Starting phenix.real_space_refine on Wed Mar 4 15:52:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qi9_4553/03_2026/6qi9_4553.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qi9_4553/03_2026/6qi9_4553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qi9_4553/03_2026/6qi9_4553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qi9_4553/03_2026/6qi9_4553.map" model { file = "/net/cci-nas-00/data/ceres_data/6qi9_4553/03_2026/6qi9_4553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qi9_4553/03_2026/6qi9_4553.cif" } resolution = 4.63 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= 0.002 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 10 5.49 5 S 68 5.16 5 C 9112 2.51 5 N 2538 2.21 5 O 2831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14559 Number of models: 1 Model: "" Number of chains: 11 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: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2084 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 259} 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: "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: 3.12, per 1000 atoms: 0.21 Number of scatterers: 14559 At special positions: 0 Unit cell: (135.89, 129.47, 80.25, 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 68 16.00 P 10 15.00 O 2831 8.00 N 2538 7.00 C 9112 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 490.9 milliseconds 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 20 sheets defined 52.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 3.584A pdb=" N ALA A 16 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER A 17 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 18 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.615A pdb=" N CYS A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.651A pdb=" N ILE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 4.214A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.738A pdb=" N LEU A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 247' Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 275 through 290 removed outlier: 3.664A pdb=" N ILE A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.999A pdb=" N MET A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 removed outlier: 4.061A pdb=" N PHE A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 removed outlier: 3.686A pdb=" N ILE A 350 " --> pdb=" O PRO A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.787A pdb=" N ASP A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 382 removed outlier: 4.027A pdb=" N ILE A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 removed outlier: 4.015A pdb=" N LEU A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.634A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 4.139A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 removed outlier: 4.020A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 455 removed outlier: 3.760A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.832A pdb=" N LEU B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 removed outlier: 3.599A pdb=" N ASN B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.892A pdb=" N ASP B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 244' Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 279 through 288 removed outlier: 4.144A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.449A pdb=" N PHE B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 356 removed outlier: 4.136A pdb=" N LEU B 355 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP B 356 " --> pdb=" O ASP B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 356' Processing helix chain 'B' and resid 367 through 383 removed outlier: 4.071A pdb=" N GLN B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 374 " --> pdb=" O GLU B 370 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.659A pdb=" N LEU B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.887A pdb=" N GLN B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 removed outlier: 3.875A pdb=" N ASN B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.660A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.772A pdb=" N LEU B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.520A pdb=" N ALA B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.819A pdb=" N SER C 17 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 removed outlier: 3.766A pdb=" N ARG C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 removed outlier: 3.660A pdb=" N ALA C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 108 through 117 removed outlier: 4.318A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 279 through 290 removed outlier: 3.864A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 308 through 318 removed outlier: 4.417A pdb=" N PHE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.769A pdb=" N GLY C 349 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.629A pdb=" N LEU C 355 " --> pdb=" O PRO C 351 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 356' Processing helix chain 'C' and resid 367 through 382 removed outlier: 3.651A pdb=" N LYS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.676A pdb=" N LEU C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 410 through 420 removed outlier: 3.565A pdb=" N LEU C 415 " --> pdb=" O THR C 411 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU C 416 " --> pdb=" O PRO C 412 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 435 removed outlier: 4.203A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.652A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 4.376A pdb=" N VAL D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 removed outlier: 3.691A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.604A pdb=" N ARG D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 