Starting phenix.real_space_refine on Sat Mar 7 13:23:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u67_26362/03_2026/7u67_26362.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u67_26362/03_2026/7u67_26362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u67_26362/03_2026/7u67_26362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u67_26362/03_2026/7u67_26362.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u67_26362/03_2026/7u67_26362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u67_26362/03_2026/7u67_26362.map" } resolution = 2.5 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= 0.006 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22158 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 120 5.16 5 C 17262 2.51 5 N 4674 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 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: 26778 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3733 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 454} Chain breaks: 6 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 9, 'GLU:plan': 24, 'ASP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 183 Chain: "G" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 697 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, C, B, F, E, J, I, H, L, K Time building chain proxies: 3.74, per 1000 atoms: 0.14 Number of scatterers: 26778 At special positions: 0 Unit cell: (132.344, 138.868, 138.868, 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 120 16.00 P 18 15.00 Mg 6 11.99 O 4698 8.00 N 4674 7.00 C 17262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 924.4 milliseconds 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 12 sheets defined 67.9% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 24 through 41 removed outlier: 3.565A pdb=" N LEU A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.580A pdb=" N LYS A 51 " --> pdb=" O LEU A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 65 through 91 removed outlier: 3.528A pdb=" N GLU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 removed outlier: 3.919A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 141 removed outlier: 3.720A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 139 " --> pdb=" O TRP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 Processing helix chain 'A' and resid 167 through 181 removed outlier: 3.810A pdb=" N GLU A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.611A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.789A pdb=" N HIS A 227 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.730A pdb=" N MET A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.605A pdb=" N GLY A 300 " --> pdb=" O HIS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.672A pdb=" N ALA A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 355 removed outlier: 4.005A pdb=" N VAL A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.718A pdb=" N LEU A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 414 removed outlier: 3.585A pdb=" N LEU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.961A pdb=" N LEU A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 448 through 460 Processing helix chain 'A' and resid 468 through 487 removed outlier: 3.529A pdb=" N ILE A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 501 Processing helix chain 'G' and resid 5 through 21 Processing helix chain 'G' and resid 62 through 84 removed outlier: 4.020A pdb=" N TRP G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 62 through 84 removed outlier: 4.020A pdb=" N TRP J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 21 Processing helix chain 'I' and resid 62 through 84 removed outlier: 4.020A pdb=" N TRP I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 62 through 84 removed outlier: 4.020A pdb=" N TRP H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 21 Processing helix chain 'L' and resid 62 through 84 removed outlier: 4.020A pdb=" N TRP L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 21 Processing helix chain 'K' and resid 62 through 84 removed outlier: 4.020A pdb=" N TRP K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.564A pdb=" N LEU D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D 35 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG D 36 " --> pdb=" O PHE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 48 through 51 removed outlier: 3.581A pdb=" N LYS D 51 " --> pdb=" O LEU D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 65 through 91 removed outlier: 3.529A pdb=" N GLU D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.919A pdb=" N GLU D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 110 " --> pdb=" O PHE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 141 removed outlier: 3.721A pdb=" N ILE D 132 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG D 139 " --> pdb=" O TRP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 167 through 181 removed outlier: 3.811A pdb=" N GLU D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU D 172 " --> pdb=" O PRO D 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 195 removed outlier: 3.611A pdb=" N ILE D 190 " --> pdb=" O ASN D 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'D' and resid 223 through 227 removed outlier: 3.789A pdb=" N HIS D 227 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 239 through 251 Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.730A pdb=" N MET D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 287 through 300 removed outlier: 3.605A pdb=" N GLY D 300 " --> pdb=" O HIS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 317 removed outlier: 3.671A pdb=" N ALA D 315 " --> pdb=" O VAL D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 355 removed outlier: 4.005A pdb=" N VAL D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) Proline residue: D 346 - end of helix Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 373 through 390 removed outlier: 3.718A pdb=" N LEU D 379 " --> pdb=" O CYS D 375 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 380 " --> pdb=" O SER D 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 414 removed outlier: 3.584A pdb=" N LEU D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 removed outlier: 3.962A pdb=" N LEU D 418 " --> pdb=" O TYR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 437 through 445 Processing helix chain 'D' and resid 448 through 460 Processing helix chain 'D' and resid 468 through 487 removed outlier: 3.529A pdb=" N ILE D 485 " --> pdb=" O LEU D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 501 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 24 through 41 removed outlier: 3.565A pdb=" N LEU C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.581A pdb=" N LYS C 51 " --> pdb=" O LEU C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 65 through 91 removed outlier: 3.528A pdb=" N GLU C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 removed outlier: 3.919A pdb=" N GLU C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 141 removed outlier: 3.720A pdb=" N ILE C 132 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 139 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 145 Processing helix chain 'C' and resid 167 through 181 removed outlier: 3.811A pdb=" N GLU C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 172 " --> pdb=" O PRO C 168 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 removed outlier: 3.611A pdb=" N ILE C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.789A pdb=" N HIS C 227 