Starting phenix.real_space_refine on Thu Sep 18 06:48:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qi8_4552/09_2025/6qi8_4552.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qi8_4552/09_2025/6qi8_4552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qi8_4552/09_2025/6qi8_4552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qi8_4552/09_2025/6qi8_4552.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qi8_4552/09_2025/6qi8_4552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qi8_4552/09_2025/6qi8_4552.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 69 5.16 5 C 9244 2.51 5 N 2584 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14789 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2423 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2369 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain breaks: 2 Chain: "C" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2401 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 305} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2287 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2585 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2562 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.27 Number of scatterers: 14789 At special positions: 0 Unit cell: (135.16, 128.62, 80.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 12 15.00 O 2880 8.00 N 2584 7.00 C 9244 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 726.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 22 sheets defined 49.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 removed outlier: 3.509A pdb=" N VAL A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 removed outlier: 3.543A pdb=" N ILE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 107 through 117 removed outlier: 3.575A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.508A pdb=" N LEU A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 244' Processing helix chain 'A' and resid 275 through 290 removed outlier: 3.638A pdb=" N LYS A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.601A pdb=" N MET A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.578A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 367 through 382 removed outlier: 4.028A pdb=" N LYS A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.958A pdb=" N HIS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.969A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 415 removed outlier: 3.585A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 removed outlier: 3.554A pdb=" N GLU A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 455 removed outlier: 3.527A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 removed outlier: 4.315A pdb=" N ALA B 48 " --> pdb=" O ASN B 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.849A pdb=" N ALA B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.977A pdb=" N ASN B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 247 removed outlier: 3.774A pdb=" N ASP B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.944A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.739A pdb=" N THR B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 318 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 381 removed outlier: 3.760A pdb=" N ILE B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 377 " --> pdb=" O GLN B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.568A pdb=" N LEU B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 3.535A pdb=" N LYS B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.510A pdb=" N VAL B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.819A pdb=" N ASN B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.865A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.604A pdb=" N ASP B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 4.242A pdb=" N SER C 17 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS C 18 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 14 through 19' Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.523A pdb=" N ALA C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 removed outlier: 3.754A pdb=" N ALA C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.898A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 removed outlier: 3.656A pdb=" N VAL C 245 " --> pdb=" O HIS C 241 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 248' Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 279 through 290 removed outlier: 3.984A pdb=" N LYS C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.518A pdb=" N PHE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.693A pdb=" N ASP C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.618A pdb=" N LYS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.860A pdb=" N LEU C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.900A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 409 " --> pdb=" O TYR C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.794A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.996A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.604A pdb=" N ALA C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 65 removed outlier: 3.723A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 removed outlier: 3.694A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.553A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 124 removed outlier: 3.862A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.606A pdb=" N ILE D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 287 " --> pdb=" O TRP D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.577A pdb=" N MET D 303 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.612A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 removed outlier: 3.702A pdb=" N ASP D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.646A pdb=" N LYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 removed outlier: 3.525A pdb=" N THR