272 through 280 removed outlier: 3.915A pdb=" N ILE D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.544A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 352 removed outlier: 3.579A pdb=" N ASP D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 377 Processing helix chain 'D' and resid 383 through 395 removed outlier: 3.893A pdb=" N TYR D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 391 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 393 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 417 removed outlier: 4.280A pdb=" N ILE D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 405 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 411 " --> pdb=" O THR D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 427 removed outlier: 3.520A pdb=" N ILE D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 451 removed outlier: 3.650A pdb=" N GLN D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP D 448 " --> pdb=" O LYS D 444 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE D 450 " --> pdb=" O TYR D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 66 removed outlier: 3.969A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY E 66 " --> pdb=" O MET E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.710A pdb=" N ILE E 86 " --> pdb=" O GLY E 82 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 109 removed outlier: 3.866A pdb=" N ILE E 108 " --> pdb=" O GLY E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.725A pdb=" N ARG E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 253 removed outlier: 3.592A pdb=" N ASP E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 264 removed outlier: 3.702A pdb=" N SER E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP E 264 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 removed outlier: 3.869A pdb=" N ARG E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 removed outlier: 3.566A pdb=" N MET E 303 " --> pdb=" O GLU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 314 removed outlier: 3.642A pdb=" N PHE E 309 " --> pdb=" O ASP E 305 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 346 No H-bonds generated for 'chain 'E' and resid 345 through 346' Processing helix chain 'E' and resid 347 through 351 Processing helix chain 'E' and resid 364 through 377 removed outlier: 3.713A pdb=" N LYS E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 373 " --> pdb=" O GLN E 369 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU E 377 " --> pdb=" O ILE E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 395 removed outlier: 3.845A pdb=" N THR E 391 " --> pdb=" O TYR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 414 removed outlier: 3.596A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 removed outlier: 4.069A pdb=" N ILE E 426 " --> pdb=" O GLN E 422 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 452 removed outlier: 3.981A pdb=" N GLN E 441 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 452 " --> pdb=" O ASP E 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 65 removed outlier: 3.769A pdb=" N ALA F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 95 removed outlier: 3.986A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 114 through 125 removed outlier: 3.655A pdb=" N LEU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 250 Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 270 through 283 removed outlier: 3.852A pdb=" N GLU F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 280 " --> pdb=" O ILE F 276 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.544A pdb=" N PHE F 309 " --> pdb=" O ASP F 305 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 377 removed outlier: 3.505A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG F 372 " --> pdb=" O LYS F 368 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 373 " --> pdb=" O GLN F 369 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 374 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.708A pdb=" N THR F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 405 removed outlier: 3.544A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE F 403 " --> pdb=" O LEU F 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU F 405 " --> pdb=" O TYR F 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 398 through 405' Processing helix chain 'F' and resid 406 through 417 removed outlier: 4.593A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG F 414 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG F 416 " --> pdb=" O VAL F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 433 removed outlier: 3.523A pdb=" N ARG F 428 " --> pdb=" O ASP F 424 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 452 removed outlier: 3.977A pdb=" N MET F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.633A pdb=" N LEU A 39 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 7.203A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 96 removed outlier: 3.567A pdb=" N CYS A 94 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.643A pdb=" N ALA B 36 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 39 " --> pdb=" O ALA B 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 97 removed outlier: 4.074A pdb=" N CYS B 94 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 300 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'C' and resid 65 through 69 Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.196A pdb=" N ASP C 302 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 328 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AB3, first strand: chain 'D' and resid 73 through 76 removed outlier: 5.974A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 104 removed outlier: 5.361A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AB6, first