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 239 through 251 Processing helix chain 'C' and resid 260 through 271 removed outlier: 3.730A pdb=" N MET C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 287 through 300 removed outlier: 3.605A pdb=" N GLY C 300 " --> pdb=" O HIS C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 317 removed outlier: 3.671A pdb=" N ALA C 315 " --> pdb=" O VAL C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 355 removed outlier: 4.005A pdb=" N VAL C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Proline residue: C 346 - end of helix Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 373 through 390 removed outlier: 3.719A pdb=" N LEU C 379 " --> pdb=" O CYS C 375 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 381 " --> pdb=" O ASP C 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 414 removed outlier: 3.584A pdb=" N LEU C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.962A pdb=" N LEU C 418 " --> pdb=" O TYR C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 437 through 445 Processing helix chain 'C' and resid 448 through 460 Processing helix chain 'C' and resid 468 through 487 removed outlier: 3.529A pdb=" N ILE C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 24 through 41 removed outlier: 3.564A pdb=" N LEU B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 36 " --> pdb=" O PHE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 48 through 51 removed outlier: 3.581A pdb=" N LYS B 51 " --> pdb=" O LEU B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 65 through 91 removed outlier: 3.528A pdb=" N GLU B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.919A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 141 removed outlier: 3.720A pdb=" N ILE B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 139 " --> pdb=" O TRP B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 145 Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.810A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.611A pdb=" N ILE B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 223 through 227 removed outlier: 3.789A pdb=" N HIS B 227 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 239 through 251 Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.730A pdb=" N MET B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 287 through 300 removed outlier: 3.605A pdb=" N GLY B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 317 removed outlier: 3.672A pdb=" N ALA B 315 " --> pdb=" O VAL B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 355 removed outlier: 4.005A pdb=" N VAL B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.717A pdb=" N LEU B 379 " --> pdb=" O CYS B 375 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 381 " --> pdb=" O ASP B 377 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 414 removed outlier: 3.585A pdb=" N LEU B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.961A pdb=" N LEU B 418 " --> pdb=" O TYR B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 437 through 445 Processing helix chain 'B' and resid 448 through 460 Processing helix chain 'B' and resid 468 through 487 removed outlier: 3.529A pdb=" N ILE B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 501 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 24 through 41 removed outlier: 3.565A pdb=" N LEU F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE F 32 " --> pdb=" O ILE F 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG F 36 " --> pdb=" O PHE F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 48 through 51 removed outlier: 3.580A pdb=" N LYS F 51 " --> pdb=" O LEU F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 65 through 91 removed outlier: 3.528A pdb=" N GLU F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU F 90 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.919A pdb=" N GLU F 107 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 110 " --> pdb=" O PHE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 141 removed outlier: 3.721A pdb=" N ILE F 132 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG F 139 " --> pdb=" O TRP F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 145 Processing helix chain 'F' and resid 167 through 181 removed outlier: 3.811A pdb=" N GLU F 171 " --> pdb=" O GLU F 167 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU F 172 " --> pdb=" O PRO F 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS F 181 " --> pdb=" O ARG F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.612A pdb=" N ILE F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 208 Processing helix chain 'F' and resid 223 through 227 removed outlier: 3.788A pdb=" N HIS F 227 " --> pdb=" O GLU F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 238 No H-bonds generated for 'chain 'F' and resid 236 through 238' Processing helix chain 'F' and resid 239 through 251 Processing helix chain 'F' and resid 260 through 271 removed outlier: 3.730A pdb=" N MET F 264 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 287 through 300 removed outlier: 3.605A pdb=" N GLY F 300 " --> pdb=" O HIS F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 317 removed outlier: 3.672A pdb=" N ALA F 315 " --> pdb=" O VAL F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 355 removed outlier: 4.004A pdb=" N VAL F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) Proline residue: F 346 - end of helix Processing helix chain 'F' and resid 355 through 362 Processing helix chain 'F' and resid 373 through 390 removed outlier: 3.718A pdb=" N LEU F 379 " --> pdb=" O CYS F 375 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS F 380 " --> pdb=" O SER F 376 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F 381 " --> pdb=" O ASP F 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 414 removed outlier: 3.585A pdb=" N LEU F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU F 400 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 419 removed outlier: 3.961A pdb=" N LEU F 418 " --> pdb=" O TYR F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 432 Processing helix chain 'F' and resid 437 through 445 Processing helix chain 'F' and resid 448 through 460 Processing helix chain 'F' and resid 468 through 487 removed outlier: 3.529A pdb=" N ILE F 485 " --> pdb=" O LEU F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 501 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.565A pdb=" N LEU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG E 36 " --> pdb=" O PHE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.581A pdb=" N LYS E 51 " --> pdb=" O LEU E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 65 through 91 removed outlier: 3.528A pdb=" N GLU E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 116 removed outlier: 3.919A pdb=" N GLU E 107 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL E 110 " --> pdb=" O PHE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 141 removed outlier: 3.720A pdb=" N ILE E 132 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG E 139 " --> pdb=" O TRP E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 145 Processing helix chain 'E' and resid 167 through 181 removed outlier: 3.811A pdb=" N GLU E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU E 172 " --> pdb=" O PRO E 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 195 removed outlier: 3.611A pdb=" N ILE E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 223 through 227 removed outlier: 3.789A pdb=" N HIS E 227 " --> pdb=" O GLU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 