D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 393 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.840A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 422 through 432 removed outlier: 3.702A pdb=" N ILE D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 453 removed outlier: 3.700A pdb=" N THR D 440 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN D 453 " --> pdb=" O ALA D 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 66 removed outlier: 3.989A pdb=" N ALA E 56 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.662A pdb=" N ALA E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 119 through 125 Processing helix chain 'E' and resid 244 through 253 removed outlier: 3.781A pdb=" N ASP E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 264 Processing helix chain 'E' and resid 270 through 284 removed outlier: 4.188A pdb=" N GLU E 274 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 304 Processing helix chain 'E' and resid 305 through 313 removed outlier: 3.532A pdb=" N SER E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 removed outlier: 3.739A pdb=" N ASP E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 378 removed outlier: 3.632A pdb=" N LYS E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU E 377 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 378 " --> pdb=" O ARG E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 395 removed outlier: 3.593A pdb=" N VAL E 389 " --> pdb=" O ASP E 385 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.850A pdb=" N ALA E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 427 removed outlier: 3.856A pdb=" N ILE E 426 " --> pdb=" O GLN E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 438 through 452 removed outlier: 4.131A pdb=" N TYR E 442 " --> pdb=" O ARG E 438 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 452 " --> pdb=" O ASP E 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 24 removed outlier: 3.757A pdb=" N GLY F 23 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA F 24 " --> pdb=" O ARG F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 20 through 24' Processing helix chain 'F' and resid 49 through 65 removed outlier: 3.744A pdb=" N ARG F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY F 57 " --> pdb=" O ARG F 53 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.935A pdb=" N ALA F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 94 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.645A pdb=" N ILE F 108 " --> pdb=" O GLY F 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 109' Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 244 through 250 removed outlier: 3.633A pdb=" N VAL F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 264 Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.540A pdb=" N ALA F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.663A pdb=" N SER F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.878A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 377 removed outlier: 3.774A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU F 371 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG F 372 " --> pdb=" O LYS F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.647A pdb=" N THR F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 392 " --> pdb=" O THR F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 416 removed outlier: 4.250A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 433 removed outlier: 3.963A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 452 removed outlier: 3.560A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.637A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 360 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.437A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438 removed outlier: 4.277A pdb=" N ILE F 356 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR F 328 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.601A pdb=" N CYS B 94 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP B 302 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET B 96 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 360 " --> pdb=" O LEU E 434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 69 Processing sheet with id=AB2, first strand: chain 'C' and resid 94 through 97 Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AB4, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB6, first strand: chain 'D' and resid 325 through 328 removed outlier: 6.683A pdb=" N VAL D 73 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N THR D 328 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE D 75 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 102 through 104 removed outlier: 6.737A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 104 removed outlier: 5.933A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL E 73 " --> pdb=" O MET E 326 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N THR E 328 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE E 75 " --> pdb=" O THR E 328 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 130 Processing sheet with id=AC2, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'F' and resid 332 through 334 435 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4978 1.34 - 1.46: 2664 1.46 - 1.58: 7195 1.58 - 1.70: 18 1.70 - 1.81: 120 Bond restraints: 14975 Sorted by residual: bond pdb=" N LYS B 7 " pdb=" CA LYS B 7 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.23e-02 6.61e+03 5.88e+00 bond pdb=" CA THR C 10 " pdb=" CB THR C 10 " ideal model delta sigma weight residual 1.532 1.564 -0.033 1.36e-02 5.41e+03 5.79e+00 bond pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.23e-02 6.61e+03 5.72e+00 bond pdb=" N LYS C 7 " pdb=" CA LYS C 7 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.56e+00 bond pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.59e+00 ... (remaining 14970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 