strand: chain 'E' and resid 100 through 103 removed outlier: 3.938A pdb=" N THR E 101 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU E 296 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA E 327 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE E 298 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL E 73 " --> pdb=" O MET E 326 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR E 328 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE E 75 " --> pdb=" O THR E 328 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 127 through 129 Processing sheet with id=AB8, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AB9, first strand: chain 'F' and resid 42 through 43 removed outlier: 4.128A pdb=" N SER F 43 " --> pdb=" O MET F 46 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET F 46 " --> pdb=" O SER F 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 100 through 101 removed outlier: 6.695A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 332 through 334 removed outlier: 3.590A pdb=" N THR F 333 " --> pdb=" O SER F 342 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1221 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: 1.76 Time building geometry restraints manager: 1.74 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: 4880 1.34 - 1.46: 2501 1.46 - 1.58: 7226 1.58 - 1.69: 15 1.69 - 1.81: 118 Bond restraints: 14740 Sorted by residual: bond pdb=" C VAL F 10 " pdb=" N PRO F 11 " ideal model delta sigma weight residual 1.332 1.365 -0.033 8.20e-03 1.49e+04 1.59e+01 bond pdb=" N THR F 419 " pdb=" CA THR F 419 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.01e+00 bond pdb=" C THR F 359 " pdb=" N THR F 360 " ideal model delta sigma weight residual 1.329 1.302 0.027 1.21e-02 6.83e+03 4.91e+00 bond pdb=" N THR E 419 " pdb=" CA THR E 419 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.62e+00 bond pdb=" CA GLU C 5 " pdb=" CB GLU C 5 " ideal model delta sigma weight residual 1.528 1.559 -0.030 1.67e-02 3.59e+03 3.29e+00 ... (remaining 14735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18270 1.79 - 3.58: 1390 3.58 - 5.37: 162 5.37 - 7.16: 72 7.16 - 8.96: 16 Bond angle restraints: 19910 Sorted by residual: angle pdb=" C ILE F 306 " pdb=" CA ILE F 306 " pdb=" CB ILE F 306 " ideal model delta sigma weight residual 111.29 103.31 7.98 1.64e+00 3.72e-01 2.37e+01 angle pdb=" C ILE E 291 " pdb=" N ILE E 292 " pdb=" CA ILE E 292 " ideal model delta sigma weight residual 123.33 119.37 3.96 8.70e-01 1.32e+00 2.07e+01 angle pdb=" C GLU E 378 " pdb=" N ASP E 379 " pdb=" CA ASP E 379 " ideal model delta sigma weight residual 122.46 128.83 -6.37 1.41e+00 5.03e-01 2.04e+01 angle pdb=" N ASP D 379 " pdb=" CA ASP D 379 " pdb=" C ASP D 379 " ideal model delta sigma weight residual 111.24 117.31 -6.07 1.38e+00 5.25e-01 1.93e+01 angle pdb=" C ILE F 13 " pdb=" N ARG F 14 " pdb=" CA ARG F 14 " ideal model delta sigma weight residual 121.19 128.11 -6.92 1.59e+00 3.96e-01 1.90e+01 ... (remaining 19905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 8295 23.42 - 46.84: 670 46.84 - 70.26: 81 70.26 - 93.68: 20 93.68 - 117.10: 6 Dihedral angle restraints: 9072 sinusoidal: 3677 harmonic: 5395 Sorted by residual: 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 -177.10 117.10 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" CA VAL E 10 " pdb=" C VAL E 10 " pdb=" N PRO E 11 " pdb=" CA PRO E 11 " ideal model delta harmonic sigma weight residual 180.00 150.82 29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ARG E 416 " pdb=" C ARG E 416 " pdb=" N LYS E 417 " pdb=" CA LYS E 417 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 9069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1965 0.077 - 0.154: 360 0.154 - 0.230: 33 0.230 - 0.307: 3 0.307 - 0.384: 1 Chirality restraints: 2362 Sorted by residual: chirality pdb=" CB ILE D 332 " pdb=" CA ILE D 332 " pdb=" CG1 ILE D 332 " pdb=" CG2 ILE D 332 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB ILE D 298 " pdb=" CA ILE D 298 " pdb=" CG1 ILE D 298 " pdb=" CG2 ILE D 298 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA THR C 10 " pdb=" N THR C 10 " pdb=" C THR C 10 " pdb=" CB THR C 10 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2359 not shown) Planarity restraints: 2538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 346 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO B 347 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 292 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO D 293 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 293 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 293 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 10 " 0.041 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO E 11 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 11 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 11 " 0.035 5.00e-02 4.00e+02 ... (remaining 2535 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 227 2.57 - 3.16: 11893 3.16 - 3.74: 22981 3.74 - 4.32: 30113 4.32 - 4.90: 46739 Nonbonded interactions: 111953 Sorted by model distance: nonbonded pdb=" OD2 ASP E 435 " pdb=" NH1 ARG E 438 " model vdw 1.993 3.120 nonbonded pdb=" OG SER E 383 " pdb=" OD1 ASP E 385 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR A 104 " pdb=" OG1 THR F 116 " model vdw 2.260 3.040 nonbonded pdb=" O SER E 339 " pdb=" OG SER E 339 " model vdw 2.261 3.040 nonbonded pdb=" O SER A 17 " pdb=" OG SER A 17 " model vdw 2.265 3.040 ... (remaining 111948 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 'E' and (resid 8 through 127 or resid 129 or resid 243 through 269 or (re \ sid 270 and (name N or name CA or name C or name O or name CB )) or resid 271 th \ rough 282 or (resid 283 and (name N or name CA or name C or name O