0.044 0.244 5919 Planarity : 0.004 0.057 6543 Dihedral : 7.857 151.505 5381 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.54 % Allowed : 11.37 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.12), residues: 4807 helix: 1.27 (0.10), residues: 2627 sheet: -0.37 (0.22), residues: 499 loop : -0.81 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 41 TYR 0.021 0.001 TYR a 11 PHE 0.025 0.001 PHE L 53 TRP 0.021 0.002 TRP a 186 HIS 0.006 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00318 (37494) covalent geometry : angle 0.65093 (50760) hydrogen bonds : bond 0.05581 ( 2342) hydrogen bonds : angle 4.82957 ( 6906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 622 time to evaluate : 1.729 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: B 236 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.7890 (t80) REVERT: B 356 GLU cc_start: 0.8233 (tt0) cc_final: 0.7991 (tt0) REVERT: B 359 LEU cc_start: 0.9298 (mt) cc_final: 0.9013 (mt) REVERT: B 386 MET cc_start: 0.8940 (mmm) cc_final: 0.8598 (mmt) REVERT: B 415 ASP cc_start: 0.8835 (t0) cc_final: 0.8551 (m-30) REVERT: B 422 ASP cc_start: 0.8901 (t0) cc_final: 0.8377 (t0) REVERT: X 17 PHE cc_start: 0.7594 (m-10) cc_final: 0.7189 (m-80) REVERT: X 66 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8687 (pttm) REVERT: X 73 GLN cc_start: 0.8079 (tp40) cc_final: 0.7864 (mm110) REVERT: X 83 ARG cc_start: 0.9040 (ttt-90) cc_final: 0.8693 (ttm-80) REVERT: X 96 GLN cc_start: 0.8823 (pp30) cc_final: 0.8614 (pp30) REVERT: X 100 LYS cc_start: 0.9336 (tttt) cc_final: 0.9103 (ptmt) REVERT: X 113 ARG cc_start: 0.8255 (ttp-110) cc_final: 0.7990 (ttp-110) REVERT: X 145 ASN cc_start: 0.7485 (m110) cc_final: 0.6573 (t0) REVERT: H 31 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8056 (tt0) REVERT: G 200 HIS cc_start: 0.7682 (m170) cc_final: 0.7321 (m170) REVERT: F 228 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8256 (mt-10) REVERT: D 366 ARG cc_start: 0.8963 (tpt170) cc_final: 0.8711 (tpm170) REVERT: D 394 ARG cc_start: 0.8805 (ttt-90) cc_final: 0.8593 (mtp85) REVERT: D 445 MET cc_start: 0.8834 (mmt) cc_final: 0.8463 (mmm) REVERT: D 457 LYS cc_start: 0.7771 (ttpp) cc_final: 0.7507 (ttpp) REVERT: I 6 MET cc_start: 0.5875 (mtm) cc_final: 0.5382 (mmm) REVERT: I 54 PHE cc_start: 0.8475 (m-80) cc_final: 0.8249 (m-80) REVERT: J 6 MET cc_start: 0.7565 (ptp) cc_final: 0.6964 (ppp) REVERT: J 11 MET cc_start: 0.7357 (tpp) cc_final: 0.6621 (tmm) REVERT: J 16 MET cc_start: 0.7238 (ttt) cc_final: 0.6996 (tpp) REVERT: J 54 PHE cc_start: 0.8438 (m-10) cc_final: 0.7441 (t80) REVERT: L 6 MET cc_start: 0.5727 (ptp) cc_final: 0.5028 (mpp) REVERT: M 6 MET cc_start: 0.8681 (mpt) cc_final: 0.8462 (mpp) REVERT: M 42 GLN cc_start: 0.7871 (pt0) cc_final: 0.7390 (pm20) REVERT: M 55 ILE cc_start: 0.8480 (mm) cc_final: 0.8188 (mt) REVERT: N 16 MET cc_start: 0.7859 (mtp) cc_final: 0.7564 (ptp) REVERT: N 42 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7292 (mp10) REVERT: P 6 MET cc_start: 0.6232 (mmt) cc_final: 0.5585 (ptp) REVERT: P 31 LEU cc_start: 0.8738 (tp) cc_final: 0.8023 (pp) REVERT: P 65 MET cc_start: 0.7355 (mmm) cc_final: 0.6958 (mmt) REVERT: P 73 TYR cc_start: 0.8474 (t80) cc_final: 0.8226 (t80) REVERT: P 78 VAL cc_start: 0.6404 (t) cc_final: 0.6145 (t) REVERT: Q 6 MET cc_start: 0.5092 (mtp) cc_final: 0.4854 (ptt) REVERT: Q 7 ASP cc_start: 0.6650 (t70) cc_final: 0.6398 (t0) REVERT: Q 10 TYR cc_start: 0.6040 (m-80) cc_final: 0.5386 (m-80) REVERT: Q 37 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8263 (tp30) REVERT: R 11 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6090 (tpt) REVERT: R 52 GLN cc_start: 0.9323 (mm110) cc_final: 0.9114 (mm-40) REVERT: S 8 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7776 (tt) REVERT: S 11 MET cc_start: 0.8743 (tpp) cc_final: 0.8374 (mmt) REVERT: S 17 MET cc_start: 0.8868 (mmt) cc_final: 0.8651 (mmt) REVERT: S 76 PHE cc_start: 0.8123 (m-80) cc_final: 0.7191 (m-80) REVERT: Y 22 MET cc_start: 0.5950 (mmt) cc_final: 0.5246 (mmt) REVERT: Y 98 ARG cc_start: 0.8773 (tmm-80) cc_final: 0.8158 (tpt170) REVERT: a 11 TYR cc_start: 0.8377 (t80) cc_final: 0.7923 (t80) REVERT: a 15 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7956 (m90) REVERT: a 117 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8885 (mm) REVERT: a 168 MET cc_start: 0.8375 (mmt) cc_final: 0.8171 (mmm) REVERT: a 169 LYS cc_start: 0.7764 (ptmt) cc_final: 0.7517 (ttpp) REVERT: a 176 LYS cc_start: 0.8179 (tppt) cc_final: 0.7909 (tptp) REVERT: a 177 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7134 (mm-30) REVERT: a 257 MET cc_start: 0.8926 (tmm) cc_final: 0.8652 (tmm) outliers start: 97 outliers final: 40 residues processed: 690 average time/residue: 0.2282 time to fit residues: 254.8604 Evaluate side-chains 574 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 528 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 19 LEU Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 54 optimal weight: 7.9990 chunk 259 optimal weight: 0.3980 chunk 109 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 446 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 381 optimal weight: 5.9990 chunk 241 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN C 479 HIS B 26 HIS A 425 GLN A 511 GLN X 104 GLN H 14 GLN G 57 HIS G 126 ASN F 324 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS a 76 GLN a 181 GLN a 245 HIS a 252 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071961 restraints weight = 83880.788| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.25 r_work: 0.2921 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 37494 Z= 0.131 Angle : 0.584 8.570 50760 Z= 0.303 Chirality : 0.042 0.227 5919 Planarity : 0.004 0.047 6543 Dihedral : 7.161 141.818 5356 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.30 % Allowed : 12.37 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.12), residues: 4807 helix: 1.61 (0.10), residues: 2690 sheet: -0.20 (0.22), residues: 514 loop : -0.68 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 453 TYR 0.012 0.001 TYR B 236 PHE 0.036 0.001 PHE L 54 TRP 0.015 0.001 TRP a 111 HIS 0.025 0.001 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00271 (37494) covalent geometry : angle 0.58444 (50760) hydrogen bonds : bond 0.04979 ( 2342) hydrogen bonds : angle 4.52867 ( 6906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 588 time to evaluate : 1.434 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: W 130 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8825 (mtmm) REVERT: W 172 ASP cc_start: 0.8845 (m-30) cc_final: 