19429 2.01 - 4.02: 670 4.02 - 6.02: 96 6.02 - 8.03: 26 8.03 - 10.04: 11 Bond angle restraints: 20232 Sorted by residual: angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 113.53 106.69 6.84 9.80e-01 1.04e+00 4.87e+01 angle pdb=" C VAL A 6 " pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 120.82 130.86 -10.04 1.50e+00 4.44e-01 4.48e+01 angle pdb=" C VAL B 6 " pdb=" N LYS B 7 " pdb=" CA LYS B 7 " ideal model delta sigma weight residual 120.82 130.84 -10.02 1.50e+00 4.44e-01 4.46e+01 angle pdb=" C ILE E 13 " pdb=" N ARG E 14 " pdb=" CA ARG E 14 " ideal model delta sigma weight residual 121.19 129.37 -8.18 1.59e+00 3.96e-01 2.65e+01 angle pdb=" C GLU D 378 " pdb=" N ASP D 379 " pdb=" CA ASP D 379 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 ... (remaining 20227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 8927 33.36 - 66.72: 237 66.72 - 100.08: 37 100.08 - 133.44: 3 133.44 - 166.81: 2 Dihedral angle restraints: 9206 sinusoidal: 3737 harmonic: 5469 Sorted by residual: dihedral pdb=" O2A ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PA ADP C 501 " pdb=" PB ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 106.81 -166.81 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 81.57 -141.57 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O1B ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PB ADP B 501 " pdb=" PA ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 -179.11 119.10 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 9203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1993 0.063 - 0.125: 336 0.125 - 0.188: 52 0.188 - 0.251: 9 0.251 - 0.313: 5 Chirality restraints: 2395 Sorted by residual: chirality pdb=" CB VAL E 10 " pdb=" CA VAL E 10 " pdb=" CG1 VAL E 10 " pdb=" CG2 VAL E 10 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL F 10 " pdb=" CA VAL F 10 " pdb=" CG1 VAL F 10 " pdb=" CG2 VAL F 10 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA VAL F 16 " pdb=" N VAL F 16 " pdb=" C VAL F 16 " pdb=" CB VAL F 16 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2392 not shown) Planarity restraints: 2578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 327 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C VAL A 327 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL A 327 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 328 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 10 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO E 11 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 11 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 11 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 10 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO F 11 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 11 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 11 " 0.038 5.00e-02 4.00e+02 ... (remaining 2575 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 113 2.58 - 3.16: 10751 3.16 - 3.74: 21197 3.74 - 4.32: 29446 4.32 - 4.90: 48326 Nonbonded interactions: 109833 Sorted by model distance: nonbonded pdb=" CB ARG F 14 " pdb=" CG1 VAL F 242 " model vdw 1.999 3.860 nonbonded pdb=" O VAL A 6 " pdb=" OD2 ASP A 242 " model vdw 2.037 3.040 nonbonded pdb=" OG SER E 243 " pdb=" OE1 GLU E 246 " model vdw 2.300 3.040 nonbonded pdb=" O SER E 363 " pdb=" OG1 THR E 367 " model vdw 2.304 3.040 nonbonded pdb=" OG SER E 114 " pdb=" OE1 GLU E 117 " model vdw 2.314 3.040 ... (remaining 109828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 120 or resid 239 through 248 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 452 or resid 501)) selection = (chain 'B' and (resid 2 through 120 or resid 239 through 248 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 501)) selection = (chain 'C' and (resid 2 through 120 or resid 239 through 248 or resid 274 throug \ h 501)) } ncs_group { reference = (chain 'D' and (resid 23 through 282 or (resid 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 501)) selection = (chain 'E' and (resid 23 through 127 or resid 243 through 249 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 through 282 or \ (resid 283 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 4 through 451 or (resid 452 through 453 and (name N or name CA or name C or name \ O or name CB )) or resid 501)) selection = (chain 'F' and (resid 23 through 127 or resid 243 through 249 or resid 270 throu \ gh 451 or (resid 452 through 453 and (name N or name CA or name C or name O or n \ ame CB )) or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.170 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0230 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 : 0.004 0.060 14984 Z= 0.207 Angle : 0.910 10.039 20232 Z= 0.529 Chirality : 0.052 0.313 2395 Planarity : 0.006 0.068 2578 Dihedral : 16.348 166.805 5668 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.19 % Allowed : 8.69 % Favored : 91.12 % 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 aren not related in a simple way. whole: -5.84 (0.13), residues: 1875 helix: -4.93 (0.05), residues: 871 sheet: -2.18 (0.33), residues: 199 loop : -2.85 (0.16), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 404 TYR 0.009 0.001 TYR B 438 PHE 0.016 0.001 PHE F 257 TRP 0.005 0.001 TRP D 283 HIS 0.005 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00410 (14975) covalent geometry : angle 0.90958 (20232) hydrogen bonds : bond 0.34368 ( 435) hydrogen bonds : angle 9.74140 ( 1248) Misc. bond : bond 0.00213 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.3534 (mttt) cc_final: 0.3242 (tptp) REVERT: B 61 MET cc_start: 0.0763 (tpp) cc_final: 0.0241 (tpt) REVERT: B 365 LEU cc_start: 0.0754 (mt) cc_final: -0.0957 (tt) REVERT: C 113 MET cc_start: 0.0870 (tpt) cc_final: 0.0540 (ttm) REVERT: D 424 ASP cc_start: 0.1234 (m-30) cc_final: 0.0594 (m-30) REVERT: F 41 GLN cc_start: 0.3192 (tp40) cc_final: 0.2044 (mt0) REVERT: F 320 MET cc_start: -0.0532 (ptt) cc_final: -0.1426 (mtt) outliers start: 3 outliers final: 1 residues processed: 166 average time/residue: 0.1319 time to fit residues: 32.4047 Evaluate side-chains 110 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 85 GLN A 348 HIS A 420 ASN A 429 HIS B 18 HIS B 85 GLN B 115 ASN B 316 HIS C 18 HIS C 42 GLN C 247 ASN C 380 GLN C 393 HIS C 429 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN E 27 HIS E 78 GLN E 251 ASN F 251 ASN F 447 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.224660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194042 restraints weight = 20461.