or name CB )) \ or resid 284 through 501)) selection = (chain 'F' and (resid 8 through 127 or resid 242 through 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.360 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.007 0.068 14746 Z= 0.339 Angle : 1.088 8.955 19910 Z= 0.622 Chirality : 0.059 0.384 2362 Planarity : 0.007 0.067 2538 Dihedral : 17.097 117.097 5580 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.39 % Allowed : 13.56 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.16), residues: 1847 helix: -3.86 (0.11), residues: 717 sheet: -1.70 (0.36), residues: 196 loop : -2.15 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 333 TYR 0.025 0.003 TYR B 314 PHE 0.026 0.003 PHE B 300 TRP 0.006 0.002 TRP D 283 HIS 0.010 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00682 (14740) covalent geometry : angle 1.08817 (19910) hydrogen bonds : bond 0.31841 ( 439) hydrogen bonds : angle 9.61820 ( 1221) Misc. bond : bond 0.00134 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 314 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.8320 (m-10) cc_final: 0.7744 (m-10) REVERT: A 300 PHE cc_start: 0.8661 (t80) cc_final: 0.8429 (t80) REVERT: A 303 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6469 (tm-30) REVERT: A 359 MET cc_start: 0.6479 (mmp) cc_final: 0.4524 (mmp) REVERT: A 364 MET cc_start: 0.8229 (mtm) cc_final: 0.7958 (ttm) REVERT: A 369 GLN cc_start: 0.9292 (tt0) cc_final: 0.8655 (tm-30) REVERT: A 373 GLN cc_start: 0.9640 (mp10) cc_final: 0.9306 (mp10) REVERT: B 53 VAL cc_start: 0.9067 (t) cc_final: 0.8848 (t) REVERT: B 61 MET cc_start: 0.9096 (tpp) cc_final: 0.8895 (tpp) REVERT: B 66 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7670 (p) REVERT: B 337 VAL cc_start: 0.8888 (t) cc_final: 0.8661 (p) REVERT: C 112 LEU cc_start: 0.9298 (mt) cc_final: 0.9055 (mm) REVERT: C 317 ARG cc_start: 0.9080 (tmm160) cc_final: 0.8478 (ttp80) REVERT: C 371 MET cc_start: 0.9116 (ttm) cc_final: 0.8447 (mtp) REVERT: C 384 ILE cc_start: 0.9590 (mt) cc_final: 0.9345 (mm) REVERT: D 117 GLU cc_start: 0.9177 (tp30) cc_final: 0.8908 (tp30) REVERT: D 125 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7460 (tpt90) REVERT: D 311 PHE cc_start: 0.9395 (t80) cc_final: 0.8734 (t80) REVERT: D 320 MET cc_start: 0.3982 (mtt) cc_final: 0.2872 (ptt) REVERT: D 326 MET cc_start: 0.7138 (mmp) cc_final: 0.6474 (mmp) REVERT: E 25 HIS cc_start: 0.8544 (m-70) cc_final: 0.7994 (m90) REVERT: E 324 LEU cc_start: 0.8715 (tp) cc_final: 0.8172 (tp) REVERT: E 404 GLN cc_start: 0.8361 (tt0) cc_final: 0.8024 (tm-30) REVERT: E 430 TYR cc_start: 0.9079 (t80) cc_final: 0.8873 (t80) REVERT: F 29 ARG cc_start: 0.9196 (mpp80) cc_final: 0.8982 (mpt-90) REVERT: F 62 MET cc_start: 0.9360 (mtp) cc_final: 0.9088 (mtp) REVERT: F 67 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8792 (mmmt) REVERT: F 317 GLU cc_start: 0.8801 (tp30) cc_final: 0.8383 (tp30) REVERT: F 326 MET cc_start: 0.9181 (ptp) cc_final: 0.8876 (mtm) outliers start: 6 outliers final: 1 residues processed: 320 average time/residue: 0.1329 time to fit residues: 59.6815 Evaluate side-chains 214 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 212 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS B 85 GLN B 305 HIS B 380 GLN B 393 HIS B 451 GLN C 42 GLN C 247 ASN C 348 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.103545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080172 restraints weight = 47589.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082712 restraints weight = 30797.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084457 restraints weight = 22440.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.085588 restraints weight = 17834.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086569 restraints weight = 15193.779| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14746 Z= 0.131 Angle : 0.684 8.533 19910 Z= 0.341 Chirality : 0.046 0.196 2362 Planarity : 0.005 0.057 2538 Dihedral : 9.001 114.449 2070 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.26 % Allowed : 5.27 % Favored : 94.47 % 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 are not related in a simple way. whole: -3.35 (0.18), residues: 1847 helix: -2.48 (0.14), residues: 832 sheet: -1.22 (0.37), residues: 191 loop : -2.05 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 416 TYR 0.028 0.002 TYR E 387 PHE 0.020 0.001 PHE D 309 TRP 0.002 0.001 TRP D 283 HIS 0.004 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00279 (14740) covalent geometry : angle 0.68374 (19910) hydrogen bonds : bond 0.04271 ( 439) hydrogen bonds : angle 5.37199 ( 1221) Misc. bond : bond 0.00119 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 321 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASN cc_start: 0.9201 (m-40) cc_final: 0.8916 (m-40) REVERT: A 301 VAL cc_start: 0.8795 (t) cc_final: 0.7481 (t) REVERT: A 303 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 369 GLN cc_start: 0.9278 (tt0) cc_final: 0.8649 (tm-30) REVERT: A 373 GLN cc_start: 0.9552 (mp10) cc_final: 0.9315 (mp10) REVERT: B 44 ASN cc_start: 0.8987 (t0) cc_final: 0.8638 (t0) REVERT: B 61 MET cc_start: 0.9121 (tpp) cc_final: 0.8739 (tpp) REVERT: B 85 GLN cc_start: 0.9427 (mm-40) cc_final: 0.8594 (mt0) REVERT: B 113 MET cc_start: 0.8758 (mtt) cc_final: 0.8555 (mtt) REVERT: B 364 MET cc_start: 0.8443 (mmp) cc_final: 0.8221 (mmp) REVERT: B 420 ASN cc_start: 0.8650 (m-40) cc_final: 0.8320 (t0) REVERT: C 102 TYR cc_start: 0.7521 (m-80) cc_final: 0.7249 (m-80) REVERT: C 108 LYS cc_start: 0.9079 (ttmt) cc_final: 0.8847 (mtmt) REVERT: C 113 MET cc_start: 0.8940 (tpt) cc_final: 0.8189 (tpt) REVERT: C 300 PHE cc_start: 0.8900 (t80) cc_final: 0.8696 (t80) REVERT: C 371 MET cc_start: 0.8958 (ttm) cc_final: 0.8682 (mtm) REVERT: C 384 ILE cc_start: 0.9453 (mt) cc_final: 