238 No H-bonds generated for 'chain 'E' and resid 236 through 238' Processing helix chain 'E' and resid 239 through 251 Processing helix chain 'E' and resid 260 through 271 removed outlier: 3.731A pdb=" N MET E 264 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 287 through 300 removed outlier: 3.606A pdb=" N GLY E 300 " --> pdb=" O HIS E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 317 removed outlier: 3.671A pdb=" N ALA E 315 " --> pdb=" O VAL E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 355 removed outlier: 4.004A pdb=" N VAL E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Proline residue: E 346 - end of helix Processing helix chain 'E' and resid 355 through 362 Processing helix chain 'E' and resid 373 through 390 removed outlier: 3.718A pdb=" N LEU E 379 " --> pdb=" O CYS E 375 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 380 " --> pdb=" O SER E 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 381 " --> pdb=" O ASP E 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 414 removed outlier: 3.585A pdb=" N LEU E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 400 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 419 removed outlier: 3.962A pdb=" N LEU E 418 " --> pdb=" O TYR E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 432 Processing helix chain 'E' and resid 437 through 445 Processing helix chain 'E' and resid 448 through 460 Processing helix chain 'E' and resid 468 through 487 removed outlier: 3.530A pdb=" N ILE E 485 " --> pdb=" O LEU E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 215 removed outlier: 6.716A pdb=" N ARG A 214 " --> pdb=" O GLY A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 24 through 32 removed outlier: 6.574A pdb=" N ASP G 39 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR G 59 " --> pdb=" O ASP G 39 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE G 41 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR G 57 " --> pdb=" O ILE G 41 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU G 43 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR G 55 " --> pdb=" O LEU G 43 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE G 45 " --> pdb=" O ILE G 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 24 through 32 removed outlier: 6.574A pdb=" N ASP J 39 " --> pdb=" O TYR J 59 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR J 59 " --> pdb=" O ASP J 39 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE J 41 " --> pdb=" O THR J 57 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR J 57 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU J 43 " --> pdb=" O THR J 55 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR J 55 " --> pdb=" O LEU J 43 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE J 45 " --> pdb=" O ILE J 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 24 through 32 removed outlier: 6.574A pdb=" N ASP I 39 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR I 59 " --> pdb=" O ASP I 39 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE I 41 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR I 57 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU I 43 " --> pdb=" O THR I 55 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR I 55 " --> pdb=" O LEU I 43 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE I 45 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 32 removed outlier: 6.574A pdb=" N ASP H 39 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR H 59 " --> pdb=" O ASP H 39 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE H 41 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR H 57 " --> pdb=" O ILE H 41 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU H 43 " --> pdb=" O THR H 55 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR H 55 " --> pdb=" O LEU H 43 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE H 45 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 24 through 32 removed outlier: 6.574A pdb=" N ASP L 39 " --> pdb=" O TYR L 59 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR L 59 " --> pdb=" O ASP L 39 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE L 41 " --> pdb=" O THR L 57 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR L 57 " --> pdb=" O ILE L 41 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU L 43 " --> pdb=" O THR L 55 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR L 55 " --> pdb=" O LEU L 43 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE L 45 " --> pdb=" O ILE L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 24 through 32 removed outlier: 6.575A pdb=" N ASP K 39 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR K 59 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE K 41 " --> pdb=" O THR K 57 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR K 57 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU K 43 " --> pdb=" O THR K 55 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR K 55 " --> pdb=" O LEU K 43 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE K 45 " --> pdb=" O ILE K 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 214 through 215 removed outlier: 6.716A pdb=" N ARG D 214 " --> pdb=" O GLY D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 214 through 215 removed outlier: 6.717A pdb=" N ARG C 214 " --> pdb=" O GLY C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 214 through 215 removed outlier: 6.717A pdb=" N ARG B 214 " --> pdb=" O GLY B 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 214 through 215 removed outlier: 6.716A pdb=" N ARG F 214 " --> pdb=" O GLY F 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 214 through 215 removed outlier: 6.717A pdb=" N ARG E 214 " --> pdb=" O GLY E 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1428 hydrogen bonds defined for protein. 4212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4225 1.31 - 1.44: 7992 1.44 - 1.56: 15017 1.56 - 1.68: 30 1.68 - 1.81: 192 Bond restraints: 27456 Sorted by residual: bond pdb=" C LEU C 140 " pdb=" O LEU C 140 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" C LEU E 140 " pdb=" O LEU E 140 " ideal model delta sigma weight residual 1.235 1.190 0.044 1.25e-02 6.40e+03 1.26e+01 bond pdb=" C LEU A 140 " pdb=" O LEU A 140 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.25e-02 6.40e+03 1.25e+01 bond pdb=" C LEU B 140 " pdb=" O LEU B 140 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.25e-02 6.40e+03 1.25e+01 bond pdb=" C LEU F 140 " pdb=" O LEU F 140 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.25e-02 6.40e+03 1.23e+01 ... (remaining 27451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 37122 3.82 - 7.64: 204 7.64 - 11.46: 18 11.46 - 15.28: 0 15.28 - 19.11: 12 Bond angle restraints: 37356 Sorted by residual: angle pdb=" PB GTP A 601 " pdb=" O3B GTP A 601 " pdb=" PG GTP A 601 " ideal model delta sigma weight residual 120.50 139.61 -19.11 3.00e+00 1.11e-01 4.06e+01 angle pdb=" PB GTP D 601 " pdb=" O3B GTP D 601 " pdb=" PG GTP D 601 " ideal model delta sigma weight residual 120.50 139.60 -19.10 3.00e+00 1.11e-01 4.05e+01 angle pdb=" PB GTP C 601 " pdb=" O3B GTP C 601 " pdb=" PG GTP C 601 " ideal model delta sigma weight residual 120.50 139.60 -19.10 3.00e+00 1.11e-01 4.05e+01 angle pdb=" PB GTP F 601 " pdb=" O3B GTP F 601 " pdb=" PG GTP F 601 " ideal model delta sigma weight residual 120.50 139.59 -19.09 3.00e+00 1.11e-01 4.05e+01 angle pdb=" PB GTP E 601 " pdb=" O3B GTP E 601 " pdb=" PG GTP E 601 " ideal model delta sigma weight residual 120.50 139.58 -19.08 3.00e+00 