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.198733 restraints weight = 13093.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.201965 restraints weight = 9513.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.204226 restraints weight = 7554.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.205644 restraints weight = 6393.461| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4301 r_free = 0.4301 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4301 r_free = 0.4301 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0752 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14984 Z= 0.149 Angle : 0.719 10.098 20232 Z= 0.355 Chirality : 0.045 0.297 2395 Planarity : 0.005 0.063 2578 Dihedral : 10.097 175.936 2113 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.08 % Allowed : 12.88 % Favored : 86.04 % 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 aren not related in a simple way. whole: -4.48 (0.15), residues: 1875 helix: -3.67 (0.11), residues: 920 sheet: -1.45 (0.35), residues: 192 loop : -2.21 (0.19), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 339 TYR 0.016 0.002 TYR E 446 PHE 0.019 0.002 PHE C 300 TRP 0.006 0.001 TRP E 283 HIS 0.010 0.002 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00313 (14975) covalent geometry : angle 0.71911 (20232) hydrogen bonds : bond 0.04356 ( 435) hydrogen bonds : angle 5.09865 ( 1248) Misc. bond : bond 0.00067 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 371 MET cc_start: 0.0431 (tmm) cc_final: 0.0196 (tmm) REVERT: B 11 LYS cc_start: 0.3185 (mttt) cc_final: 0.2675 (tptp) REVERT: B 61 MET cc_start: 0.1074 (tpp) cc_final: 0.0367 (tpt) REVERT: B 276 ARG cc_start: 0.3397 (mtt180) cc_final: 0.3172 (mtt180) REVERT: B 303 GLU cc_start: 0.3753 (mt-10) cc_final: 0.3121 (tt0) REVERT: E 285 GLU cc_start: 0.4901 (pm20) cc_final: 0.4482 (tp30) REVERT: E 298 ILE cc_start: 0.1569 (mm) cc_final: 0.1311 (mt) REVERT: E 320 MET cc_start: -0.0753 (tpt) cc_final: -0.1536 (tpt) REVERT: E 326 MET cc_start: 0.1129 (mpp) cc_final: 0.0566 (ptp) REVERT: E 401 TYR cc_start: 0.3220 (t80) cc_final: 0.2405 (t80) REVERT: F 41 GLN cc_start: 0.4244 (tp40) cc_final: 0.1952 (tm-30) REVERT: F 90 MET cc_start: 0.0589 (tmm) cc_final: 0.0248 (tmm) REVERT: F 113 MET cc_start: -0.0590 (ptp) cc_final: -0.1019 (ptt) REVERT: F 320 MET cc_start: -0.0286 (ptt) cc_final: -0.1351 (mtt) outliers start: 17 outliers final: 5 residues processed: 135 average time/residue: 0.1196 time to fit residues: 24.9231 Evaluate side-chains 107 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain E residue 245 HIS Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN B 241 HIS C 18 HIS C 429 HIS D 27 HIS D 78 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 329 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 344 HIS F 251 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.235542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.208262 restraints weight = 21125.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.213131 restraints weight = 13359.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.216513 restraints weight = 9461.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.218763 restraints weight = 7294.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.220457 restraints weight = 6039.720| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4420 r_free = 0.4420 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4420 r_free = 0.4420 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1544 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 14984 Z= 0.232 Angle : 0.927 14.675 20232 Z= 0.455 Chirality : 0.051 0.404 2395 Planarity : 0.006 0.060 2578 Dihedral : 10.083 140.230 2113 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.73 % Allowed : 15.36 % Favored : 81.92 % Cbeta Deviations : 0.06 % 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 aren not related in a simple way. whole: -3.79 (0.16), residues: 1875 helix: -2.84 (0.13), residues: 893 sheet: -2.14 (0.35), residues: 178 loop : -1.98 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 118 TYR 0.023 0.003 TYR F 340 PHE 0.027 0.003 PHE A 312 TRP 0.009 0.001 TRP D 283 HIS 0.025 0.003 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00498 (14975) covalent geometry : angle 0.92709 (20232) hydrogen bonds : bond 0.05228 ( 435) hydrogen bonds : angle 5.52172 ( 1248) Misc. bond : bond 0.00128 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 HIS cc_start: 0.1159 (OUTLIER) cc_final: 0.0155 (t-90) REVERT: B 61 MET cc_start: 0.1371 (tpp) cc_final: 0.0770 (tpt) REVERT: B 113 MET cc_start: 0.1637 (tpt) cc_final: 0.1295 (mmp) REVERT: B 364 MET cc_start: -0.0195 (ttp) cc_final: -0.0573 (ptp) REVERT: C 96 MET cc_start: 0.4076 (mmt) cc_final: 0.3417 (mpp) REVERT: C 113 MET cc_start: 0.2752 (ttt) cc_final: 0.2414 (ttt) REVERT: C 364 MET cc_start: 0.3034 (mtt) cc_final: -0.0072 (ttp) REVERT: D 346 ILE cc_start: 0.0465 (OUTLIER) cc_final: 0.0045 (mt) REVERT: E 320 MET cc_start: -0.0703 (tpt) cc_final: -0.1367 (tpt) REVERT: E 336 ARG cc_start: 0.1667 (ttt90) cc_final: 0.1461 (tpp80) REVERT: F 41 GLN cc_start: 0.4931 (tp40) cc_final: 0.3471 (tm-30) REVERT: F 90 MET cc_start: 0.0608 (tmm) cc_final: 0.0041 (tmm) REVERT: F 320 MET cc_start: 0.1244 (ptt) cc_final: -0.0489 (mtt) REVERT: F 328 THR cc_start: 0.0702 (OUTLIER) cc_final: 0.0231 (t) outliers start: 43 outliers final: 17 residues processed: 161 average time/residue: 0.1152 time to fit residues: 28.6493 Evaluate side-chains 133 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 62 optimal weight: 8.9990 chunk 8 optimal weight: 0.0040 chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 107 optimal weight: 0.0970 chunk 128 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS C 18 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 HIS E 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.233920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.206615 restraints weight = 20653.