0.9194 (mm) REVERT: C 410 LEU cc_start: 0.9328 (mt) cc_final: 0.9105 (tt) REVERT: C 428 GLU cc_start: 0.8937 (pt0) cc_final: 0.8596 (pm20) REVERT: D 117 GLU cc_start: 0.9199 (tp30) cc_final: 0.8955 (tp30) REVERT: D 309 PHE cc_start: 0.6082 (m-80) cc_final: 0.5845 (m-10) REVERT: D 320 MET cc_start: 0.4500 (mtt) cc_final: 0.3027 (ptt) REVERT: D 326 MET cc_start: 0.6799 (mmp) cc_final: 0.6391 (mmp) REVERT: D 351 LEU cc_start: 0.7438 (mt) cc_final: 0.6958 (mt) REVERT: D 414 ARG cc_start: 0.9148 (mtp-110) cc_final: 0.8864 (ttp80) REVERT: D 415 LYS cc_start: 0.8180 (tppt) cc_final: 0.7728 (tppt) REVERT: E 62 MET cc_start: 0.7460 (tpp) cc_final: 0.6881 (tpp) REVERT: E 300 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7584 (mt-10) REVERT: E 374 ARG cc_start: 0.8784 (mmm160) cc_final: 0.8501 (mmm160) REVERT: E 404 GLN cc_start: 0.8810 (tt0) cc_final: 0.8251 (tm-30) REVERT: E 405 LEU cc_start: 0.9458 (mt) cc_final: 0.9154 (mm) REVERT: E 452 PHE cc_start: 0.6936 (m-80) cc_final: 0.6530 (m-80) REVERT: F 58 VAL cc_start: 0.9457 (t) cc_final: 0.9232 (p) REVERT: F 61 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8149 (mm-30) REVERT: F 62 MET cc_start: 0.9059 (mtp) cc_final: 0.8627 (mtp) REVERT: F 73 VAL cc_start: 0.9352 (t) cc_final: 0.9060 (t) REVERT: F 74 LEU cc_start: 0.9179 (tp) cc_final: 0.8659 (tp) REVERT: F 119 LEU cc_start: 0.9333 (mt) cc_final: 0.9024 (mt) REVERT: F 317 GLU cc_start: 0.8680 (tp30) cc_final: 0.8342 (tp30) outliers start: 4 outliers final: 0 residues processed: 324 average time/residue: 0.1137 time to fit residues: 53.6822 Evaluate side-chains 226 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 67 optimal weight: 0.0970 chunk 120 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 170 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN C 247 ASN C 305 HIS D 313 ASN ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN F 25 HIS F 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.104119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081054 restraints weight = 48473.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083570 restraints weight = 31234.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.085411 restraints weight = 22685.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.086503 restraints weight = 17999.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087409 restraints weight = 15363.077| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14746 Z= 0.115 Angle : 0.647 8.811 19910 Z= 0.317 Chirality : 0.044 0.249 2362 Planarity : 0.004 0.054 2538 Dihedral : 8.502 111.948 2070 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.18), residues: 1847 helix: -1.78 (0.16), residues: 829 sheet: -1.02 (0.38), residues: 191 loop : -1.73 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 124 TYR 0.018 0.001 TYR B 405 PHE 0.018 0.001 PHE D 309 TRP 0.001 0.000 TRP D 283 HIS 0.003 0.001 HIS F 302 Details of bonding type rmsd covalent geometry : bond 0.00246 (14740) covalent geometry : angle 0.64677 (19910) hydrogen bonds : bond 0.03746 ( 439) hydrogen bonds : angle 4.85392 ( 1221) Misc. bond : bond 0.00091 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 313 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.8447 (t) cc_final: 0.7875 (t) REVERT: A 369 GLN cc_start: 0.9208 (tt0) cc_final: 0.8574 (tm-30) REVERT: A 373 GLN cc_start: 0.9549 (mp10) cc_final: 0.9153 (mp10) REVERT: A 408 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8351 (mm110) REVERT: B 42 GLN cc_start: 0.8603 (mm110) cc_final: 0.8355 (mp10) REVERT: B 44 ASN cc_start: 0.9000 (t0) cc_final: 0.8697 (t0) REVERT: B 420 ASN cc_start: 0.8612 (m-40) cc_final: 0.8311 (t0) REVERT: C 86 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8571 (mp0) REVERT: C 102 TYR cc_start: 0.7564 (m-80) cc_final: 0.7273 (m-80) REVERT: C 113 MET cc_start: 0.8900 (tpt) cc_final: 0.8107 (tpt) REVERT: C 436 LEU cc_start: 0.8915 (mm) cc_final: 0.8593 (tp) REVERT: C 447 LEU cc_start: 0.9126 (mm) cc_final: 0.8919 (tp) REVERT: D 68 ILE cc_start: 0.7207 (tp) cc_final: 0.6903 (tp) REVERT: D 90 MET cc_start: 0.8779 (tmm) cc_final: 0.7810 (mmp) REVERT: D 92 GLN cc_start: 0.7348 (tm-30) cc_final: 0.7135 (tm-30) REVERT: D 97 ASP cc_start: 0.8119 (p0) cc_final: 0.7615 (t70) REVERT: D 113 MET cc_start: 0.5814 (ptt) cc_final: 0.4255 (mmt) REVERT: D 277 ASN cc_start: 0.7752 (p0) cc_final: 0.7523 (p0) REVERT: D 311 PHE cc_start: 0.9336 (t80) cc_final: 0.8787 (t80) REVERT: D 320 MET cc_start: 0.4440 (mtt) cc_final: 0.2939 (ptt) REVERT: D 326 MET cc_start: 0.7119 (mmp) cc_final: 0.6043 (mmp) REVERT: D 338 THR cc_start: 0.8454 (t) cc_final: 0.8252 (m) REVERT: D 351 LEU cc_start: 0.7444 (mt) cc_final: 0.7219 (mt) REVERT: D 414 ARG cc_start: 0.9015 (mtp-110) cc_final: 0.8811 (ttp80) REVERT: E 62 MET cc_start: 0.7430 (tpp) cc_final: 0.6445 (tpp) REVERT: E 68 ILE cc_start: 0.9221 (tp) cc_final: 0.8996 (tp) REVERT: E 90 MET cc_start: 0.9139 (mmm) cc_final: 0.8602 (mmm) REVERT: E 113 MET cc_start: 0.8831 (ttp) cc_final: 0.8628 (ppp) REVERT: E 297 PHE cc_start: 0.9105 (t80) cc_final: 0.8686 (t80) REVERT: E 300 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7452 (mt-10) REVERT: E 324 LEU cc_start: 0.8556 (tp) cc_final: 0.8287 (tp) REVERT: E 374 ARG cc_start: 0.8847 (mmm160) cc_final: 0.8502 (mmm160) REVERT: E 404 GLN cc_start: 0.8717 (tt0) cc_final: 0.8220 (tm-30) REVERT: E 405 LEU cc_start: 0.9407 (mt) cc_final: 0.9138 (mm) REVERT: E 427 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8536 (mmtm) REVERT: E 450 PHE cc_start: 0.7265 (t80) cc_final: 0.7016 (t80) REVERT: E 452 PHE cc_start: 0.6956 (m-80) cc_final: 0.6512 (m-80) REVERT: F 88 MET cc_start: 0.8093 (ptm) cc_final: 0.7803 (ptm) REVERT: F 303 MET cc_start: 0.9097 (mmm) cc_final: 0.8623 (mpp) REVERT: F 305 ASP cc_start: 0.9115 (p0) cc_final: 0.8822 (p0) REVERT: F 317 GLU cc_start: 0.8692 (tp30) cc_final: 0.8360 (tp30) outliers start: 2 outliers final: 0 residues processed: 315 average time/residue: 0.1154 time to fit residues: 52.9530 Evaluate side-chains 227 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS C 247 ASN C 332 ASN D 245 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.102714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079915 restraints weight = 48555.