1.11e-01 4.04e+01 ... (remaining 37351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 15498 33.32 - 66.64: 552 66.64 - 99.96: 30 99.96 - 133.28: 12 133.28 - 166.59: 18 Dihedral angle restraints: 16110 sinusoidal: 6168 harmonic: 9942 Sorted by residual: dihedral pdb=" C8 GTP F 601 " pdb=" C1' GTP F 601 " pdb=" N9 GTP F 601 " pdb=" O4' GTP F 601 " ideal model delta sinusoidal sigma weight residual 104.59 -62.00 166.59 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP D 601 " pdb=" C1' GTP D 601 " pdb=" N9 GTP D 601 " pdb=" O4' GTP D 601 " ideal model delta sinusoidal sigma weight residual 104.59 -62.00 166.59 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP B 601 " pdb=" C1' GTP B 601 " pdb=" N9 GTP B 601 " pdb=" O4' GTP B 601 " ideal model delta sinusoidal sigma weight residual 104.59 -61.97 166.57 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 16107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3622 0.058 - 0.117: 416 0.117 - 0.175: 39 0.175 - 0.234: 45 0.234 - 0.292: 18 Chirality restraints: 4140 Sorted by residual: chirality pdb=" CA ARG C 415 " pdb=" N ARG C 415 " pdb=" C ARG C 415 " pdb=" CB ARG C 415 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ARG E 415 " pdb=" N ARG E 415 " pdb=" C ARG E 415 " pdb=" CB ARG E 415 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ARG F 415 " pdb=" N ARG F 415 " pdb=" C ARG F 415 " pdb=" CB ARG F 415 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4137 not shown) Planarity restraints: 4668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 77 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C GLY C 77 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY C 77 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 78 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 77 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C GLY E 77 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY E 77 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG E 78 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 77 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C GLY B 77 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY B 77 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG B 78 " -0.014 2.00e-02 2.50e+03 ... (remaining 4665 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 583 2.71 - 3.26: 25099 3.26 - 3.80: 40919 3.80 - 4.35: 53504 4.35 - 4.90: 90801 Nonbonded interactions: 210906 Sorted by model distance: nonbonded pdb=" NE2 HIS B 117 " pdb="MG MG B 602 " model vdw 2.161 2.250 nonbonded pdb=" NE2 HIS F 117 " pdb="MG MG F 602 " model vdw 2.162 2.250 nonbonded pdb=" NE2 HIS A 117 " pdb="MG MG A 602 " model vdw 2.162 2.250 nonbonded pdb=" NE2 HIS C 117 " pdb="MG MG C 602 " model vdw 2.162 2.250 nonbonded pdb=" NE2 HIS D 117 " pdb="MG MG D 602 " model vdw 2.162 2.250 ... (remaining 210901 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'C' selection = chain 'B' selection = chain 'F' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'I' selection = chain 'H' selection = chain 'L' selection = chain 'K' } 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 19.200 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 0.057 27456 Z= 0.317 Angle : 0.748 19.105 37356 Z= 0.389 Chirality : 0.047 0.292 4140 Planarity : 0.004 0.040 4668 Dihedral : 17.774 166.595 9654 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.91 % Allowed : 16.67 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3264 helix: 0.03 (0.11), residues: 2148 sheet: 1.62 (0.42), residues: 162 loop : -0.55 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 154 TYR 0.018 0.001 TYR B 272 PHE 0.013 0.001 PHE E 286 TRP 0.016 0.001 TRP H 73 HIS 0.003 0.001 HIS E 445 Details of bonding type rmsd covalent geometry : bond 0.00513 (27456) covalent geometry : angle 0.74783 (37356) hydrogen bonds : bond 0.25905 ( 1428) hydrogen bonds : angle 6.05603 ( 4212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 563 time to evaluate : 0.857 Fit side-chains REVERT: A 192 LEU cc_start: 0.8518 (tp) cc_final: 0.8295 (tp) REVERT: A 286 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7396 (p90) REVERT: A 382 TYR cc_start: 0.8069 (m-80) cc_final: 0.7609 (m-80) REVERT: A 398 ARG cc_start: 0.7528 (ttp-110) cc_final: 0.7130 (ttp-110) REVERT: A 400 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7404 (mt-10) REVERT: A 499 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7163 (mtp180) REVERT: D 26 HIS cc_start: 0.7694 (t70) cc_final: 0.7489 (t70) REVERT: D 82 LYS cc_start: 0.7860 (mttp) cc_final: 0.7658 (mttm) REVERT: D 174 ARG cc_start: 0.8161 (ptp90) cc_final: 0.7949 (ptm160) REVERT: D 237 LEU cc_start: 0.8453 (tp) cc_final: 0.8163 (tt) REVERT: D 382 TYR cc_start: 0.8161 (m-80) cc_final: 0.7865 (m-80) REVERT: D 398 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.6661 (ttp-110) REVERT: D 498 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7498 (mtm-85) REVERT: C 66 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7451 (mtt-85) REVERT: C 82 LYS cc_start: 0.7959 (mttp) cc_final: 0.7731 (mttm) REVERT: C 118 ASP cc_start: 0.6854 (m-30) cc_final: 0.6555 (t0) REVERT: C 134 ASP cc_start: 0.7775 (m-30) cc_final: 0.7562 (m-30) REVERT: C 237 LEU cc_start: 0.8487 (tp) cc_final: 0.8239 (tt) REVERT: C 382 TYR cc_start: 0.8154 (m-80) cc_final: 0.7840 (m-80) REVERT: C 398 ARG cc_start: 0.7674 (ttp-110) cc_final: 0.6737 (ttp-110) REVERT: C 421 SER cc_start: 0.8214 (m) cc_final: 0.8005 (p) REVERT: B 23 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8389 (mmmt) REVERT: B 66 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7398 (mtt-85) REVERT: B 154 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8094 (mtm-85) REVERT: B 184 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6441 (tm-30) REVERT: B 382 TYR cc_start: 0.7975 (m-80) cc_final: 0.7501 (m-80) REVERT: B 434 VAL cc_start: 0.8148 (t) cc_final: 0.7859 (t) REVERT: F 75 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7931 (tp40) REVERT: F 382 TYR cc_start: 0.7812 (m-80) cc_final: 0.7588 (m-80) REVERT: F 499 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7192 (mtp180) REVERT: E 66 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7378 (mtt-85) REVERT: E 134 ASP cc_start: 0.7761 (m-30) cc_final: 0.7511 (m-30) REVERT: E 154 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7991 (mtm180) REVERT: E 217 TRP cc_start: 0.8819 (p-90) cc_final: 0.8308 (p90) REVERT: E 382 TYR cc_start: 0.8017 (m-80) cc_final: 0.7711 (m-80) REVERT: E 473 GLU cc_start: 0.6680 (tm-30) cc_final: 0.6469 (tm-30) REVERT: E 498 ARG cc_start: 0.8070 (mtp-110) cc_final: 0.7867 (mtp180) REVERT: E 499 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7195 (mtp180) outliers start: 24 outliers final: 9 residues processed: 575 average time/residue: 0.8746 time to fit residues: 558.0258 Evaluate side-chains 534 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 521 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain I residue 40 CYS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain K residue 40 CYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 499 ARG Chi-restraints excluded: chain E residue 499 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 HIS D 384 ASN C 69 HIS B 251 ASN E 69 HIS E 251 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116374 restraints weight = 33689.971| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.39 r_work: 0.3420 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27456 Z= 0.147 Angle : 0.534 7.050 37356 Z= 0.272 Chirality : 0.039 0.124 4140 Planarity : 0.004 0.042 