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.211396 restraints weight = 13198.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.214590 restraints weight = 9416.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.216550 restraints weight = 7368.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.218380 restraints weight = 6203.009| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1346 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14984 Z= 0.110 Angle : 0.650 11.204 20232 Z= 0.306 Chirality : 0.043 0.170 2395 Planarity : 0.004 0.052 2578 Dihedral : 9.213 129.647 2113 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.33 % Allowed : 17.20 % Favored : 81.47 % 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 aren not related in a simple way. whole: -3.12 (0.17), residues: 1875 helix: -2.22 (0.14), residues: 920 sheet: -1.74 (0.34), residues: 184 loop : -1.72 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.012 0.001 TYR B 405 PHE 0.022 0.001 PHE C 300 TRP 0.004 0.001 TRP E 283 HIS 0.008 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00234 (14975) covalent geometry : angle 0.65011 (20232) hydrogen bonds : bond 0.03239 ( 435) hydrogen bonds : angle 4.50997 ( 1248) Misc. bond : bond 0.00066 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1042 (mmp) cc_final: 0.0139 (tpp) REVERT: A 371 MET cc_start: 0.1303 (tmm) cc_final: 0.0902 (tmm) REVERT: B 61 MET cc_start: 0.0766 (tpp) cc_final: 0.0063 (tpt) REVERT: B 364 MET cc_start: -0.0461 (ttp) cc_final: -0.0794 (ptt) REVERT: C 96 MET cc_start: 0.4242 (mmt) cc_final: 0.3662 (mmp) REVERT: C 102 TYR cc_start: 0.3919 (m-80) cc_final: 0.3333 (m-80) REVERT: C 113 MET cc_start: 0.2133 (ttt) cc_final: 0.1870 (ttt) REVERT: C 364 MET cc_start: 0.2655 (mtt) cc_final: -0.0175 (ttp) REVERT: E 320 MET cc_start: -0.0363 (tpt) cc_final: -0.0881 (tpt) REVERT: E 336 ARG cc_start: 0.1219 (ttt90) cc_final: 0.1016 (tpp80) REVERT: F 41 GLN cc_start: 0.4624 (tp40) cc_final: 0.4211 (mm-40) REVERT: F 65 GLU cc_start: -0.3294 (OUTLIER) cc_final: -0.4119 (mm-30) REVERT: F 113 MET cc_start: -0.0842 (ptp) cc_final: -0.1506 (ptt) REVERT: F 320 MET cc_start: 0.0717 (ptt) cc_final: -0.0855 (mtt) REVERT: F 404 GLN cc_start: -0.1682 (OUTLIER) cc_final: -0.4936 (tm-30) outliers start: 21 outliers final: 9 residues processed: 137 average time/residue: 0.1287 time to fit residues: 26.4420 Evaluate side-chains 120 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain E residue 245 HIS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 180 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 69 optimal weight: 0.0270 chunk 120 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.236017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.209070 restraints weight = 20688.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.213626 restraints weight = 13323.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.216834 restraints weight = 9624.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.218970 restraints weight = 7533.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.220588 restraints weight = 6283.038| |-----------------------------------------------------------------------------| r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1433 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14984 Z= 0.110 Angle : 0.638 9.747 20232 Z= 0.301 Chirality : 0.043 0.173 2395 Planarity : 0.004 0.045 2578 Dihedral : 8.868 117.028 2113 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.33 % Allowed : 18.46 % Favored : 80.20 % 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 aren not related in a simple way. whole: -2.67 (0.18), residues: 1875 helix: -1.82 (0.15), residues: 925 sheet: -1.57 (0.35), residues: 187 loop : -1.53 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 372 TYR 0.011 0.001 TYR B 405 PHE 0.020 0.001 PHE C 300 TRP 0.003 0.000 TRP D 283 HIS 0.006 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00232 (14975) covalent geometry : angle 0.63810 (20232) hydrogen bonds : bond 0.03043 ( 435) hydrogen bonds : angle 4.29385 ( 1248) Misc. bond : bond 0.00081 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.0964 (mmp) cc_final: 0.0376 (mmp) REVERT: A 371 MET cc_start: 0.2423 (tmm) cc_final: 0.1545 (tmm) REVERT: B 364 MET cc_start: -0.0515 (ttp) cc_final: -0.0760 (ptt) REVERT: C 96 MET cc_start: 0.4382 (mmt) cc_final: 0.3492 (mmp) REVERT: C 364 MET cc_start: 0.2842 (mtt) cc_final: -0.0138 (ttp) REVERT: D 49 GLN cc_start: 0.5350 (mm-40) cc_final: 0.5074 (mt0) REVERT: D 62 MET cc_start: 0.4231 (tpp) cc_final: 0.3878 (mmp) REVERT: D 88 MET cc_start: -0.1390 (mtp) cc_final: -0.2443 (mtp) REVERT: E 88 MET cc_start: 0.5127 (tpt) cc_final: 0.4883 (tpp) REVERT: E 320 MET cc_start: -0.0367 (tpt) cc_final: -0.0680 (tpt) REVERT: E 336 ARG cc_start: 0.1418 (ttt90) cc_final: 0.1006 (tpp80) REVERT: F 41 GLN cc_start: 0.4548 (tp40) cc_final: 0.4201 (mm-40) REVERT: F 65 GLU cc_start: -0.3239 (OUTLIER) cc_final: -0.4941 (mt-10) REVERT: F 113 MET cc_start: -0.1052 (ptp) cc_final: -0.1819 (ptt) REVERT: F 320 MET cc_start: 0.0447 (ptt) cc_final: -0.0989 (mtt) REVERT: F 382 MET cc_start: -0.1366 (mmt) cc_final: -0.2210 (mmm) outliers start: 21 outliers final: 12 residues processed: 136 average time/residue: 0.1145 time to fit residues: 24.2343 Evaluate side-chains 125 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 5 optimal weight: 0.9980 chunk 179 optimal weight: 0.0000 chunk 6 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 100 optimal weight: 0.0010 chunk 132 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 0.0670 chunk 165 optimal weight: 0.0570 overall best weight: 0.