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082378 restraints weight = 31597.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083978 restraints weight = 23123.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.085272 restraints weight = 18483.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.086054 restraints weight = 15667.088| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14746 Z= 0.139 Angle : 0.655 7.999 19910 Z= 0.320 Chirality : 0.045 0.172 2362 Planarity : 0.004 0.054 2538 Dihedral : 8.461 111.368 2070 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.19), residues: 1847 helix: -1.34 (0.17), residues: 831 sheet: -0.80 (0.38), residues: 185 loop : -1.57 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 438 TYR 0.018 0.001 TYR E 442 PHE 0.014 0.001 PHE B 116 TRP 0.014 0.002 TRP D 283 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00300 (14740) covalent geometry : angle 0.65483 (19910) hydrogen bonds : bond 0.03340 ( 439) hydrogen bonds : angle 4.68600 ( 1221) Misc. bond : bond 0.00143 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 68 LEU cc_start: 0.8022 (tp) cc_final: 0.7819 (mm) REVERT: A 300 PHE cc_start: 0.8566 (t80) cc_final: 0.8260 (t80) REVERT: A 301 VAL cc_start: 0.8429 (t) cc_final: 0.7918 (t) REVERT: A 369 GLN cc_start: 0.9240 (tt0) cc_final: 0.8627 (tm-30) REVERT: A 373 GLN cc_start: 0.9548 (mp10) cc_final: 0.9061 (mp10) REVERT: A 408 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8550 (tp-100) REVERT: B 44 ASN cc_start: 0.9032 (t0) cc_final: 0.8699 (t0) REVERT: B 61 MET cc_start: 0.8468 (tpp) cc_final: 0.8243 (tpp) REVERT: B 364 MET cc_start: 0.8000 (mmp) cc_final: 0.7495 (mmp) REVERT: B 420 ASN cc_start: 0.8820 (m-40) cc_final: 0.8485 (t0) REVERT: B 431 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8795 (mt-10) REVERT: C 86 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8555 (mp0) REVERT: C 102 TYR cc_start: 0.7696 (m-80) cc_final: 0.7332 (m-80) REVERT: C 113 MET cc_start: 0.8914 (tpt) cc_final: 0.8148 (tpt) REVERT: C 436 LEU cc_start: 0.8997 (mm) cc_final: 0.8664 (tp) REVERT: D 68 ILE cc_start: 0.7359 (tp) cc_final: 0.7014 (tp) REVERT: D 90 MET cc_start: 0.8797 (tmm) cc_final: 0.7838 (mmp) REVERT: D 92 GLN cc_start: 0.7315 (tm-30) cc_final: 0.6999 (tm-30) REVERT: D 97 ASP cc_start: 0.8121 (p0) cc_final: 0.7627 (t70) REVERT: D 299 ASP cc_start: 0.7977 (m-30) cc_final: 0.7101 (t0) REVERT: D 311 PHE cc_start: 0.9300 (t80) cc_final: 0.8801 (t80) REVERT: D 320 MET cc_start: 0.4511 (mtt) cc_final: 0.2995 (ptt) REVERT: D 326 MET cc_start: 0.6651 (mmp) cc_final: 0.4722 (ppp) REVERT: D 338 THR cc_start: 0.8416 (t) cc_final: 0.8188 (m) REVERT: D 349 ASP cc_start: 0.8999 (p0) cc_final: 0.8694 (p0) REVERT: D 433 PHE cc_start: 0.6872 (m-80) cc_final: 0.6604 (m-80) REVERT: D 444 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8537 (mtpp) REVERT: E 61 GLU cc_start: 0.8519 (pt0) cc_final: 0.7463 (tt0) REVERT: E 62 MET cc_start: 0.7492 (tpp) cc_final: 0.6525 (tpp) REVERT: E 68 ILE cc_start: 0.9249 (tp) cc_final: 0.9036 (tp) REVERT: E 90 MET cc_start: 0.9089 (mmm) cc_final: 0.8668 (mmt) REVERT: E 115 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8182 (tttm) REVERT: E 297 PHE cc_start: 0.9085 (t80) cc_final: 0.8697 (t80) REVERT: E 300 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7575 (mt-10) REVERT: E 324 LEU cc_start: 0.8498 (tp) cc_final: 0.8258 (tp) REVERT: E 325 ILE cc_start: 0.8431 (mt) cc_final: 0.8221 (mt) REVERT: E 351 LEU cc_start: 0.8977 (tp) cc_final: 0.8777 (tp) REVERT: E 374 ARG cc_start: 0.8853 (mmm160) cc_final: 0.8469 (mmm160) REVERT: E 404 GLN cc_start: 0.8682 (tt0) cc_final: 0.8169 (tm-30) REVERT: E 405 LEU cc_start: 0.9429 (mt) cc_final: 0.9129 (mm) REVERT: E 427 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8540 (mmtm) REVERT: E 452 PHE cc_start: 0.7047 (m-80) cc_final: 0.6626 (m-80) REVERT: F 88 MET cc_start: 0.8154 (ptm) cc_final: 0.7804 (ptm) REVERT: F 303 MET cc_start: 0.9172 (mmm) cc_final: 0.8703 (mpp) REVERT: F 305 ASP cc_start: 0.9133 (p0) cc_final: 0.8820 (p0) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.1096 time to fit residues: 47.9403 Evaluate side-chains 219 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 129 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 82 optimal weight: 0.0020 chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 148 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 overall best weight: 2.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 380 GLN C 385 ASN D 245 HIS D 404 GLN F 25 HIS F 49 GLN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.077938 restraints weight = 49503.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080369 restraints weight = 32099.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082106 restraints weight = 23495.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083320 restraints weight = 18621.