4668 Dihedral : 12.346 177.466 3818 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.02 % Allowed : 17.81 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3264 helix: 0.96 (0.11), residues: 2178 sheet: 1.70 (0.43), residues: 162 loop : -0.67 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 64 TYR 0.012 0.001 TYR J 28 PHE 0.014 0.001 PHE C 106 TRP 0.017 0.001 TRP K 73 HIS 0.009 0.001 HIS D 445 Details of bonding type rmsd covalent geometry : bond 0.00334 (27456) covalent geometry : angle 0.53354 (37356) hydrogen bonds : bond 0.06156 ( 1428) hydrogen bonds : angle 3.93575 ( 4212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 529 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: A 286 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7500 (p90) REVERT: A 382 TYR cc_start: 0.8194 (m-80) cc_final: 0.7899 (m-80) REVERT: A 397 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8008 (mt-10) REVERT: A 499 ARG cc_start: 0.8312 (mtp180) cc_final: 0.8049 (mtp180) REVERT: G 73 TRP cc_start: 0.7526 (t60) cc_final: 0.7199 (t60) REVERT: K 73 TRP cc_start: 0.7717 (t60) cc_final: 0.7439 (t60) REVERT: D 41 ASN cc_start: 0.8582 (m110) cc_final: 0.8371 (m110) REVERT: D 237 LEU cc_start: 0.8847 (tp) cc_final: 0.8590 (tt) REVERT: D 291 LEU cc_start: 0.7828 (tp) cc_final: 0.7556 (tp) REVERT: D 498 ARG cc_start: 0.8355 (mtp-110) cc_final: 0.7982 (mtm-85) REVERT: C 121 ASN cc_start: 0.8757 (m-40) cc_final: 0.8342 (m-40) REVERT: C 291 LEU cc_start: 0.7712 (tp) cc_final: 0.7435 (tp) REVERT: C 382 TYR cc_start: 0.8245 (m-80) cc_final: 0.7923 (m-80) REVERT: C 469 PHE cc_start: 0.8469 (t80) cc_final: 0.8222 (t80) REVERT: B 33 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7850 (mp0) REVERT: B 64 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7714 (mtm-85) REVERT: B 66 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7579 (mtt-85) REVERT: B 154 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.8261 (mtm-85) REVERT: B 434 VAL cc_start: 0.8263 (t) cc_final: 0.7974 (t) REVERT: F 286 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7472 (p90) REVERT: F 382 TYR cc_start: 0.7966 (m-80) cc_final: 0.7628 (m-80) REVERT: F 421 SER cc_start: 0.8446 (m) cc_final: 0.8229 (t) REVERT: E 33 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7673 (mp0) REVERT: E 154 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8225 (mtm180) REVERT: E 217 TRP cc_start: 0.8848 (p-90) cc_final: 0.8527 (p90) REVERT: E 239 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7304 (mm-30) REVERT: E 499 ARG cc_start: 0.8113 (mtp180) cc_final: 0.7910 (mtp180) outliers start: 53 outliers final: 10 residues processed: 550 average time/residue: 0.8744 time to fit residues: 536.6135 Evaluate side-chains 535 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 520 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 459 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 98 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 239 optimal weight: 0.0470 chunk 65 optimal weight: 0.1980 chunk 233 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN D 445 HIS F 41 ASN F 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118938 restraints weight = 33892.969| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.40 r_work: 0.3459 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27456 Z= 0.100 Angle : 0.465 6.646 37356 Z= 0.232 Chirality : 0.037 0.117 4140 Planarity : 0.004 0.042 4668 Dihedral : 11.401 173.476 3800 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.17 % Allowed : 17.39 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3264 helix: 1.46 (0.12), residues: 2190 sheet: 2.20 (0.43), residues: 162 loop : -0.48 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 499 TYR 0.023 0.001 TYR E 382 PHE 0.011 0.001 PHE A 127 TRP 0.019 0.001 TRP K 73 HIS 0.009 0.001 HIS D 445 Details of bonding type rmsd covalent geometry : bond 0.00207 (27456) covalent geometry : angle 0.46545 (37356) hydrogen bonds : bond 0.04486 ( 1428) hydrogen bonds : angle 3.58821 ( 4212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 525 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7495 (p90) REVERT: A 382 TYR cc_start: 0.8154 (m-80) cc_final: 0.7858 (m-80) REVERT: A 482 GLN cc_start: 0.8413 (mt0) cc_final: 0.8109 (mt0) REVERT: A 499 ARG cc_start: 0.8295 (mtp180) cc_final: 0.8018 (mtp180) REVERT: G 73 TRP cc_start: 0.7628 (t60) cc_final: 0.7356 (t60) REVERT: D 118 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7450 (t0) REVERT: D 237 LEU cc_start: 0.8808 (tp) cc_final: 0.8573 (tt) REVERT: D 382 TYR cc_start: 0.8187 (m-80) cc_final: 0.7845 (m-80) REVERT: C 75 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: C 382 TYR cc_start: 0.8192 (m-80) cc_final: 0.7909 (m-80) REVERT: C 469 PHE cc_start: 0.8393 (t80) cc_final: 0.8162 (t80) REVERT: B 382 TYR cc_start: 0.8283 (m-10) cc_final: 0.7998 (m-80) REVERT: B 434 VAL cc_start: 0.8228 (t) cc_final: 0.7937 (t) REVERT: F 197 MET cc_start: 0.8526 (mmt) cc_final: 0.8287 (mmt) REVERT: F 286 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7524 (p90) REVERT: F 382 TYR cc_start: 0.7935 (m-80) cc_final: 0.7628 (m-80) REVERT: E 154 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8201 (mtm180) REVERT: E 217 TRP cc_start: 0.8820 (p-90) cc_final: 0.8545 (p90) REVERT: E 239 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7329 (mm-30) outliers start: 57 outliers final: 15 residues processed: 551 average time/residue: 0.8517 time to fit residues: 524.4840 Evaluate side-chains 542 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 522 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain I residue 75 ASN Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 434 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 125 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 251 optimal weight: 0.0670 chunk 148 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 326 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 287 optimal weight: 0.0770 chunk 116 optimal weight: 6.9990 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN D 445 HIS B 342 ASN F 342 ASN E 294 HIS E 365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.137443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117847 restraints weight = 33624.445| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.38 r_work: 0.3443 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27456 Z= 0.111 Angle : 0.480 6.621 37356 Z= 0.239 Chirality : 0.038 0.131 4140 Planarity : 0.004 0.042 4668 Dihedral : 11.232 179.757 3800 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.93 % Allowed : 17.12 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.16), residues: 3264 helix: 1.58 (0.12), residues: 2202 sheet: 2.21 (0.43), residues: 162 loop : -0.51 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 498 TYR 0.010 0.001 TYR J 28 PHE 0.013 0.001 PHE A 127 TRP 0.029 0.001 TRP K 73 HIS 0.008 0.001 HIS D 445 Details of bonding type rmsd covalent geometry : bond 0.00245 (27456) covalent geometry : angle 0.48012 (37356) hydrogen bonds : bond 0.04779 ( 1428) hydrogen bonds : angle 3.49507 ( 4212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 533 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7560 (p90) REVERT: A 382 TYR cc_start: 0.8141 (m-80) cc_final: 0.7877 (m-80) REVERT: A 415 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7650 (ttm170) REVERT: A 482 GLN cc_start: 0.8445 (mt0) cc_final: 0.8119 (mt0) REVERT: G 73 TRP cc_start: 0.7705 (t60) cc_final: 0.7370 (t60) REVERT: J 46 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5807 (mt-10) REVERT: D 75 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: D 121 ASN cc_start: 0.8618 (m110) cc_final: 0.8234 (m-40) REVERT: D 178 GLN cc_start: 0.8627 (tp40) cc_final: 0.8382 (tp40) REVERT: D 184 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: D 237 LEU cc_start: 0.8886 (tp) cc_final: 0.8667 (tt) REVERT: D 291 LEU cc_start: 0.7820 (tp) cc_final: 0.7499 (tp) REVERT: D 382 TYR cc_start: 0.8182 (m-80) cc_final: 0.7840 (m-80) REVERT: D 469 PHE cc_start: 0.8357 (t80) cc_final: 0.8137 (t80) REVERT: C 75 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: C 184 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: C 291 LEU cc_start: 0.7696 (tp) cc_final: 0.7422 (tp) REVERT: C 382 TYR cc_start: 0.8194 (m-80) cc_final: 0.7906 (m-80) REVERT: C 469 PHE cc_start: 0.8391 (t80) cc_final: 0.8173 (t80) REVERT: B 66 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7535 (mtt-85) REVERT: B 75 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: F 286 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7542 (p90) REVERT: F 382 TYR cc_start: 0.7972 (m-80) cc_final: 0.7695 (m-80) REVERT: E 78 ARG cc_start: 0.8564 (ttt90) cc_final: 0.8310 (ttt90) REVERT: E 154 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8254 (mtm180) REVERT: E 217 TRP cc_start: 0.8824 (p-90) cc_final: 0.8541 (p90) REVERT: E 239 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7356 (mm-30) outliers start: 77 outliers final: 27 residues processed: 572 average time/residue: 0.8504 time to fit residues: 543.5883 Evaluate side-chains 567 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 530 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 422 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 248 optimal weight: 7.9990 chunk 321 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 328 optimal weight: 0.6980 chunk 310 optimal weight: 4.9990 chunk 278 optimal weight: 0.9980 chunk 141 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: D 445 HIS B 342 ASN F 342 ASN E 294 HIS E 365 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119015 restraints weight = 33671.825| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.38 r_work: 0.3461 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27456 Z= 0.098 Angle : 0.466 6.582 37356 Z= 0.231 Chirality : 0.037 0.165 4140 Planarity : 0.003 0.042 4668 Dihedral : 10.892 173.739 3800 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.12 % Allowed : 17.31 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.16), residues: 3264 helix: 1.73 (0.12), residues: 2190 sheet: 2.33 (0.43), residues: 162 loop : -0.44 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 498 TYR 0.014 0.001 TYR B 455 PHE 0.010 0.001 PHE E 286 TRP 0.033 0.001 TRP K 73 HIS 0.008 0.001 HIS D 445 Details of bonding type rmsd covalent geometry : bond 0.00211 (27456) covalent geometry : angle 0.46616 (37356) hydrogen bonds : bond 0.04259 ( 1428) hydrogen bonds : angle 3.41096 ( 4212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 538 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7990 (tmt170) REVERT: A 184 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: A 286 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7525 (p90) REVERT: A 382 TYR cc_start: 0.8116 (m-80) cc_final: 0.7854 (m-80) REVERT: A 459 VAL cc_start: 0.8845 (t) cc_final: 0.8637 (t) REVERT: A 482 GLN cc_start: 0.8444 (mt0) cc_final: 0.8081 (mt0) REVERT: J 46 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5749 (mt-10) REVERT: D 75 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: D 79 TYR cc_start: 0.8093 (t80) cc_final: 0.7873 (t80) REVERT: D 118 ASP cc_start: 0.7687 (t0) cc_final: 0.7465 (t0) REVERT: D 184 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: C 75 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: C 184 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: C 382 TYR cc_start: 0.8170 (m-80) cc_final: 0.7869 (m-80) REVERT: C 469 PHE cc_start: 0.8371 (t80) cc_final: 0.8135 (t80) REVERT: B 66 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7425 (mtt-85) REVERT: B 118 ASP cc_start: 0.7499 (m-30) cc_final: 0.7233 (t0) REVERT: B 184 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: F 184 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: F 197 MET cc_start: 0.8476 (mmt) cc_final: 0.8263 (mmt) REVERT: F 286 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7491 (p90) REVERT: F 382 TYR cc_start: 0.7950 (m-80) cc_final: 0.7670 (m-80) REVERT: F 415 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7411 (ttm-80) REVERT: E 75 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: E 154 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8248 (mtm180) REVERT: E 184 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: E 217 TRP cc_start: 0.8809 (p-90) cc_final: 0.8553 (p90) REVERT: E 239 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7373 (mm-30) REVERT: E 382 TYR cc_start: 0.8297 (m-10) cc_final: 0.8028 (m-80) outliers start: 82 outliers final: 33 residues processed: 577 average time/residue: 0.8481 time to fit residues: 547.2294 Evaluate side-chains 578 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 530 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 434 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 192 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 ASN D 365 ASN D 445 HIS C 11 ASN C 365 ASN B 342 ASN F 133 ASN F 342 ASN E 294 HIS E 365 ASN E 389 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117169 restraints weight = 33748.240| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.39 r_work: 0.3432 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27456 Z= 0.125 Angle : 0.493 6.634 37356 Z= 0.247 Chirality : 0.038 0.139 4140 Planarity : 0.004 0.042 4668 Dihedral : 10.740 173.288 3800 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.74 % Allowed : 17.69 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.16), residues: 3264 helix: 1.63 (0.12), residues: 2190 sheet: 2.35 (0.44), residues: 156 loop : -0.54 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 499 TYR 0.012 0.001 TYR J 28 PHE 0.014 0.001 PHE E 286 TRP 0.042 0.001 TRP J 73 HIS 0.008 0.001 HIS D 445 Details of bonding type rmsd covalent geometry : bond 0.00289 (27456) covalent geometry : angle 0.49288 (37356) hydrogen bonds : bond 0.05022 ( 1428) hydrogen bonds : angle 3.46438 ( 4212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 534 time to evaluate : 0.888 Fit side-chains REVERT: A 15 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7971 (tmt170) REVERT: A 184 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: A 286 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7537 (p90) REVERT: A 382 TYR cc_start: 0.8110 (m-80) cc_final: 0.7852 (m-80) REVERT: A 482 GLN cc_start: 0.8476 (mt0) cc_final: 0.8148 (mt0) REVERT: J 46 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5741 (mt-10) REVERT: D 75 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: D 178 GLN cc_start: 0.8612 (tp40) cc_final: 0.8392 (tp40) REVERT: D 184 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: D 291 LEU cc_start: 0.7785 (tp) cc_final: 0.7444 (tp) REVERT: C 75 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: C 184 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: C 291 LEU cc_start: 0.7686 (tp) cc_final: 0.7430 (tp) REVERT: C 382 TYR cc_start: 0.8187 (m-80) cc_final: 0.7936 (m-80) REVERT: B 64 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7428 (mtm180) REVERT: B 66 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7600 (mtt-85) REVERT: B 184 