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.235479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.207714 restraints weight = 20269.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.212463 restraints weight = 12763.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.215817 restraints weight = 9090.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.218148 restraints weight = 7047.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.219769 restraints weight = 5813.341| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1336 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14984 Z= 0.094 Angle : 0.603 10.416 20232 Z= 0.280 Chirality : 0.042 0.165 2395 Planarity : 0.003 0.048 2578 Dihedral : 8.561 117.380 2113 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.33 % Allowed : 18.65 % Favored : 80.01 % 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 aren not related in a simple way. whole: -2.17 (0.18), residues: 1875 helix: -1.36 (0.16), residues: 917 sheet: -1.39 (0.35), residues: 189 loop : -1.33 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 372 TYR 0.011 0.001 TYR E 401 PHE 0.025 0.001 PHE C 300 TRP 0.001 0.000 TRP D 283 HIS 0.005 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00196 (14975) covalent geometry : angle 0.60285 (20232) hydrogen bonds : bond 0.02577 ( 435) hydrogen bonds : angle 4.02129 ( 1248) Misc. bond : bond 0.00061 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.0905 (mmp) cc_final: 0.0016 (tpp) REVERT: A 371 MET cc_start: 0.1257 (tmm) cc_final: 0.0629 (tmm) REVERT: A 450 GLN cc_start: 0.3198 (OUTLIER) cc_final: 0.2418 (tp-100) REVERT: B 61 MET cc_start: 0.0766 (tpp) cc_final: 0.0475 (tpt) REVERT: B 364 MET cc_start: -0.0088 (ttp) cc_final: -0.0642 (ptt) REVERT: C 96 MET cc_start: 0.4204 (mmt) cc_final: 0.3332 (mmp) REVERT: C 102 TYR cc_start: 0.4604 (m-80) cc_final: 0.3266 (m-80) REVERT: C 364 MET cc_start: 0.2402 (mtt) cc_final: -0.0487 (ttp) REVERT: C 403 LEU cc_start: 0.2334 (OUTLIER) cc_final: 0.2026 (tp) REVERT: D 49 GLN cc_start: 0.5462 (mm-40) cc_final: 0.5166 (mt0) REVERT: D 62 MET cc_start: 0.4205 (tpp) cc_final: 0.3890 (mmp) REVERT: D 88 MET cc_start: -0.1532 (mtp) cc_final: -0.2616 (mtp) REVERT: E 88 MET cc_start: 0.4947 (tpt) cc_final: 0.4659 (tpp) REVERT: E 320 MET cc_start: -0.0216 (tpt) cc_final: -0.0454 (tpt) REVERT: E 336 ARG cc_start: 0.1129 (ttt90) cc_final: 0.0772 (tpp80) REVERT: E 416 ARG cc_start: 0.1610 (ppt170) cc_final: 0.0555 (ttm110) REVERT: F 41 GLN cc_start: 0.4525 (tp40) cc_final: 0.4297 (mm-40) REVERT: F 65 GLU cc_start: -0.3637 (OUTLIER) cc_final: -0.4314 (mm-30) REVERT: F 113 MET cc_start: -0.0813 (ptp) cc_final: -0.1477 (ptt) REVERT: F 320 MET cc_start: 0.0471 (ptt) cc_final: -0.0638 (mtt) REVERT: F 325 ILE cc_start: 0.1717 (OUTLIER) cc_final: 0.0894 (mm) REVERT: F 382 MET cc_start: -0.1651 (mmt) cc_final: -0.2254 (mmm) REVERT: F 404 GLN cc_start: -0.1534 (OUTLIER) cc_final: -0.4891 (tm-30) outliers start: 21 outliers final: 10 residues processed: 141 average time/residue: 0.1253 time to fit residues: 26.9501 Evaluate side-chains 129 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 147 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 0.2980 chunk 57 optimal weight: 0.0980 chunk 139 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 109 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.236466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.208885 restraints weight = 20502.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.213582 restraints weight = 13057.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.216887 restraints weight = 9375.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.219128 restraints weight = 7286.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.220768 restraints weight = 6035.783| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1419 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14984 Z= 0.101 Angle : 0.612 9.225 20232 Z= 0.288 Chirality : 0.042 0.160 2395 Planarity : 0.003 0.042 2578 Dihedral : 8.481 121.455 2113 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.52 % Allowed : 18.85 % Favored : 79.63 % 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 aren not related in a simple way. whole: -1.91 (0.19), residues: 1875 helix: -1.12 (0.16), residues: 918 sheet: -1.38 (0.37), residues: 176 loop : -1.21 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.010 0.001 TYR B 405 PHE 0.023 0.001 PHE C 300 TRP 0.003 0.000 TRP D 283 HIS 0.004 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00212 (14975) covalent geometry : angle 0.61169 (20232) hydrogen bonds : bond 0.02627 ( 435) hydrogen bonds : angle 4.01794 ( 1248) Misc. bond : bond 0.00065 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1064 (mmp) cc_final: 0.0486 (mmp) REVERT: A 364 MET cc_start: 0.0437 (pmm) cc_final: -0.0194 (pmm) REVERT: A 371 MET cc_start: 0.1507 (tmm) cc_final: 0.0682 (tmm) REVERT: B 364 MET cc_start: 0.0000 (ttp) cc_final: -0.0726 (ptt) REVERT: C 96 MET cc_start: 0.4325 (mmt) cc_final: 0.3557 (mmp) REVERT: C 364 MET cc_start: 0.2823 (mtt) cc_final: -0.0153 (ttp) REVERT: D 49 GLN cc_start: 0.5798 (mm-40) cc_final: 0.5263 (mt0) REVERT: D 62 MET cc_start: 0.4354 (tpp) cc_final: 0.4075 (mmp) REVERT: D 88 MET cc_start: -0.1194 (mtp) cc_final: -0.2197 (mtp) REVERT: E 416 ARG cc_start: 0.1712 (ppt170) cc_final: 0.0041 (mmt-90) REVERT: E 420 GLU cc_start: 0.6332 (pm20) cc_final: 0.5991 (mp0) REVERT: F 41 GLN cc_start: 0.4581 (tp40) cc_final: 0.4321 (mm-40) REVERT: F 65 GLU cc_start: -0.3982 (OUTLIER) cc_final: -0.4910 (mm-30) REVERT: F 113 MET cc_start: -0.0979 (ptp) cc_final: -0.1834 (ptt) REVERT: F 320 MET cc_start: 0.0575 (ptt) cc_final: -0.0638 (mtt) REVERT: F 325 ILE cc_start: 0.1832 (OUTLIER) cc_final: 0.0926 (mm) REVERT: F 382 MET cc_start: -0.1551 (mmt) cc_final: -0.2174 (mmm) REVERT: F 404 GLN cc_start: -0.1495 (OUTLIER) cc_final: -0.4840 (tm-30) outliers start: 24 outliers final: 16 residues processed: 139 average time/residue: 0.1231 time to fit residues: 26.1582 Evaluate side-chains 130 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 140 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 115 optimal weight: 0.0970 chunk 150 optimal weight: 0.0970 chunk 103 optimal weight: 3.9990 chunk 174 optimal weight: 0.4980 chunk 141 optimal weight: 0.6980 chunk 40 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.237389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.210400 restraints weight = 20256.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.214826 restraints weight = 13026.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.217984 restraints weight = 9431.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.220207 restraints weight = 7389.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.221781 restraints weight = 6181.843| |-----------------------------------------------------------------------------| r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1381 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14984 Z= 0.096 Angle : 0.608 9.718 20232 Z= 0.284 Chirality : 0.042 0.176 2395 Planarity : 0.003 0.058 2578 Dihedral : 8.358 120.326 2113 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.46 % Allowed : 19.04 % Favored : 79.51 % 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 aren not related in a simple way. whole: -1.56 (0.19), residues: 1875 helix: -0.79 (0.17), residues: 921 sheet: -1.16 (0.38), residues: 175 loop : -1.11 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 336 TYR 0.010 0.001 TYR B 405 PHE 0.028 0.001 PHE C 300 TRP 0.002 0.000 TRP D 283 HIS 0.008 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00204 (14975) covalent geometry : angle 0.60800 (20232) hydrogen bonds : bond 0.02565 ( 435) hydrogen bonds : angle 3.88445 ( 1248) Misc. bond : bond 0.00077 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1151 (mmp) cc_final: 0.0593 (mmp) REVERT: A 364 MET cc_start: 0.0282 (pmm) cc_final: -0.3175 (ttm) REVERT: A 371 MET cc_start: 0.1249 (tmm) cc_final: 0.0562 (tmm) REVERT: B 364 MET cc_start: 0.0042 (ttp) cc_final: -0.0648 (ptt) REVERT: B 371 MET cc_start: 0.3799 (tpp) cc_final: 0.0266 (ptt) REVERT: C 96 MET cc_start: 0.4235 (mmt) cc_final: 0.3508 (mmp) REVERT: C 306 MET cc_start: 0.3450 (pmm) cc_final: -0.0078 (ttt) REVERT: C 364 MET cc_start: 0.2595 (mtt) cc_final: -0.0097 (ttp) REVERT: C 403 LEU cc_start: 0.2310 (OUTLIER) cc_final: 0.2029 (tp) REVERT: D 49 GLN cc_start: 0.6154 (mm-40) cc_final: 0.5510 (mt0) REVERT: D 62 MET cc_start: 0.4358 (tpp) cc_final: 0.4142 (mmp) REVERT: D 88 MET cc_start: -0.1264 (mtp) cc_final: -0.2297 (mtp) REVERT: D 330 ARG cc_start: 0.4827 (tpt-90) cc_final: 0.3764 (ptm160) REVERT: E 88 MET cc_start: 0.4919 (tpt) cc_final: 0.4525 (tpp) REVERT: E 416 ARG cc_start: 0.1673 (ppt170) cc_final: 0.0418 (mmt-90) REVERT: E 420 GLU cc_start: 0.6249 (pm20) cc_final: 0.5861 (mp0) REVERT: F 65 GLU cc_start: -0.4118 (OUTLIER) cc_final: -0.4927 (mm-30) REVERT: F 320 MET cc_start: 0.0654 (ptt) cc_final: -0.0647 (mtt) REVERT: F 325 ILE cc_start: 0.1842 (OUTLIER) cc_final: 0.1008 (mm) REVERT: F 382 MET cc_start: -0.1833 (mmt) cc_final: -0.2327 (mmm) outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 0.1265 time to fit residues: 26.4777 Evaluate side-chains 134 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain E residue 401 TYR Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 97 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 117 optimal weight: 0.0870 chunk 130 optimal weight: 9.9990 chunk 128 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.238726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.211615 restraints weight = 20609.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.216253 restraints weight = 13302.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.219443 restraints weight = 9580.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.221353 restraints weight = 7524.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.223186 restraints weight = 6362.188| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1439 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14984 Z= 0.098 Angle : 0.618 10.026 20232 Z= 0.287 Chirality : 0.042 0.164 2395 Planarity : 0.003 0.041 2578 Dihedral : 8.290 121.605 2113 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.40 % Allowed : 19.42 % Favored : 79.19 % 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 aren not related in a simple way. whole: -1.44 (0.19), residues: 1875 helix: -0.68 (0.17), residues: 924 sheet: -1.05 (0.38), residues: 178 loop : -1.08 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 336 TYR 0.010 0.001 TYR B 405 PHE 0.021 0.001 PHE C 300 TRP 0.004 0.000 TRP D 283 HIS 0.003 0.001 HIS E 25 Details of bonding type rmsd covalent geometry : bond 0.00207 (14975) covalent geometry : angle 0.61849 (20232) hydrogen bonds : bond 0.02515 ( 435) hydrogen bonds : angle 3.88490 ( 1248) Misc. bond : bond 0.00071 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1215 (mmp) cc_final: 0.0440 (tpp) REVERT: A 364 MET cc_start: 0.0199 (pmm) cc_final: -0.3194 (ttm) REVERT: B 364 MET cc_start: 0.0147 (ttp) cc_final: -0.0554 (ptt) REVERT: B 371 MET cc_start: 0.3834 (tpp) cc_final: 0.0318 (ptt) REVERT: C 96 MET cc_start: 0.4286 (mmt) cc_final: 0.3524 (mmp) REVERT: C 306 MET cc_start: 0.3327 (pmm) cc_final: 0.0315 (ttt) REVERT: C 364 MET cc_start: 0.2391 (mtt) cc_final: -0.0127 (ttp) REVERT: C 403 LEU cc_start: 0.2251 (OUTLIER) cc_final: 