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.084178 restraints weight = 15740.002| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14746 Z= 0.164 Angle : 0.671 8.137 19910 Z= 0.330 Chirality : 0.045 0.173 2362 Planarity : 0.004 0.069 2538 Dihedral : 8.510 110.948 2070 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.19), residues: 1847 helix: -1.15 (0.17), residues: 838 sheet: -0.75 (0.39), residues: 185 loop : -1.50 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 46 TYR 0.016 0.002 TYR E 442 PHE 0.020 0.002 PHE E 450 TRP 0.019 0.002 TRP D 283 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00353 (14740) covalent geometry : angle 0.67073 (19910) hydrogen bonds : bond 0.03321 ( 439) hydrogen bonds : angle 4.70070 ( 1221) Misc. bond : bond 0.00275 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASN cc_start: 0.9197 (m-40) cc_final: 0.8986 (m-40) REVERT: A 300 PHE cc_start: 0.8678 (t80) cc_final: 0.8292 (t80) REVERT: A 301 VAL cc_start: 0.8529 (t) cc_final: 0.7957 (t) REVERT: A 369 GLN cc_start: 0.9258 (tt0) cc_final: 0.8737 (tm-30) REVERT: A 373 GLN cc_start: 0.9546 (mp10) cc_final: 0.9054 (mp10) REVERT: A 408 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8607 (tp-100) REVERT: B 42 GLN cc_start: 0.8518 (mm110) cc_final: 0.8175 (mp10) REVERT: B 44 ASN cc_start: 0.9106 (t0) cc_final: 0.8386 (t0) REVERT: B 61 MET cc_start: 0.8807 (tpp) cc_final: 0.8510 (tpp) REVERT: B 112 LEU cc_start: 0.9232 (mm) cc_final: 0.8947 (pp) REVERT: B 371 MET cc_start: 0.9382 (mtt) cc_final: 0.9177 (mtt) REVERT: B 420 ASN cc_start: 0.8902 (m-40) cc_final: 0.8571 (t0) REVERT: C 86 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8443 (tp30) REVERT: C 102 TYR cc_start: 0.7721 (m-80) cc_final: 0.7370 (m-80) REVERT: C 113 MET cc_start: 0.8909 (tpt) cc_final: 0.8130 (tpt) REVERT: C 436 LEU cc_start: 0.9069 (mm) cc_final: 0.8739 (tp) REVERT: D 68 ILE cc_start: 0.7408 (tp) cc_final: 0.7120 (tp) REVERT: D 74 LEU cc_start: 0.8750 (mm) cc_final: 0.8386 (mm) REVERT: D 90 MET cc_start: 0.8767 (tmm) cc_final: 0.7836 (mmp) REVERT: D 92 GLN cc_start: 0.7402 (tm-30) cc_final: 0.7163 (tm-30) REVERT: D 97 ASP cc_start: 0.8144 (p0) cc_final: 0.7677 (t70) REVERT: D 113 MET cc_start: 0.5875 (ptt) cc_final: 0.4397 (mmt) REVERT: D 299 ASP cc_start: 0.7864 (m-30) cc_final: 0.7470 (t0) REVERT: D 311 PHE cc_start: 0.9343 (t80) cc_final: 0.8812 (t80) REVERT: D 320 MET cc_start: 0.4676 (mtt) cc_final: 0.3214 (ptt) REVERT: D 326 MET cc_start: 0.7187 (mmp) cc_final: 0.6524 (mmp) REVERT: D 338 THR cc_start: 0.8419 (t) cc_final: 0.8205 (m) REVERT: D 349 ASP cc_start: 0.9017 (p0) cc_final: 0.8750 (p0) REVERT: D 351 LEU cc_start: 0.7400 (mt) cc_final: 0.7082 (mt) REVERT: D 417 LYS cc_start: 0.8379 (tmtt) cc_final: 0.8110 (tmtt) REVERT: D 433 PHE cc_start: 0.7062 (m-80) cc_final: 0.6630 (m-80) REVERT: D 444 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8640 (mtpp) REVERT: E 61 GLU cc_start: 0.8530 (pt0) cc_final: 0.7504 (tt0) REVERT: E 62 MET cc_start: 0.7516 (tpp) cc_final: 0.6505 (tpp) REVERT: E 68 ILE cc_start: 0.9215 (tp) cc_final: 0.8973 (tp) REVERT: E 90 MET cc_start: 0.9033 (mmm) cc_final: 0.8646 (mmm) REVERT: E 113 MET cc_start: 0.8743 (ppp) cc_final: 0.8204 (ppp) REVERT: E 297 PHE cc_start: 0.9108 (t80) cc_final: 0.8805 (t80) REVERT: E 299 ASP cc_start: 0.7569 (t70) cc_final: 0.7366 (t0) REVERT: E 300 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7532 (mt-10) REVERT: E 325 ILE cc_start: 0.8467 (mt) cc_final: 0.8204 (mt) REVERT: E 351 LEU cc_start: 0.9022 (tp) cc_final: 0.8694 (tp) REVERT: E 374 ARG cc_start: 0.8934 (mmm160) cc_final: 0.8525 (mmm160) REVERT: E 404 GLN cc_start: 0.8737 (tt0) cc_final: 0.8243 (tm-30) REVERT: E 427 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8179 (mmmm) REVERT: E 452 PHE cc_start: 0.7050 (m-80) cc_final: 0.6662 (m-80) REVERT: F 88 MET cc_start: 0.8146 (ptm) cc_final: 0.7849 (ptm) REVERT: F 303 MET cc_start: 0.9232 (mmm) cc_final: 0.8725 (mpp) REVERT: F 305 ASP cc_start: 0.9270 (p0) cc_final: 0.8958 (p0) REVERT: F 397 THR cc_start: 0.7210 (p) cc_final: 0.6993 (p) outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.1111 time to fit residues: 47.4769 Evaluate side-chains 217 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 52 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 152 optimal weight: 0.0570 chunk 158 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 450 GLN C 18 HIS C 247 ASN C 380 GLN C 420 ASN D 245 HIS ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS F 49 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.100368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078077 restraints weight = 48905.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080437 restraints weight = 32215.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082118 restraints weight = 23767.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083207 restraints weight = 19004.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.084097 restraints weight = 16245.239| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14746 Z= 0.167 Angle : 0.682 9.047 19910 Z= 0.337 Chirality : 0.046 0.206 2362 Planarity : 0.006 0.180 2538 Dihedral : 8.497 111.658 2070 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.06 % Allowed : 2.70 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.19), residues: 1847 helix: -1.00 (0.17), residues: 827 sheet: -0.77 (0.39), residues: 185 loop : -1.53 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 404 TYR 0.017 0.002 TYR E 442 PHE 0.018 0.002 PHE F 452 TRP 0.016 0.002 TRP D 283 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00361 (14740) covalent geometry : angle 0.68187 (19910) hydrogen bonds : bond 0.03303 ( 439) hydrogen bonds : angle 4.78590 ( 1221) Misc. bond : bond 0.00240 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 108 LYS cc_start: 0.8111 (ptpt) cc_final: 0.7894 (ptmt) REVERT: A 115 ASN cc_start: 0.9186 (m-40) cc_final: 0.8924 (m-40) REVERT: A 300 PHE cc_start: 0.8702 (t80) cc_final: 0.8342 (t80) REVERT: A 301 VAL cc_start: 0.8471 (t) cc_final: 0.7853 (t) REVERT: A 369 GLN cc_start: 0.9219 (tt0) cc_final: 0.8786 (tm-30) REVERT: A 373 GLN cc_start: 0.9542 (mp10) cc_final: 0.9115 (mp10) REVERT: A 408 