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: F 184 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: F 286 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7510 (p90) REVERT: F 382 TYR cc_start: 0.7962 (m-80) cc_final: 0.7716 (m-80) REVERT: F 415 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7484 (ttm-80) REVERT: E 75 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: E 154 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8220 (mtm-85) REVERT: E 184 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: E 217 TRP cc_start: 0.8831 (p-90) cc_final: 0.8557 (p90) REVERT: E 239 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7394 (mm-30) REVERT: E 317 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7559 (mp0) outliers start: 72 outliers final: 36 residues processed: 571 average time/residue: 0.8556 time to fit residues: 545.6037 Evaluate side-chains 577 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 524 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 491 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 313 optimal weight: 6.9990 chunk 289 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 324 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN D 11 ASN D 41 ASN D 290 GLN D 445 HIS B 342 ASN B 384 ASN F 342 ASN E 365 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113778 restraints weight = 33316.128| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.37 r_work: 0.3384 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 27456 Z= 0.239 Angle : 0.609 10.349 37356 Z= 0.309 Chirality : 0.044 0.224 4140 Planarity : 0.005 0.043 4668 Dihedral : 10.908 178.936 3800 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.85 % Allowed : 18.30 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 3264 helix: 1.33 (0.12), residues: 2166 sheet: 1.96 (0.43), residues: 162 loop : -0.68 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 154 TYR 0.018 0.002 TYR J 28 PHE 0.028 0.002 PHE E 286 TRP 0.037 0.002 TRP G 73 HIS 0.008 0.001 HIS D 445 Details of bonding type rmsd covalent geometry : bond 0.00592 (27456) covalent geometry : angle 0.60894 (37356) hydrogen bonds : bond 0.07139 ( 1428) hydrogen bonds : angle 3.74254 ( 4212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 529 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7808 (tmt170) REVERT: A 286 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7575 (p90) REVERT: A 382 TYR cc_start: 0.8160 (m-80) cc_final: 0.7855 (m-80) REVERT: A 482 GLN cc_start: 0.8557 (mt0) cc_final: 0.8283 (mt0) REVERT: J 46 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5686 (mt-10) REVERT: D 75 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: D 184 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: C 75 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: C 118 ASP cc_start: 0.7721 (t0) cc_final: 0.7471 (t0) REVERT: C 121 ASN cc_start: 0.8594 (m-40) cc_final: 0.8331 (m-40) REVERT: C 184 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: C 317 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: C 382 TYR cc_start: 0.8234 (m-80) cc_final: 0.7952 (m-80) REVERT: B 64 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7750 (mtm-85) REVERT: B 66 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7722 (mtt-85) REVERT: B 75 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: F 286 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7551 (p90) REVERT: F 382 TYR cc_start: 0.7985 (m-80) cc_final: 0.7709 (m-80) REVERT: F 415 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7521 (ttm-80) REVERT: E 71 MET cc_start: 0.8010 (mmm) cc_final: 0.7698 (mtt) REVERT: E 154 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8190 (mtm-85) REVERT: E 217 TRP cc_start: 0.8831 (p-90) cc_final: 0.8572 (p90) REVERT: E 317 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7477 (mp0) outliers start: 75 outliers final: 36 residues processed: 571 average time/residue: 0.8493 time to fit residues: 541.6156 Evaluate side-chains 576 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 527 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 491 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 201 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 322 optimal weight: 0.9980 chunk 320 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 chunk 328 optimal weight: 0.9990 chunk 239 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN D 365 ASN D 445 HIS C 11 ASN B 342 ASN B 384 ASN F 342 ASN E 13 HIS E 365 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.136758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117150 restraints weight = 33826.762| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.38 r_work: 0.3432 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27456 Z= 0.115 Angle : 0.499 7.892 37356 Z= 0.253 Chirality : 0.038 0.239 4140 Planarity : 0.004 0.045 4668 Dihedral : 10.699 178.309 3800 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.51 % Allowed : 19.29 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.16), residues: 3264 helix: 1.52 (0.12), residues: 2190 sheet: 2.05 (0.43), residues: 162 loop : -0.61 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 154 TYR 0.014 0.001 TYR B 382 PHE 0.012 0.001 PHE E 286 TRP 0.053 0.001 TRP G 73 HIS 0.012 0.001 HIS D 445 Details of bonding type rmsd covalent geometry : bond 0.00254 (27456) covalent geometry : angle 0.49901 (37356) hydrogen bonds : bond 0.04953 ( 1428) hydrogen bonds : angle 3.54646 ( 4212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 526 time to evaluate : 0.950 Fit side-chains REVERT: A 15 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7961 (tmt170) REVERT: A 184 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: A 286 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7517 (p90) REVERT: A 382 TYR cc_start: 0.8120 (m-80) cc_final: 0.7866 (m-80) REVERT: A 482 GLN cc_start: 0.8464 (mt0) cc_final: 0.8183 (mt0) REVERT: J 46 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5652 (mt-10) REVERT: D 75 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: D 79 TYR cc_start: 0.8106 (t80) cc_final: 0.7868 (t80) REVERT: D 184 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: D 291 LEU cc_start: 0.7787 (tp) cc_final: 0.7498 (tp) REVERT: C 75 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: C 121 ASN cc_start: 0.8552 (m-40) cc_final: 0.8254 (m-40) REVERT: C 184 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6991 (tm-30) REVERT: C 291 LEU cc_start: 0.7740 (tp) cc_final: 0.7534 (tp) REVERT: C 382 TYR cc_start: 0.8175 (m-80) cc_final: 0.7891 (m-80) REVERT: B 66 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7545 (mtt-85) REVERT: B 75 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: B 184 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: F 197 MET cc_start: 0.8464 (mmt) cc_final: 0.8205 (mmt) REVERT: F 286 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7510 (p90) REVERT: F 317 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: F 382 TYR cc_start: 0.7964 (m-80) cc_final: 0.7723 (m-80) REVERT: F 415 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7421 (ttm-80) REVERT: E 71 MET cc_start: 0.7860 (mmm) cc_final: 0.7494 (mtt) REVERT: E 75 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: E 154 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.8216 (mtm-85) REVERT: E 217 TRP cc_start: 0.8799 (p-90) cc_final: 0.8574 (p90) REVERT: E 317 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7601 (mp0) outliers start: 66 outliers final: 35 residues processed: 561 average