0.8584 (m-30) REVERT: C 262 ASP cc_start: 0.8185 (m-30) cc_final: 0.7965 (m-30) REVERT: B 236 TYR cc_start: 0.9163 (OUTLIER) cc_final: 0.7782 (t80) REVERT: B 356 GLU cc_start: 0.8244 (tt0) cc_final: 0.7984 (tt0) REVERT: B 359 LEU cc_start: 0.9275 (mt) cc_final: 0.9014 (mt) REVERT: B 386 MET cc_start: 0.8914 (mmm) cc_final: 0.8586 (mmt) REVERT: B 415 ASP cc_start: 0.8667 (t0) cc_final: 0.8373 (m-30) REVERT: B 434 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8361 (mtmm) REVERT: X 2 ASN cc_start: 0.7394 (t0) cc_final: 0.6993 (p0) REVERT: X 17 PHE cc_start: 0.7462 (m-10) cc_final: 0.7086 (m-80) REVERT: X 66 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8664 (pttm) REVERT: X 73 GLN cc_start: 0.8140 (tp40) cc_final: 0.7890 (mm110) REVERT: X 78 GLN cc_start: 0.8319 (pp30) cc_final: 0.8045 (pp30) REVERT: X 96 GLN cc_start: 0.8790 (pp30) cc_final: 0.8456 (pp30) REVERT: X 100 LYS cc_start: 0.9334 (tttt) cc_final: 0.9091 (ptmt) REVERT: X 113 ARG cc_start: 0.8343 (ttp-110) cc_final: 0.8085 (ttp-110) REVERT: X 145 ASN cc_start: 0.7591 (m110) cc_final: 0.6578 (t0) REVERT: G 200 HIS cc_start: 0.7777 (m170) cc_final: 0.7359 (m170) REVERT: F 228 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8191 (mt-10) REVERT: D 386 ASP cc_start: 0.8108 (m-30) cc_final: 0.7604 (m-30) REVERT: D 457 LYS cc_start: 0.7797 (ttpp) cc_final: 0.7564 (ttpp) REVERT: I 6 MET cc_start: 0.5882 (mtm) cc_final: 0.5355 (mmm) REVERT: I 53 PHE cc_start: 0.8268 (t80) cc_final: 0.8066 (t80) REVERT: I 65 MET cc_start: 0.8026 (mmt) cc_final: 0.7757 (mmm) REVERT: I 73 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7685 (t80) REVERT: J 11 MET cc_start: 0.7403 (tpp) cc_final: 0.6601 (tmm) REVERT: J 16 MET cc_start: 0.7258 (ttt) cc_final: 0.7057 (tpp) REVERT: J 54 PHE cc_start: 0.8423 (m-10) cc_final: 0.7416 (t80) REVERT: L 6 MET cc_start: 0.5490 (ptp) cc_final: 0.5230 (mpp) REVERT: L 28 ILE cc_start: 0.8974 (mm) cc_final: 0.8597 (mt) REVERT: L 35 PHE cc_start: 0.7575 (t80) cc_final: 0.7022 (t80) REVERT: M 17 MET cc_start: 0.7687 (mmm) cc_final: 0.6531 (mpp) REVERT: M 55 ILE cc_start: 0.8553 (mm) cc_final: 0.8296 (mt) REVERT: N 42 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7382 (mp10) REVERT: P 6 MET cc_start: 0.6050 (mmt) cc_final: 0.5437 (ptp) REVERT: P 17 MET cc_start: 0.7771 (mtt) cc_final: 0.7426 (tpt) REVERT: P 65 MET cc_start: 0.7431 (mmm) cc_final: 0.7194 (mmt) REVERT: P 73 TYR cc_start: 0.8517 (t80) cc_final: 0.8315 (t80) REVERT: Q 7 ASP cc_start: 0.6403 (t70) cc_final: 0.5861 (t0) REVERT: Q 10 TYR cc_start: 0.5977 (m-80) cc_final: 0.5419 (m-80) REVERT: Q 11 MET cc_start: 0.5723 (tpp) cc_final: 0.4126 (tmm) REVERT: R 11 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.5898 (tpt) REVERT: R 52 GLN cc_start: 0.9374 (mm110) cc_final: 0.9012 (mm-40) REVERT: S 6 MET cc_start: 0.6266 (mmm) cc_final: 0.6003 (mmm) REVERT: S 75 MET cc_start: 0.9135 (tmm) cc_final: 0.8807 (tmm) REVERT: S 76 PHE cc_start: 0.8054 (m-80) cc_final: 0.7093 (m-80) REVERT: Y 22 MET cc_start: 0.5922 (mmt) cc_final: 0.5271 (mmt) REVERT: Y 51 HIS cc_start: 0.7468 (m90) cc_final: 0.7068 (m90) REVERT: Y 98 ARG cc_start: 0.8724 (tmm-80) cc_final: 0.8195 (tpt170) REVERT: Y 104 GLN cc_start: 0.8820 (tt0) cc_final: 0.8436 (pt0) REVERT: a 11 TYR cc_start: 0.8324 (t80) cc_final: 0.8089 (t80) REVERT: a 15 HIS cc_start: 0.8521 (m90) cc_final: 0.8250 (m-70) REVERT: a 65 LYS cc_start: 0.4481 (mttt) cc_final: 0.3903 (mmtp) REVERT: a 117 LEU cc_start: 0.9060 (mm) cc_final: 0.8837 (mm) REVERT: a 169 LYS cc_start: 0.7831 (ptmt) cc_final: 0.7564 (pttm) REVERT: a 176 LYS cc_start: 0.8162 (tppt) cc_final: 0.7930 (tptp) REVERT: a 177 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7220 (mm-30) REVERT: a 234 GLN cc_start: 0.6749 (mt0) cc_final: 0.6504 (mp10) REVERT: a 257 MET cc_start: 0.8897 (tmm) cc_final: 0.8683 (tmm) outliers start: 88 outliers final: 52 residues processed: 645 average time/residue: 0.2283 time to fit residues: 237.6942 Evaluate side-chains 583 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 527 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 347 LEU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain I residue 73 TYR Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 215 optimal weight: 2.9990 chunk 469 optimal weight: 0.9990 chunk 395 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 349 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 383 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN W 139 ASN C 172 GLN C 479 HIS B 484 GLN A 358 ASN X 85 GLN X 104 GLN H 24 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.096791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.067481 restraints weight = 84088.823| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.27 r_work: 0.2819 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 37494 Z= 0.230 Angle : 0.650 9.086 50760 Z= 0.337 Chirality : 0.045 0.168 5919 Planarity : 0.004 0.048 6543 Dihedral : 7.039 127.763 5355 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.01 % Allowed : 13.88 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4807 helix: 1.64 (0.10), residues: 2699 sheet: -0.22 (0.22), residues: 529 loop : -0.67 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 41 TYR 0.027 0.002 TYR C 492 PHE 0.030 0.002 PHE L 53 TRP 0.027 0.002 TRP a 235 HIS 0.007 0.001 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00541 (37494) covalent geometry : angle 0.64962 (50760) hydrogen bonds : bond 0.05298 ( 2342) hydrogen bonds : angle 4.56852 ( 6906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 549 time to evaluate : 1.464 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: W 130 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8895 (mtmm) REVERT: W 172 ASP cc_start: 0.8829 (m-30) cc_final: 0.8605 (m-30) REVERT: C 225 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9268 (m) REVERT: B 236 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.7691 (t80) REVERT: B 356 GLU cc_start: 0.8295 (tt0) cc_final: 0.8010 (tt0) REVERT: B 359 LEU cc_start: 0.9443 (mt) cc_final: 0.9169 (mt) REVERT: B 386 MET cc_start: 0.9159 (mmm) cc_final: 0.8670 (mmt) REVERT: B 466 SER cc_start: 0.9166 (m) cc_final: 0.8923 (p) REVERT: A 20 ASN cc_start: 0.8545 (m-40) cc_final: 0.8192 (p0) REVERT: A 236 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8880 (t80) REVERT: A 422 ASP cc_start: 0.8686 (m-30) cc_final: 0.8423 (t0) REVERT: X 2 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7035 (p0) REVERT: X 17 PHE cc_start: 0.7519 (m-10) cc_final: 0.7150 (m-80) REVERT: X 66 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8609 (pttm) REVERT: X 96 GLN cc_start: 0.8850 (pp30) cc_final: 0.8096 (pp30) REVERT: X 100 LYS cc_start: 0.9328 (tttt) cc_final: 0.9114 (ptmt) REVERT: X 145 ASN cc_start: 0.7301 (m110) cc_final: 0.6360 (t0) REVERT: G 178 MET cc_start: 0.8666 (pmm) cc_final: 0.8192 (pmm) REVERT: G 200 HIS cc_start: 0.7959 (m170) cc_final: 0.7580 (m170) REVERT: G 246 MET cc_start: 0.9177 (mmp) cc_final: 0.8968 (mmp) REVERT: F 228 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8411 (mt-10) REVERT: F 379 MET cc_start: 0.8770 (ttm) cc_final: 0.8498 (tpp) REVERT: E 242 ASP cc_start: 0.8164 (t0) cc_final: 0.7939 (t0) REVERT: D 56 MET cc_start: 0.9324 (mmm) cc_final: 0.9086 (mmm) REVERT: D 301 ASP cc_start: 0.8755 (t0) cc_final: 0.8476 (t0) REVERT: D 386 ASP cc_start: 0.8138 (m-30) cc_final: 0.7892 (m-30) REVERT: D 457 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7757 (ttpp) REVERT: I 6 MET cc_start: 0.6009 (mtm) cc_final: 0.5475 (mmm) REVERT: I 52 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7288 (mm-40) REVERT: I 65 MET cc_start: 0.8150 (mmt) cc_final: 0.7904 (mmm) REVERT: J 6 MET cc_start: 0.7409 (ptp) cc_final: 0.6720 (ppp) REVERT: J 11 MET cc_start: 0.7234 (tpp) cc_final: 0.6624 (tmm) REVERT: L 6 MET cc_start: 0.5634 (ptp) cc_final: 0.5234 (mpp) REVERT: L 11 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6122 (tpp) REVERT: L 28 ILE cc_start: 0.8876 (mm) cc_final: 0.8511 (mt) REVERT: L 35 PHE cc_start: 0.7382 (t80) cc_final: 0.7011 (t80) REVERT: M 17 MET cc_start: 0.7651 (mmm) cc_final: 0.7297 (mmm) REVERT: M 42 GLN cc_start: 0.8017 (pt0) cc_final: 0.7344 (pm20) REVERT: M 55 ILE cc_start: 0.8552 (mm) cc_final: 0.8220 (mt) REVERT: N 34 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8363 (mmmm) REVERT: N 37 GLU cc_start: 0.8818 (tt0) cc_final: 0.8480 (tt0) REVERT: N 42 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7660 (mp10) REVERT: O 46 ILE cc_start: 0.8788 (pt) cc_final: 0.8480 (mt) REVERT: P 6 MET cc_start: 0.5720 (mmt) cc_final: 0.5010 (ptp) REVERT: P 73 TYR cc_start: 0.8465 (t80) cc_final: 0.8195 (t80) REVERT: Q 7 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.5911 (t0) REVERT: R 61 ASP cc_start: 0.9266 (m-30) cc_final: 0.8934 (t0) REVERT: S 8 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7310 (tt) REVERT: S 75 MET cc_start: 0.9096 (tmm) cc_final: 0.8658 (tmm) REVERT: S 76 PHE cc_start: 0.8093 (m-80) cc_final: 0.7463 (m-80) REVERT: Y 22 MET cc_start: 0.5983 (mmt) cc_final: 0.5733 (mmt) REVERT: Y 51 HIS cc_start: 0.7434 (m90) cc_final: 0.7001 (m90) REVERT: Y 83 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7765 (ttp80) REVERT: Y 98 ARG cc_start: 0.8785 (tmm-80) cc_final: 0.8247 (tpt170) REVERT: Y 104 GLN cc_start: 0.8730 (tt0) cc_final: 0.8313 (pt0) REVERT: a 11 TYR cc_start: 0.8487 (t80) cc_final: 0.8219 (t80) REVERT: a 15 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8187 (m90) REVERT: a 65 LYS cc_start: 0.4413 (mttt) cc_final: 0.3837 (mmtp) REVERT: a 117 LEU cc_start: 0.9090 (mm) cc_final: 0.8871 (mm) REVERT: a 118 MET cc_start: 0.8555 (tpp) cc_final: 0.8350 (tpp) REVERT: a 177 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7165 (mm-30) REVERT: a 234 GLN cc_start: 0.7009 (mt0) cc_final: 0.6621 (mp10) REVERT: a 257 MET cc_start: 0.8887 (tmm) cc_final: 0.8678 (tmm) outliers start: 115 outliers final: 73 residues processed: 626 average time/residue: 0.2257 time to fit residues: 229.8681 Evaluate side-chains 600 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 518 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 7 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 191 optimal weight: 6.9990 chunk 372 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 429 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 291 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 75 optimal weight: 0.9980 chunk 432 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 85 GLN X 104 GLN H 5 HIS ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN Y 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.069645 restraints weight = 83190.792| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.28 r_work: 0.2872 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37494 Z= 0.124 Angle : 0.579 10.702 50760 Z= 0.296 Chirality : 0.041 0.155 5919 Planarity : 0.004 0.048 6543 Dihedral : 6.626 125.047 5354 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.27 % Allowed : 15.40 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.12), residues: 4807 helix: 1.87 (0.10), residues: 2690 sheet: -0.05 (0.22), residues: 509 loop : -0.61 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 83 TYR 0.021 0.001 TYR C 474 PHE 0.025 0.001 PHE Q 53 TRP 0.016 0.001 TRP a 235 HIS 0.009 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00257 (37494) covalent geometry : angle 0.57885 (50760) hydrogen bonds : bond 0.04654 ( 2342) hydrogen bonds : angle 4.35076 ( 6906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 549 time to evaluate : 1.373 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: W 12 LYS cc_start: 0.9341 (tttp) cc_final: 0.8817 (ttmm) REVERT: W 130 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8852 (mtmm) REVERT: B 236 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.7582 (t80) REVERT: B 386 MET cc_start: 0.9088 (mmm) cc_final: 0.8684 (mmt) REVERT: B 434 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8330 (mtmm) REVERT: B 466 SER cc_start: 0.9086 (m) cc_final: 0.8876 (p) REVERT: A 20 ASN cc_start: 0.8462 (m-40) cc_final: 0.8164 (p0) REVERT: A 422 ASP cc_start: 0.8647 (m-30) cc_final: 0.8358 (t0) REVERT: X 2 ASN cc_start: 0.7334 (t0) cc_final: 0.6761 (p0) REVERT: X 17 PHE cc_start: 0.7511 (m-10) cc_final: 0.7137 (m-80) REVERT: X 96 GLN cc_start: 0.8800 (pp30) cc_final: 0.8455 (pp30) REVERT: X 100 LYS cc_start: 0.9301 (tttt) cc_final: 0.9055 (ptmt) REVERT: X 145 ASN cc_start: 0.7295 (m110) cc_final: 0.6334 (t0) REVERT: G 178 MET cc_start: 0.8712 (pmm) cc_final: 0.8235 (pmm) REVERT: G 200 HIS cc_start: 0.7868 (m170) cc_final: 0.7410 (m170) REVERT: F 228 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8286 (mt-10) REVERT: F 379 MET cc_start: 0.8684 (ttm) cc_final: 0.8464 (tpp) REVERT: E 340 THR cc_start: 0.9198 (m) cc_final: 0.8928 (p) REVERT: D 56 MET cc_start: 0.9099 (mmm) cc_final: 0.8897 (mmm) REVERT: D 301 ASP cc_start: 0.8731 (t0) cc_final: 0.8463 (t0) REVERT: D 457 LYS cc_start: 0.7961 (ttpp) cc_final: 0.7696 (ttpp) REVERT: I 6 MET cc_start: 0.5875 (mtm) cc_final: 0.5341 (mmm) REVERT: I 52 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7395 (mm-40) REVERT: I 65 MET cc_start: 0.8099 (mmt) cc_final: 0.7853 (mmm) REVERT: J 11 MET cc_start: 0.7309 (tpp) cc_final: 0.6628 (tmm) REVERT: J 54 PHE cc_start: 0.8308 (m-10) cc_final: 0.7326 (t80) REVERT: J 73 TYR cc_start: 0.5955 (t80) cc_final: 0.4350 (m-80) REVERT: L 6 MET cc_start: 0.5562 (ptp) cc_final: 0.5202 (mpp) REVERT: L 11 MET cc_start: 0.7405 (mpp) cc_final: 0.6079 (tpp) REVERT: L 17 MET cc_start: 0.8058 (mmp) cc_final: 0.7795 (mmp) REVERT: L 28 ILE cc_start: 0.8844 (mm) cc_final: 0.8503 (mt) REVERT: L 35 PHE cc_start: 0.7227 (t80) cc_final: 0.6688 (t80) REVERT: M 17 MET cc_start: 0.7720 (mmm) cc_final: 0.7425 (mmm) REVERT: M 55 ILE cc_start: 0.8546 (mm) cc_final: 0.8284 (mt) REVERT: N 37 GLU cc_start: 0.8752 (tt0) cc_final: 0.8387 (tt0) REVERT: N 42 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7496 (mp10) REVERT: N 46 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8136 (pt) REVERT: O 46 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8544 (mt) REVERT: P 6 MET cc_start: 0.5687 (mmt) cc_final: 0.5066 (ptp) REVERT: P 17 MET cc_start: 0.7826 (mtt) cc_final: 0.7320 (tpt) REVERT: P 73 TYR cc_start: 0.8448 (t80) cc_final: 0.8213 (t80) REVERT: R 61 ASP cc_start: 0.9126 (m-30) cc_final: 0.8832 (t0) REVERT: S 8 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7263 (tt) REVERT: S 75 MET cc_start: 0.9115 (tmm) cc_final: 0.8665 (tmm) REVERT: S 76 PHE cc_start: 0.7922 (m-80) cc_final: 0.7604 (m-80) REVERT: Y 22 MET cc_start: 0.5882 (mmt) cc_final: 0.5177 (mmt) REVERT: Y 51 HIS cc_start: 0.7462 (m90) cc_final: 0.7124 (m-70) REVERT: Y 98 ARG cc_start: 0.8796 (tmm-80) cc_final: 0.8231 (tpt170) REVERT: Y 104 GLN cc_start: 0.8746 (tt0) cc_final: 0.8503 (pt0) REVERT: a 11 TYR cc_start: 0.8450 (t80) cc_final: 0.8013 (t80) REVERT: a 15 HIS cc_start: 0.8403 (OUTLIER) cc_final: 0.8107 (m-70) REVERT: a 65 LYS cc_start: 0.4445 (mttt) cc_final: 0.3850 (mmtp) REVERT: a 93 MET cc_start: 0.6860 (mpp) cc_final: 0.6562 (mpp) REVERT: a 117 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8787 (mm) REVERT: a 118 MET cc_start: 0.8536 (tpp) cc_final: 0.8277 (tpp) REVERT: a 177 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7036 (mm-30) REVERT: a 234 GLN cc_start: 0.6965 (mt0) cc_final: 0.6594 (mp10) outliers start: 87 outliers final: 57 residues processed: 608 average time/residue: 0.2244 time to fit residues: 222.8240 Evaluate side-chains 571 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 508 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 10 optimal weight: 10.0000 chunk 375 optimal weight: 0.5980 chunk 374 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 249 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 340 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 139 ASN C 172 GLN C 479 HIS ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN H 56 HIS D 243 ASN O 3 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.069990 restraints weight = 82987.434| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.20 r_work: 0.2886 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37494 Z= 0.122 Angle : 0.575 12.586 50760 Z= 0.293 Chirality : 0.041 0.199 5919 Planarity : 0.004 0.047 6543 Dihedral : 6.310 123.186 5353 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.48 % Allowed : 15.50 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.12), residues: 4807 helix: 1.93 (0.10), residues: 2691 sheet: -0.01 (0.23), residues: 510 loop : -0.48 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG Y 83 TYR 0.012 0.001 TYR C 474 PHE 0.030 0.001 PHE Q 53 TRP 0.035 0.001 TRP a 235 HIS 0.010 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00256 (37494) covalent geometry : angle 0.57538 (50760) hydrogen bonds : bond 0.04469 ( 2342) hydrogen bonds : angle 4.24764 ( 6906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 522 time to evaluate : 1.360 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: W 130 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8843 (mtmm) REVERT: W 147 MET cc_start: 0.8330 (ptp) cc_final: 0.7292 (tpt) REVERT: B 236 TYR cc_start: 0.9265 (OUTLIER) cc_final: 0.7449 (t80) REVERT: B 386 MET cc_start: 0.9050 (mmm) cc_final: 0.8565 (mmm) REVERT: B 399 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8503 (mm-40) REVERT: B 434 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8441 (mtmm) REVERT: A 20 ASN cc_start: 0.8454 (m-40) cc_final: 0.8166 (p0) REVERT: X 2 ASN cc_start: 0.7412 (t0) cc_final: 0.6893 (p0) REVERT: X 17 PHE cc_start: 0.7492 (m-10) cc_final: 0.7138 (m-80) REVERT: X 66 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8489 (pttm) REVERT: X 88 ASP cc_start: 0.9257 (t0) cc_final: 0.8764 (m-30) REVERT: X 98 ARG cc_start: 0.8735 (ttm170) cc_final: 0.8533 (ttm170) REVERT: X 119 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7976 (tp30) REVERT: X 145 ASN cc_start: 0.7201 (m110) cc_final: 0.6233 (t0) REVERT: G 178 MET cc_start: 0.8712 (pmm) cc_final: 0.8177 (pmm) REVERT: G 200 HIS cc_start: 0.7850 (m170) cc_final: 0.7392 (m170) REVERT: F 228 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8239 (mt-10) REVERT: E 340 THR cc_start: 0.9171 (m) cc_final: 0.8916 (p) REVERT: E 345 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8125 (t0) REVERT: D 56 MET cc_start: 0.9049 (mmm) cc_final: 0.8843 (mmm) REVERT: D 301 ASP cc_start: 0.8737 (t0) cc_final: 0.8483 (t0) REVERT: D 457 LYS cc_start: 0.7955 (ttpp) cc_final: 0.7692 (ttpp) REVERT: I 6 MET cc_start: 0.6093 (mtm) cc_final: 0.5505 (mmm) REVERT: I 52 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7492 (mm-40) REVERT: I 65 MET cc_start: 0.8100 (mmt) cc_final: 0.7849 (mmm) REVERT: J 11 MET cc_start: 0.7189 (tpp) cc_final: 0.6424 (tmm) REVERT: J 54 PHE cc_start: 0.8270 (m-10) cc_final: 0.7157 (t80) REVERT: J 73 TYR cc_start: 0.6075 (t80) cc_final: 0.4357 (m-80) REVERT: L 6 MET cc_start: 0.5650 (ptp) cc_final: 0.5328 (mpp) REVERT: L 11 MET cc_start: 0.7501 (mpp) cc_final: 0.6342 (tpp) REVERT: L 16 MET cc_start: 0.7548 (tpp) cc_final: 0.6665 (mmm) REVERT: L 28 ILE cc_start: 0.8743 (mm) cc_final: 0.8451 (mt) REVERT: L 35 PHE cc_start: 0.7238 (t80) cc_final: 0.6882 (t80) REVERT: M 17 MET cc_start: 0.7700 (mmm) cc_final: 0.7425 (mmm) REVERT: M 55 ILE cc_start: 0.8535 (mm) cc_final: 0.8293 (mt) REVERT: N 42 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7444 (mp10) REVERT: N 46 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8159 (pt) REVERT: O 46 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8546 (mt) REVERT: P 6 MET cc_start: 0.5873 (mmt) cc_final: 0.5226 (ptp) REVERT: P 17 MET cc_start: 0.7682 (mtt) cc_final: 0.7121 (tpt) REVERT: P 35 PHE cc_start: 0.8440 (t80) cc_final: 0.8174 (t80) REVERT: R 61 ASP cc_start: 0.9135 (m-30) cc_final: 0.8894 (t0) REVERT: S 6 MET cc_start: 0.6099 (mmm) cc_final: 0.5865 (mmm) REVERT: S 8 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7223 (tt) REVERT: S 75 MET cc_start: 0.9104 (tmm) cc_final: 0.8702 (tmm) REVERT: S 76 PHE cc_start: 0.8011 (m-80) cc_final: 0.7733 (m-80) REVERT: Y 22 MET cc_start: 0.5869 (mmt) cc_final: 0.5176 (mmt) REVERT: Y 51 HIS cc_start: 0.7418 (m90) cc_final: 0.6940 (m90) REVERT: Y 93 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8645 (mp0) REVERT: a 65 LYS cc_start: 0.4505 (mttt) cc_final: 0.3896 (mmtp) REVERT: a 93 MET cc_start: 0.7128 (mpp) cc_final: 0.6927 (mpp) REVERT: a 117 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8785 (mm) REVERT: a 118 MET cc_start: 0.8547 (tpp) cc_final: 0.8251 (tpp) REVERT: a 167 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7663 (ttmm) REVERT: a 177 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6991 (mm-30) REVERT: a 234 GLN cc_start: 0.6904 (mt0) cc_final: 0.6526 (mp10) outliers start: 95 outliers final: 59 residues processed: 589 average time/residue: 0.2259 time to fit residues: 215.6060 Evaluate side-chains 567 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 500 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 34 LYS Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 357 optimal weight: 4.9990 chunk 410 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 140 optimal weight: 0.0970 chunk 97 optimal weight: 0.7980 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN A 425 GLN ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN H 24 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.067973 restraints weight = 83260.270| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.20 r_work: 0.2842 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37494 Z= 0.176 Angle : 0.608 10.423 50760 Z= 0.311 Chirality : 0.042 0.219 5919 Planarity : 0.004 0.048 6543 Dihedral : 6.251 124.325 5349 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.25 % Allowed : 16.10 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.12), residues: 4807 helix: 1.90 (0.10), residues: 2693 sheet: -0.05 (0.22), residues: 532 loop : -0.47 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 82 TYR 0.015 0.001 TYR F 297 PHE 0.025 0.001 PHE Q 53 TRP 0.038 0.001 TRP a 235 HIS 0.005 0.001 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00405 (37494) covalent geometry : angle 0.60760 (50760) hydrogen bonds : bond 0.04722 ( 2342) hydrogen bonds : angle 4.31812 ( 6906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 517 time to evaluate : 1.504 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: W 12 LYS cc_start: 0.9359 (tttp) cc_final: 0.8832 (ttmm) REVERT: W 130 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8880 (mtmm) REVERT: W 147 MET cc_start: 0.8422 (ptp) cc_final: 0.7335 (tpt) REVERT: B 236 TYR cc_start: 0.9340 (OUTLIER) cc_final: 0.7410 (t80) REVERT: B 386 MET cc_start: 0.9090 (mmm) cc_final: 0.8730 (mmt) REVERT: A 20 ASN cc_start: 0.8495 (m-40) cc_final: 0.8128 (p0) REVERT: X 2 ASN cc_start: 0.7341 (t0) cc_final: 0.6845 (p0) REVERT: X 17 PHE cc_start: 0.7498 (m-10) cc_final: 0.7159 (m-80) REVERT: X 66 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8489 (pttm) REVERT: X 119 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7955 (tp30) REVERT: X 145 ASN cc_start: 0.7261 (m110) cc_final: 0.6319 (t0) REVERT: G 178 MET cc_start: 0.8754 (pmm) cc_final: 0.8291 (pmm) REVERT: G 200 HIS cc_start: 0.7866 (m170) cc_final: 0.7392 (m170) REVERT: G 246 MET cc_start: 0.9095 (mmp) cc_final: 0.8874 (mmp) REVERT: F 228 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8300 (mt-10) REVERT: E 340 THR cc_start: 0.9187 (m) cc_final: 0.8943 (p) REVERT: D 301 ASP cc_start: 0.8844 (t0) cc_final: 0.8599 (t0) REVERT: D 432 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: D 457 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7758 (ttpp) REVERT: I 6 MET cc_start: 0.6233 (mtm) cc_final: 0.5687 (mmm) REVERT: I 52 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7672 (mm-40) REVERT: I 65 MET cc_start: 0.8126 (mmt) cc_final: 0.7874 (mmm) REVERT: J 11 MET cc_start: 0.7332 (tpp) cc_final: 0.6405 (tmm) REVERT: J 16 MET cc_start: 0.7521 (tmm) cc_final: 0.7319 (tmm) REVERT: J 54 PHE cc_start: 0.8294 (m-10) cc_final: 0.7187 (t80) REVERT: J 73 TYR cc_start: 0.6084 (t80) cc_final: 0.4371 (m-80) REVERT: L 6 MET cc_start: 0.5585 (ptp) cc_final: 0.5245 (mpp) REVERT: L 11 MET cc_start: 0.7524 (mpp) cc_final: 0.6394 (tpp) REVERT: L 28 ILE cc_start: 0.8874 (mm) cc_final: 0.8526 (mt) REVERT: L 35 PHE cc_start: 0.7360 (t80) cc_final: 0.6952 (t80) REVERT: M 55 ILE cc_start: 0.8535 (mm) cc_final: 0.8184 (mt) REVERT: M 63 ILE cc_start: 0.8767 (mp) cc_final: 0.8556 (mt) REVERT: N 17 MET cc_start: 0.7016 (mmp) cc_final: 0.6801 (mmm) REVERT: N 42 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7554 (mp10) REVERT: N 46 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8149 (pt) REVERT: N 74 VAL cc_start: 0.8625 (t) cc_final: 0.8199 (p) REVERT: O 34 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7855 (mmtp) REVERT: O 46 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8562 (mt) REVERT: P 6 MET cc_start: 0.5605 (mmt) cc_final: 0.4984 (ptp) REVERT: P 16 MET cc_start: 0.7514 (mtm) cc_final: 0.7220 (mmm) REVERT: P 17 MET cc_start: 0.7711 (mtt) cc_final: 0.7229 (tpt) REVERT: P 37 GLU cc_start: 0.8093 (tt0) cc_final: 0.7820 (tt0) REVERT: S 5 ASN cc_start: 0.2859 (m110) cc_final: 0.2368 (t0) REVERT: S 6 MET cc_start: 0.6000 (mmm) cc_final: 0.5713 (mmm) REVERT: S 8 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7311 (tt) REVERT: S 16 MET cc_start: 0.8541 (mtm) cc_final: 0.8264 (mtp) REVERT: S 75 MET cc_start: 0.9116 (tmm) cc_final: 0.8672 (tmm) REVERT: S 76 PHE cc_start: 0.8071 (m-80) cc_final: 0.7735 (m-80) REVERT: Y 22 MET cc_start: 0.5805 (mmt) cc_final: 0.5028 (mmt) REVERT: Y 51 HIS cc_start: 0.7509 (m90) cc_final: 0.6997 (m90) REVERT: Y 93 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8650 (mp0) REVERT: Y 98 ARG cc_start: 0.8861 (tmm-80) cc_final: 0.8438 (tpt170) REVERT: Y 104 GLN cc_start: 0.8704 (pt0) cc_final: 0.8272 (pm20) REVERT: a 117 LEU cc_start: 0.9060 (mm) cc_final: 0.8839 (mm) REVERT: a 118 MET cc_start: 0.8547 (tpp) cc_final: 0.8239 (tpp) REVERT: a 167 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7632 (ttmm) REVERT: a 168 MET cc_start: 0.8567 (mmm) cc_final: 0.8337 (mmt) REVERT: a 177 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7014 (mm-30) REVERT: a 234 GLN cc_start: 0.6856 (mt0) cc_final: 0.6500 (mp10) outliers start: 86 outliers final: 64 residues processed: 578 average time/residue: 0.2187 time to fit residues: 206.5516 Evaluate side-chains 570 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 499 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 175 optimal weight: 6.9990 chunk 434 optimal weight: 20.0000 chunk 424 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 340 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 402 optimal weight: 6.9990 chunk 395 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN G 54 HIS D 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.069735 restraints weight = 83341.458| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.22 r_work: 0.2884 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37494 Z= 0.124 Angle : 0.587 11.280 50760 Z= 0.299 Chirality : 0.041 0.166 5919 Planarity : 0.004 0.048 6543 Dihedral : 6.050 121.413 5349 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.09 % Allowed : 16.50 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.12), residues: 4807 helix: 1.97 (0.10), residues: 2699 sheet: 0.03 (0.23), residues: 519 loop : -0.42 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 115 TYR 0.012 0.001 TYR C 400 PHE 0.029 0.001 PHE Y 20 TRP 0.041 0.001 TRP a 235 HIS 0.007 0.001 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00264 (37494) covalent geometry : angle 0.58749 (50760) hydrogen bonds : bond 0.04395 ( 2342) hydrogen bonds : angle 4.21148 ( 6906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 534 time to evaluate : 1.360 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: W 12 LYS cc_start: 0.9366 (tttp) cc_final: 0.8838 (ttmm) REVERT: W 130 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8859 (mtmm) REVERT: W 147 MET cc_start: 0.8274 (ptp) cc_final: 0.7258 (tpt) REVERT: C 418 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7488 (ttm-80) REVERT: B 236 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.7312 (t80) REVERT: B 386 MET cc_start: 0.9051 (mmm) cc_final: 0.8756 (mmt) REVERT: B 484 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8176 (tm-30) REVERT: A 20 ASN cc_start: 0.8520 (m-40) cc_final: 0.8174 (p0) REVERT: X 2 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.6876 (p0) REVERT: X 17 PHE cc_start: 0.7479 (m-10) cc_final: 0.7196 (m-80) REVERT: X 119 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7930 (tp30) REVERT: X 145 ASN cc_start: 0.7070 (m110) cc_final: 0.6109 (t0) REVERT: H 31 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8039 (tt0) REVERT: G 178 MET cc_start: 0.8764 (pmm) cc_final: 0.8273 (pmm) REVERT: G 200 HIS cc_start: 0.7806 (m170) cc_final: 0.7327 (m170) REVERT: F 228 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8283 (mt-10) REVERT: E 340 THR cc_start: 0.9213 (m) cc_final: 0.8956 (p) REVERT: D 301 ASP cc_start: 0.8805 (t0) cc_final: 0.8497 (t0) REVERT: D 432 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: D 457 LYS cc_start: 0.8017 (ttpp) cc_final: 0.7750 (ttpp) REVERT: I 6 MET cc_start: 0.6222 (mtm) cc_final: 0.5665 (mmm) REVERT: I 52 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7671 (mm-40) REVERT: I 65 MET cc_start: 0.8129 (mmt) cc_final: 0.7872 (mmm) REVERT: J 11 MET cc_start: 0.7299 (tpp) cc_final: 0.6349 (tmm) REVERT: J 54 PHE cc_start: 0.8241 (m-10) cc_final: 0.7137 (t80) REVERT: J 73 TYR cc_start: 0.6048 (t80) cc_final: 0.4287 (m-80) REVERT: L 6 MET cc_start: 0.5682 (ptp) cc_final: 0.5430 (mpp) REVERT: L 11 MET cc_start: 0.7483 (mpp) cc_final: 0.6425 (tpp) REVERT: L 16 MET cc_start: 0.8113 (tpp) cc_final: 0.7360 (mmm) REVERT: L 28 ILE cc_start: 0.8725 (mm) cc_final: 0.8426 (mt) REVERT: L 35 PHE cc_start: 0.7300 (t80) cc_final: 0.6942 (t80) REVERT: M 6 MET cc_start: 0.8612 (pmm) cc_final: 0.7937 (pmm) REVERT: M 17 MET cc_start: 0.7572 (mmm) cc_final: 0.7311 (mmm) REVERT: M 55 ILE cc_start: 0.8500 (mm) cc_final: 0.8236 (mt) REVERT: M 57 MET cc_start: 0.8751 (tmm) cc_final: 0.8435 (tmm) REVERT: N 42 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7462 (mp10) REVERT: N 46 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8178 (pt) REVERT: N 74 VAL cc_start: 0.8537 (t) cc_final: 0.8213 (p) REVERT: O 34 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7859 (mmtp) REVERT: O 52 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7474 (mp10) REVERT: P 6 MET cc_start: 0.5767 (mmt) cc_final: 0.5180 (ptp) REVERT: P 16 MET cc_start: 0.7516 (mtm) cc_final: 0.7244 (tpp) REVERT: P 17 MET cc_start: 0.7734 (mtt) cc_final: 0.7249 (tpt) REVERT: P 37 GLU cc_start: 0.8071 (tt0) cc_final: 0.7779 (tt0) REVERT: Q 16 MET cc_start: 0.6214 (mmm) cc_final: 0.5875 (mmm) REVERT: R 61 ASP cc_start: 0.8802 (t0) cc_final: 0.8443 (t0) REVERT: S 5 ASN cc_start: 0.2732 (m110) cc_final: 0.2359 (t0) REVERT: S 6 MET cc_start: 0.6224 (mmm) cc_final: 0.5933 (mmm) REVERT: S 8 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7104 (tt) REVERT: S 16 MET cc_start: 0.8526 (mtm) cc_final: 0.8240 (mtp) REVERT: S 75 MET cc_start: 0.9110 (tmm) cc_final: 0.8698 (tmm) REVERT: S 76 PHE cc_start: 0.7886 (m-80) cc_final: 0.7619 (m-80) REVERT: Y 22 MET cc_start: 0.5777 (mmt) cc_final: 0.5010 (mmt) REVERT: Y 51 HIS cc_start: 0.7534 (m90) cc_final: 0.6996 (m90) REVERT: Y 93 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8634 (mp0) REVERT: Y 98 ARG cc_start: 0.8886 (tmm-80) cc_final: 0.8395 (tpt170) REVERT: Y 104 GLN cc_start: 0.8624 (pt0) cc_final: 0.8191 (pm20) REVERT: a 65 LYS cc_start: 0.4496 (mttt) cc_final: 0.3900 (mmtp) REVERT: a 117 LEU cc_start: 0.9034 (mm) cc_final: 0.8804 (mm) REVERT: a 118 MET cc_start: 0.8518 (tpp) cc_final: 0.8195 (tpp) REVERT: a 167 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7618 (ttmm) REVERT: a 168 MET cc_start: 0.8515 (mmm) cc_final: 0.8273 (mmt) REVERT: a 177 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7040 (mm-30) REVERT: a 234 GLN cc_start: 0.6928 (mt0) cc_final: 0.6531 (mp10) outliers start: 80 outliers final: 61 residues processed: 590 average time/residue: 0.2213 time to fit residues: 213.0989 Evaluate side-chains 565 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 498 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 474 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 34 LYS Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 409 optimal weight: 9.9990 chunk 360 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 454 optimal weight: 3.9990 chunk 453 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 265 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN D 243 ASN Y 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.097407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.067777 restraints weight = 83526.552| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.20 r_work: 0.2833 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37494 Z= 0.172 Angle : 0.628 11.753 50760 Z= 0.321 Chirality : 0.043 0.226 5919 Planarity : 0.004 0.049 6543 Dihedral : 6.063 122.444 5349 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.04 % Allowed : 16.84 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.12), residues: 4807 helix: 1.89 (0.10), residues: 2711 sheet: -0.09 (0.22), residues: 535 loop : -0.40 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 115 TYR 0.015 0.001 TYR F 297 PHE 0.036 0.001 PHE Q 35 TRP 0.045 0.001 TRP a 235 HIS 0.009 0.001 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00399 (37494) covalent geometry : angle 0.62766 (50760) hydrogen bonds : bond 0.04669 ( 2342) hydrogen bonds : angle 4.30781 ( 6906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 503 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 123 LYS cc_start: 0.8552 (mttm) cc_final: 0.8303 (mttp) REVERT: W 130 LYS cc_start: 0.9176 (mtpp) cc_final: 0.8903 (mtmm) REVERT: W 147 MET cc_start: 0.8309 (ptp) cc_final: 0.7218 (tpt) REVERT: W 151 ILE cc_start: 0.9430 (mt) cc_final: 0.9196 (mm) REVERT: C 418 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7487 (ttm-80) REVERT: B 236 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.7335 (t80) REVERT: B 386 MET cc_start: 0.9089 (mmm) cc_final: 0.8608 (mmm) REVERT: B 484 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8419 (tm-30) REVERT: A 20 ASN cc_start: 0.8551 (m-40) cc_final: 0.8160 (p0) REVERT: X 2 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.6907 (p0) REVERT: X 17 PHE cc_start: 0.7490 (m-10) cc_final: 0.7185 (m-80) REVERT: X 119 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: H 31 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8139 (tt0) REVERT: G 178 MET cc_start: 0.8823 (pmm) cc_final: 0.8341 (pmm) REVERT: G 200 HIS cc_start: 0.7870 (m170) cc_final: 0.7384 (m170) REVERT: F 228 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8309 (mt-10) REVERT: E 323 ARG cc_start: 0.8704 (ttm-80) cc_final: 0.8384 (tpp-160) REVERT: E 340 THR cc_start: 0.9218 (m) cc_final: 0.8969 (p) REVERT: D 226 MET cc_start: 0.9243 (mtt) cc_final: 0.9033 (mtt) REVERT: D 301 ASP cc_start: 0.8864 (t0) cc_final: 0.8565 (t0) REVERT: D 432 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: D 457 LYS cc_start: 0.8082 (ttpp) cc_final: 0.7775 (ttpp) REVERT: I 6 MET cc_start: 0.6317 (mtm) cc_final: 0.5739 (mmm) REVERT: I 65 MET cc_start: 0.8138 (mmt) cc_final: 0.7886 (mmm) REVERT: J 11 MET cc_start: 0.7300 (tpp) cc_final: 0.6346 (tmm) REVERT: J 54 PHE cc_start: 0.8259 (m-10) cc_final: 0.7122 (t80) REVERT: J 73 TYR cc_start: 0.6167 (t80) cc_final: 0.4261 (m-80) REVERT: L 6 MET cc_start: 0.5700 (ptp) cc_final: 0.5345 (mpp) REVERT: L 11 MET cc_start: 0.7574 (mpp) cc_final: 0.6413 (tpp) REVERT: L 16 MET cc_start: 0.8206 (tpp) cc_final: 0.7516 (mmm) REVERT: L 28 ILE cc_start: 0.8784 (mm) cc_final: 0.8438 (mt) REVERT: L 35 PHE cc_start: 0.7328 (t80) cc_final: 0.6958 (t80) REVERT: M 6 MET cc_start: 0.8566 (pmm) cc_final: 0.7936 (pmm) REVERT: M 55 ILE cc_start: 0.8559 (mm) cc_final: 0.8252 (mt) REVERT: M 57 MET cc_start: 0.8841 (tmm) cc_final: 0.8584 (tmm) REVERT: N 42 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7574 (mp10) REVERT: N 46 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8180 (pt) REVERT: N 74 VAL cc_start: 0.8548 (t) cc_final: 0.8239 (p) REVERT: O 34 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7869 (mmtp) REVERT: O 46 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8559 (mt) REVERT: O 52 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7430 (mp10) REVERT: P 6 MET cc_start: 0.5773 (mmt) cc_final: 0.5149 (ptp) REVERT: P 16 MET cc_start: 0.7503 (mtm) cc_final: 0.7249 (tpp) REVERT: P 17 MET cc_start: 0.7777 (mtt) cc_final: 0.7373 (tpt) REVERT: P 37 GLU cc_start: 0.8047 (tt0) cc_final: 0.7736 (tt0) REVERT: R 61 ASP cc_start: 0.8855 (t0) cc_final: 0.8498 (t0) REVERT: S 5 ASN cc_start: 0.3016 (m110) cc_final: 0.2444 (t0) REVERT: S 6 MET cc_start: 0.6206 (mmm) cc_final: 0.5922 (mmm) REVERT: S 8 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7068 (tt) REVERT: S 16 MET cc_start: 0.8586 (mtm) cc_final: 0.8297 (mtp) REVERT: S 75 MET cc_start: 0.9119 (tmm) cc_final: 0.8689 (tmm) REVERT: S 76 PHE cc_start: 0.8104 (m-80) cc_final: 0.7742 (m-80) REVERT: Y 22 MET cc_start: 0.5838 (mmt) cc_final: 0.5044 (mmt) REVERT: Y 51 HIS cc_start: 0.7600 (m90) cc_final: 0.7070 (m90) REVERT: Y 93 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8638 (mp0) REVERT: Y 98 ARG cc_start: 0.8882 (tmm-80) cc_final: 0.8373 (tpt170) REVERT: Y 104 GLN cc_start: 0.8677 (pt0) cc_final: 0.8225 (pm20) REVERT: a 117 LEU cc_start: 0.9088 (mm) cc_final: 0.8868 (mm) REVERT: a 118 MET cc_start: 0.8578 (tpp) cc_final: 0.8335 (tpt) REVERT: a 167 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7664 (ttmm) REVERT: a 177 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6965 (mm-30) REVERT: a 234 GLN cc_start: 0.6981 (mt0) cc_final: 0.6602 (mp10) outliers start: 78 outliers final: 60 residues processed: 559 average time/residue: 0.2205 time to fit residues: 202.5052 Evaluate side-chains 560 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 493 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 474 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 90 optimal weight: 0.9990 chunk 368 optimal weight: 0.3980 chunk 348 optimal weight: 0.4980 chunk 30 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 362 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 235 optimal weight: 0.6980 chunk 439 optimal weight: 6.9990 chunk 284 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN B 484 GLN ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.069831 restraints weight = 83260.781| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.22 r_work: 0.2881 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37494 Z= 0.124 Angle : 0.615 12.455 50760 Z= 0.311 Chirality : 0.041 0.195 5919 Planarity : 0.004 0.048 6543 Dihedral : 5.916 119.862 5349 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.57 % Allowed : 17.33 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.12), residues: 4807 helix: 1.96 (0.10), residues: 2711 sheet: -0.03 (0.22), residues: 527 loop : -0.35 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 115 TYR 0.015 