0.1967 (tp) REVERT: D 62 MET cc_start: 0.4417 (tpp) cc_final: 0.4212 (mmp) REVERT: D 88 MET cc_start: -0.1018 (mtp) cc_final: -0.1990 (mtp) REVERT: D 330 ARG cc_start: 0.4999 (tpt-90) cc_final: 0.3619 (ptm160) REVERT: D 380 VAL cc_start: 0.3795 (m) cc_final: 0.3559 (m) REVERT: E 88 MET cc_start: 0.4917 (tpt) cc_final: 0.4673 (tpp) REVERT: E 90 MET cc_start: 0.1728 (mtt) cc_final: 0.0122 (ptp) REVERT: E 416 ARG cc_start: 0.1676 (ppt170) cc_final: 0.0475 (mmt-90) REVERT: E 420 GLU cc_start: 0.6242 (pm20) cc_final: 0.5829 (mp0) REVERT: F 65 GLU cc_start: -0.3991 (OUTLIER) cc_final: -0.4785 (mm-30) REVERT: F 90 MET cc_start: 0.0631 (tmm) cc_final: 0.0130 (tmm) REVERT: F 320 MET cc_start: 0.0531 (ptt) cc_final: -0.0732 (mtt) REVERT: F 325 ILE cc_start: 0.1846 (OUTLIER) cc_final: 0.1078 (mm) REVERT: F 382 MET cc_start: -0.1752 (mmt) cc_final: -0.2280 (mmm) REVERT: F 404 GLN cc_start: -0.0926 (OUTLIER) cc_final: -0.4505 (tm-30) outliers start: 22 outliers final: 13 residues processed: 136 average time/residue: 0.1278 time to fit residues: 26.0496 Evaluate side-chains 131 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 104 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 145 optimal weight: 0.0010 chunk 168 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN B 280 ASN C 42 GLN C 236 GLN C 241 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.244539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.219235 restraints weight = 21151.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.223806 restraints weight = 13652.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.226990 restraints weight = 9793.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.229165 restraints weight = 7600.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.230715 restraints weight = 6283.343| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1819 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14984 Z= 0.158 Angle : 0.759 10.854 20232 Z= 0.363 Chirality : 0.046 0.179 2395 Planarity : 0.004 0.047 2578 Dihedral : 8.854 127.954 2113 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.27 % Allowed : 19.29 % Favored : 79.44 % 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 aren not related in a simple way. whole: -1.95 (0.18), residues: 1875 helix: -1.08 (0.16), residues: 907 sheet: -1.40 (0.39), residues: 158 loop : -1.36 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 357 TYR 0.021 0.002 TYR F 340 PHE 0.027 0.002 PHE C 300 TRP 0.010 0.002 TRP D 283 HIS 0.015 0.002 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00348 (14975) covalent geometry : angle 0.75922 (20232) hydrogen bonds : bond 0.03631 ( 435) hydrogen bonds : angle 4.59676 ( 1248) Misc. bond : bond 0.00124 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.1370 (pmm) cc_final: -0.2161 (ttm) REVERT: A 371 MET cc_start: 0.2638 (tmm) cc_final: 0.2106 (tmm) REVERT: A 450 GLN cc_start: 0.4112 (OUTLIER) cc_final: 0.3304 (tp-100) REVERT: B 364 MET cc_start: 0.0631 (ttp) cc_final: -0.0073 (ptt) REVERT: C 96 MET cc_start: 0.3937 (mmt) cc_final: 0.3603 (mmp) REVERT: C 306 MET cc_start: 0.2362 (pmm) cc_final: 0.0023 (ttt) REVERT: C 364 MET cc_start: 0.2373 (mtt) cc_final: -0.0128 (ttp) REVERT: C 403 LEU cc_start: 0.2915 (OUTLIER) cc_final: 0.2634 (tp) REVERT: D 62 MET cc_start: 0.4656 (tpp) cc_final: 0.4366 (mmp) REVERT: D 88 MET cc_start: -0.0495 (mtp) cc_final: -0.1539 (mtp) REVERT: E 320 MET cc_start: 0.0962 (tpt) cc_final: -0.0205 (tpt) REVERT: E 416 ARG cc_start: 0.2048 (ppt170) cc_final: 0.0589 (mmt-90) REVERT: E 420 GLU cc_start: 0.6199 (pm20) cc_final: 0.5897 (mp0) REVERT: F 65 GLU cc_start: -0.4173 (OUTLIER) cc_final: -0.4995 (mm-30) REVERT: F 90 MET cc_start: 0.0660 (tmm) cc_final: 0.0382 (tmm) REVERT: F 113 MET cc_start: -0.0657 (ptp) cc_final: -0.1725 (ptt) REVERT: F 320 MET cc_start: 0.0765 (ptt) cc_final: -0.1078 (mtt) REVERT: F 325 ILE cc_start: 0.2594 (OUTLIER) cc_final: 0.2091 (mm) REVERT: F 382 MET cc_start: -0.1350 (mmt) cc_final: -0.2307 (mmt) REVERT: F 404 GLN cc_start: -0.0044 (OUTLIER) cc_final: -0.3875 (tm-30) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 0.1268 time to fit residues: 26.3107 Evaluate side-chains 130 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 245 HIS Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 179 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 160 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.244847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.218874 restraints weight = 21059.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.223743 restraints weight = 13320.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.227073 restraints weight = 9359.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.229394 restraints weight = 7190.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.230690 restraints weight = 5873.272| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1827 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 14984 Z= 0.214 Angle : 0.948 59.103 20232 Z= 0.498 Chirality : 0.050 0.957 2395 Planarity : 0.004 0.047 2578 Dihedral : 8.869 127.983 2113 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.46 % Allowed : 19.67 % Favored : 78.87 % Cbeta Deviations : 0.06 % 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 aren not related in a simple way. whole: -1.95 (0.18), residues: 1875 helix: -1.08 (0.16), residues: 907 sheet: -1.40 (0.39), residues: 158 loop : -1.36 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 64 TYR 0.018 0.002 TYR F 340 PHE 0.026 0.002 PHE C 300 TRP 0.009 0.001 TRP D 283 HIS 0.009 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00468 (14975) covalent geometry : angle 0.94780 (20232) hydrogen bonds : bond 0.03642 ( 435) hydrogen bonds : angle 4.58789 ( 1248) Misc. bond : bond 0.00133 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2279.60 seconds wall clock time: 40 minutes 27.04 seconds (2427.04 seconds total)