time/residue: 0.8463 time to fit residues: 530.9306 Evaluate side-chains 570 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 520 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 10 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 258 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN D 11 ASN D 445 HIS C 11 ASN B 13 HIS B 178 GLN B 342 ASN F 342 ASN E 365 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.134458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114782 restraints weight = 33728.945| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.38 r_work: 0.3398 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27456 Z= 0.189 Angle : 0.563 7.778 37356 Z= 0.286 Chirality : 0.042 0.268 4140 Planarity : 0.004 0.044 4668 Dihedral : 10.761 179.123 3800 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.44 % Allowed : 19.63 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.15), residues: 3264 helix: 1.42 (0.12), residues: 2166 sheet: 1.76 (0.42), residues: 168 loop : -0.67 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 154 TYR 0.015 0.002 TYR J 28 PHE 0.022 0.002 PHE E 286 TRP 0.055 0.002 TRP J 73 HIS 0.011 0.001 HIS D 445 Details of bonding type rmsd covalent geometry : bond 0.00460 (27456) covalent geometry : angle 0.56325 (37356) hydrogen bonds : bond 0.06366 ( 1428) hydrogen bonds : angle 3.67895 ( 4212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 522 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7908 (tmt170) REVERT: A 286 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7573 (p90) REVERT: A 382 TYR cc_start: 0.8160 (m-80) cc_final: 0.7881 (m-80) REVERT: A 482 GLN cc_start: 0.8564 (mt0) cc_final: 0.8265 (mt0) REVERT: J 77 MET cc_start: 0.6213 (ptp) cc_final: 0.5902 (ptp) REVERT: I 77 MET cc_start: 0.6088 (ptp) cc_final: 0.5743 (mtt) REVERT: D 75 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: D 184 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: D 291 LEU cc_start: 0.7819 (tp) cc_final: 0.7591 (tp) REVERT: C 75 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: C 184 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: C 382 TYR cc_start: 0.8219 (m-80) cc_final: 0.7935 (m-80) REVERT: B 66 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7684 (mtt-85) REVERT: B 75 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: F 184 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: F 286 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7535 (p90) REVERT: F 382 TYR cc_start: 0.8008 (m-80) cc_final: 0.7750 (m-80) REVERT: F 415 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7502 (ttm-80) REVERT: E 71 MET cc_start: 0.7977 (mmm) cc_final: 0.7706 (mtt) REVERT: E 154 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8254 (mtm-85) REVERT: E 184 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: E 217 TRP cc_start: 0.8825 (p-90) cc_final: 0.8577 (p90) REVERT: E 317 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7549 (mp0) outliers start: 64 outliers final: 39 residues processed: 557 average time/residue: 0.8591 time to fit residues: 533.8878 Evaluate side-chains 571 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 520 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 80 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN D 11 ASN D 445 HIS B 178 GLN B 342 ASN E 365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114662 restraints weight = 33556.932| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.37 r_work: 0.3397 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27456 Z= 0.193 Angle : 0.571 13.084 37356 Z= 0.290 Chirality : 0.042 0.255 4140 Planarity : 0.004 0.044 4668 Dihedral : 10.791 179.577 3800 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.13 % Allowed : 20.32 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.15), residues: 3264 helix: 1.33 (0.12), residues: 2166 sheet: 1.84 (0.42), residues: 162 loop : -0.71 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 154 TYR 0.018 0.002 TYR D 382 PHE 0.023 0.002 PHE E 286 TRP 0.070 0.002 TRP G 73 HIS 0.013 0.001 HIS D 445 Details of bonding type rmsd covalent geometry : bond 0.00473 (27456) covalent geometry : angle 0.57073 (37356) hydrogen bonds : bond 0.06389 ( 1428) hydrogen bonds : angle 3.70117 ( 4212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 527 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7898 (tmt170) REVERT: A 286 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7562 (p90) REVERT: A 382 TYR cc_start: 0.8152 (m-80) cc_final: 0.7865 (m-80) REVERT: A 482 GLN cc_start: 0.8546 (mt0) cc_final: 0.8252 (mt0) REVERT: J 46 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5921 (pm20) REVERT: J 77 MET cc_start: 0.6326 (ptp) cc_final: 0.6016 (ptp) REVERT: D 75 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: D 79 TYR cc_start: 0.8107 (t80) cc_final: 0.7899 (t80) REVERT: D 184 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: D 382 TYR cc_start: 0.8257 (m-10) cc_final: 0.8022 (m-80) REVERT: C 75 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: C 184 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: C 382 TYR cc_start: 0.8222 (m-80) cc_final: 0.7929 (m-80) REVERT: B 66 ARG cc_start: 0.7953 (mtp85) cc_final: 0.7668 (mtt-85) REVERT: B 75 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: F 184 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: F 286 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7513 (p90) REVERT: F 382 TYR cc_start: 0.8013 (m-80) cc_final: 0.7787 (m-80) REVERT: F 415 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7505 (ttm-80) REVERT: E 71 MET cc_start: 0.7981 (mmm) cc_final: 0.7719 (mtt) REVERT: E 154 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.8246 (mtm-85) REVERT: E 184 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: E 217 TRP cc_start: 0.8819 (p-90) cc_final: 0.8589 (p90) REVERT: E 317 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7571 (mp0) outliers start: 56 outliers final: 36 residues processed: 555 average time/residue: 0.8152 time to fit residues: 505.7173 Evaluate side-chains 573 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 524 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 119 optimal weight: 0.7980 chunk 229 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 284 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 324 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN D 11 ASN D 445 HIS B 178 GLN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN F 13 HIS E 365 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117139 restraints weight = 33525.567| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.37 r_work: 0.3432 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27456 Z= 0.117 Angle : 0.512 15.703 37356 Z= 0.257 Chirality : 0.038 0.165 4140 Planarity : 0.004 0.045 4668 Dihedral : 10.643 179.119 3800 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.02 % Allowed : 20.78 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.16), residues: 3264 helix: 1.60 (0.12), residues: 2172 sheet: 1.97 (0.43), residues: 162 loop : -0.63 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 154 TYR 0.015 0.001 TYR D 382 PHE 0.013 0.001 PHE E 286 TRP 0.081 0.002 TRP G 73 HIS 0.014 0.001 HIS D 445 Details of bonding type rmsd covalent geometry : bond 0.00262 (27456) covalent geometry : angle 0.51150 (37356) hydrogen bonds : bond 0.04960 ( 1428) hydrogen bonds : angle 3.56101 ( 4212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11830.42 seconds wall clock time: 200 minutes 54.04 seconds (12054.04 seconds total)