0.001 TYR a 11 PHE 0.048 0.001 PHE Q 35 TRP 0.046 0.001 TRP a 235 HIS 0.007 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00261 (37494) covalent geometry : angle 0.61545 (50760) hydrogen bonds : bond 0.04345 ( 2342) hydrogen bonds : angle 4.22114 ( 6906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 529 time to evaluate : 1.193 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: W 12 LYS cc_start: 0.9331 (tttp) cc_final: 0.8820 (ttmm) REVERT: W 130 LYS cc_start: 0.9165 (mtpp) cc_final: 0.8881 (mtmm) REVERT: W 151 ILE cc_start: 0.9388 (mt) cc_final: 0.9127 (mm) REVERT: C 418 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7420 (ttm-80) REVERT: B 10 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8614 (tm-30) REVERT: B 236 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.7340 (t80) REVERT: B 386 MET cc_start: 0.9062 (mmm) cc_final: 0.8594 (mmm) REVERT: B 419 LYS cc_start: 0.8961 (pptt) cc_final: 0.8409 (mppt) REVERT: X 2 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7037 (p0) REVERT: X 119 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: H 31 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8101 (tt0) REVERT: G 178 MET cc_start: 0.8806 (pmm) cc_final: 0.8324 (pmm) REVERT: G 200 HIS cc_start: 0.7827 (m170) cc_final: 0.7344 (m170) REVERT: F 228 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8283 (mt-10) REVERT: E 323 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8352 (tpp-160) REVERT: E 340 THR cc_start: 0.9216 (m) cc_final: 0.8999 (p) REVERT: D 226 MET cc_start: 0.9145 (mtt) cc_final: 0.8930 (mtt) REVERT: D 301 ASP cc_start: 0.8815 (t0) cc_final: 0.8579 (t0) REVERT: D 457 LYS cc_start: 0.8031 (ttpp) cc_final: 0.7756 (ttpp) REVERT: I 6 MET cc_start: 0.6270 (mtm) cc_final: 0.5695 (mmm) REVERT: I 52 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7690 (mm-40) REVERT: I 65 MET cc_start: 0.8145 (mmt) cc_final: 0.7888 (mmm) REVERT: J 11 MET cc_start: 0.7290 (tpp) cc_final: 0.6342 (tmm) REVERT: J 54 PHE cc_start: 0.8210 (m-10) cc_final: 0.7092 (t80) REVERT: J 73 TYR cc_start: 0.6028 (t80) cc_final: 0.4145 (m-80) REVERT: L 6 MET cc_start: 0.5750 (ptp) cc_final: 0.5527 (mpp) REVERT: L 11 MET cc_start: 0.7496 (mpp) cc_final: 0.6383 (tpp) REVERT: L 16 MET cc_start: 0.8105 (tpp) cc_final: 0.7524 (mmm) REVERT: L 28 ILE cc_start: 0.8636 (mm) cc_final: 0.8366 (mt) REVERT: L 35 PHE cc_start: 0.7185 (t80) cc_final: 0.6641 (t80) REVERT: L 57 MET cc_start: 0.7530 (ppp) cc_final: 0.7096 (ppp) REVERT: M 6 MET cc_start: 0.8586 (pmm) cc_final: 0.7952 (pmm) REVERT: M 17 MET cc_start: 0.7635 (mmm) cc_final: 0.7145 (mmm) REVERT: M 55 ILE cc_start: 0.8350 (mm) cc_final: 0.8055 (mt) REVERT: M 57 MET cc_start: 0.8796 (tmm) cc_final: 0.8542 (tmm) REVERT: N 16 MET cc_start: 0.7580 (ptp) cc_final: 0.7264 (ptp) REVERT: N 42 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7534 (mp10) REVERT: N 46 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8150 (pt) REVERT: N 74 VAL cc_start: 0.8524 (t) cc_final: 0.8244 (p) REVERT: O 34 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7852 (mmtp) REVERT: O 46 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8540 (mt) REVERT: O 52 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7433 (mp10) REVERT: O 65 MET cc_start: 0.8430 (tpt) cc_final: 0.7894 (mtp) REVERT: O 72 LEU cc_start: 0.9133 (mt) cc_final: 0.8908 (tt) REVERT: P 6 MET cc_start: 0.5732 (mmt) cc_final: 0.5147 (ptp) REVERT: P 17 MET cc_start: 0.7776 (mtt) cc_final: 0.7270 (tpt) REVERT: Q 17 MET cc_start: 0.6268 (mtt) cc_final: 0.6043 (mtt) REVERT: R 61 ASP cc_start: 0.8848 (t0) cc_final: 0.8482 (t0) REVERT: S 5 ASN cc_start: 0.3015 (m110) cc_final: 0.2374 (t0) REVERT: S 6 MET cc_start: 0.6218 (mmm) cc_final: 0.5942 (mmm) REVERT: S 8 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6924 (tt) REVERT: S 16 MET cc_start: 0.8473 (mtm) cc_final: 0.8170 (mtp) REVERT: S 61 ASP cc_start: 0.7778 (p0) cc_final: 0.7546 (p0) REVERT: S 75 MET cc_start: 0.9107 (tmm) cc_final: 0.8749 (tmm) REVERT: S 76 PHE cc_start: 0.7904 (m-80) cc_final: 0.7600 (m-80) REVERT: Y 22 MET cc_start: 0.5811 (mmt) cc_final: 0.5023 (mmt) REVERT: Y 51 HIS cc_start: 0.7614 (m90) cc_final: 0.7137 (m-70) REVERT: Y 93 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8602 (mp0) REVERT: Y 98 ARG cc_start: 0.8889 (tmm-80) cc_final: 0.8366 (tpt170) REVERT: Y 104 GLN cc_start: 0.8623 (pt0) cc_final: 0.8147 (pm20) REVERT: a 47 PHE cc_start: 0.8347 (t80) cc_final: 0.7904 (t80) REVERT: a 117 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8870 (mm) REVERT: a 118 MET cc_start: 0.8539 (tpp) cc_final: 0.8221 (tpp) REVERT: a 167 LYS cc_start: 0.7860 (ttmm) cc_final: 0.7623 (ttmm) REVERT: a 177 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6960 (mm-30) REVERT: a 234 GLN cc_start: 0.6861 (mt0) cc_final: 0.6430 (mp10) outliers start: 60 outliers final: 48 residues processed: 572 average time/residue: 0.2221 time to fit residues: 207.7875 Evaluate side-chains 558 residues out of total 3837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 503 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 474 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 347 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 34 LYS Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 81 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 356 optimal weight: 6.9990 chunk 435 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 366 optimal weight: 0.9980 chunk 445 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN Y 123 GLN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.068946 restraints weight = 83377.002| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.21 r_work: 0.2864 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37494 Z= 0.143 Angle : 0.628 13.104 50760 Z= 0.316 Chirality : 0.042 0.195 5919 Planarity : 0.004 0.048 6543 Dihedral : 5.881 119.294 5349 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.73 % Allowed : 17.41 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.12), residues: 4807 helix: 1.93 (0.10), residues: 2715 sheet: -0.03 (0.22), residues: 532 loop : -0.36 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 115 TYR 0.012 0.001 TYR F 297 PHE 0.042 0.001 PHE Q 35 TRP 0.048 0.001 TRP a 235 HIS 0.009 0.001 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00325 (37494) covalent geometry : angle 0.62836 (50760) hydrogen bonds : bond 0.04444 ( 2342) hydrogen bonds : angle 4.24953 ( 6906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11379.34 seconds wall clock time: 194 minutes 10.57 seconds (11650.57 seconds total)