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8566 (tp-100) REVERT: B 42 GLN cc_start: 0.8413 (mm110) cc_final: 0.8103 (mp10) REVERT: B 44 ASN cc_start: 0.9027 (t0) cc_final: 0.8322 (t0) REVERT: B 112 LEU cc_start: 0.9270 (mm) cc_final: 0.8912 (pp) REVERT: B 355 LEU cc_start: 0.9219 (tp) cc_final: 0.9013 (tp) REVERT: B 420 ASN cc_start: 0.8793 (m-40) cc_final: 0.8524 (t0) REVERT: B 425 ILE cc_start: 0.9018 (mm) cc_final: 0.8774 (mm) REVERT: C 86 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8559 (tp30) REVERT: C 96 MET cc_start: 0.8962 (ppp) cc_final: 0.8753 (ppp) REVERT: C 102 TYR cc_start: 0.7717 (m-80) cc_final: 0.7461 (m-80) REVERT: C 113 MET cc_start: 0.8831 (tpt) cc_final: 0.8047 (tpt) REVERT: C 436 LEU cc_start: 0.9048 (mm) cc_final: 0.8778 (tp) REVERT: D 68 ILE cc_start: 0.7383 (tp) cc_final: 0.6995 (tp) REVERT: D 74 LEU cc_start: 0.8778 (mm) cc_final: 0.8446 (mm) REVERT: D 90 MET cc_start: 0.8741 (tmm) cc_final: 0.7842 (mmp) REVERT: D 92 GLN cc_start: 0.7433 (tm-30) cc_final: 0.6975 (tm-30) REVERT: D 97 ASP cc_start: 0.8153 (p0) cc_final: 0.7672 (t70) REVERT: D 113 MET cc_start: 0.5606 (ptt) cc_final: 0.4143 (mmm) REVERT: D 277 ASN cc_start: 0.7773 (p0) cc_final: 0.7558 (p0) REVERT: D 299 ASP cc_start: 0.7818 (m-30) cc_final: 0.7378 (t0) REVERT: D 311 PHE cc_start: 0.9343 (t80) cc_final: 0.8807 (t80) REVERT: D 320 MET cc_start: 0.4702 (mtt) cc_final: 0.3217 (ptt) REVERT: D 326 MET cc_start: 0.7193 (mmp) cc_final: 0.6584 (mmp) REVERT: D 351 LEU cc_start: 0.7432 (mt) cc_final: 0.7164 (mt) REVERT: D 444 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8680 (mtpp) REVERT: E 61 GLU cc_start: 0.8470 (pt0) cc_final: 0.7419 (tt0) REVERT: E 62 MET cc_start: 0.7499 (tpp) cc_final: 0.6457 (tpp) REVERT: E 68 ILE cc_start: 0.9204 (tp) cc_final: 0.8940 (tp) REVERT: E 90 MET cc_start: 0.9011 (mmm) cc_final: 0.8552 (mmm) REVERT: E 113 MET cc_start: 0.8849 (ppp) cc_final: 0.8016 (ppp) REVERT: E 297 PHE cc_start: 0.9096 (t80) cc_final: 0.8807 (t80) REVERT: E 299 ASP cc_start: 0.7628 (t70) cc_final: 0.7413 (t0) REVERT: E 300 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7600 (mt-10) REVERT: E 325 ILE cc_start: 0.8516 (mt) cc_final: 0.8253 (mt) REVERT: E 351 LEU cc_start: 0.9021 (tp) cc_final: 0.8649 (tp) REVERT: E 374 ARG cc_start: 0.8933 (mmm160) cc_final: 0.8468 (mmm160) REVERT: E 404 GLN cc_start: 0.8729 (tt0) cc_final: 0.8261 (tm-30) REVERT: E 427 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8601 (mmtm) REVERT: E 452 PHE cc_start: 0.7039 (m-80) cc_final: 0.6651 (m-80) REVERT: F 61 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8311 (mm-30) REVERT: F 65 GLU cc_start: 0.8660 (mp0) cc_final: 0.8432 (mp0) REVERT: F 74 LEU cc_start: 0.9009 (tp) cc_final: 0.8689 (tp) REVERT: F 88 MET cc_start: 0.8135 (ptm) cc_final: 0.7740 (ptm) REVERT: F 303 MET cc_start: 0.9199 (mmm) cc_final: 0.8770 (mpp) REVERT: F 305 ASP cc_start: 0.9277 (p0) cc_final: 0.8908 (p0) REVERT: F 397 THR cc_start: 0.7053 (p) cc_final: 0.6830 (p) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.1123 time to fit residues: 46.0224 Evaluate side-chains 213 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 6 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 153 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN C 247 ASN C 380 GLN C 420 ASN D 245 HIS ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS F 49 GLN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.080478 restraints weight = 48346.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.083084 restraints weight = 31033.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084770 restraints weight = 22466.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.086078 restraints weight = 17851.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086949 restraints weight = 15070.137| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14746 Z= 0.117 Angle : 0.653 8.491 19910 Z= 0.317 Chirality : 0.045 0.165 2362 Planarity : 0.006 0.186 2538 Dihedral : 8.259 110.566 2070 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.06 % Allowed : 1.67 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.19), residues: 1847 helix: -0.79 (0.18), residues: 832 sheet: -0.70 (0.39), residues: 186 loop : -1.45 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 428 TYR 0.023 0.002 TYR B 314 PHE 0.017 0.001 PHE B 116 TRP 0.008 0.001 TRP D 283 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00258 (14740) covalent geometry : angle 0.65281 (19910) hydrogen bonds : bond 0.03073 ( 439) hydrogen bonds : angle 4.48418 ( 1221) Misc. bond : bond 0.00226 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 115 ASN cc_start: 0.8750 (m-40) cc_final: 0.8506 (m-40) REVERT: A 300 PHE cc_start: 0.8748 (t80) cc_final: 0.8506 (t80) REVERT: A 301 VAL cc_start: 0.8537 (t) cc_final: 0.7971 (t) REVERT: A 369 GLN cc_start: 0.9261 (tt0) cc_final: 0.8879 (tm-30) REVERT: A 408 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8603 (tp-100) REVERT: B 44 ASN cc_start: 0.9023 (t0) cc_final: 0.8565 (t0) REVERT: B 113 MET cc_start: 0.8526 (mmt) cc_final: 0.8293 (mmp) REVERT: B 364 MET cc_start: 0.7776 (mmp) cc_final: 0.7376 (mmp) REVERT: B 371 MET cc_start: 0.9254 (mtt) cc_final: 0.9005 (mtt) REVERT: B 420 ASN cc_start: 0.8759 (m-40) cc_final: 0.8409 (t0) REVERT: C 102 TYR cc_start: 0.7843 (m-80) cc_final: 0.7410 (m-80) REVERT: C 113 MET cc_start: 0.8843 (tpt) cc_final: 0.8050 (tpt) REVERT: C 436 LEU cc_start: 0.8913 (mm) cc_final: 0.8621 (tp) REVERT: C 438 TYR cc_start: 0.7620 (m-10) cc_final: 0.7413 (m-10) REVERT: D 68 ILE cc_start: 0.7371 (tp) cc_final: 0.7086 (tp) REVERT: D 74 LEU cc_start: 0.8781 (mm) cc_final: 0.8386 (mm) REVERT: D 90 MET cc_start: 0.8712 (tmm) cc_final: 0.8057 (mmp) REVERT: D 92 GLN cc_start: 0.6960 (tm-30) cc_final: 0.6575 (tm-30) REVERT: D 97 ASP cc_start: 0.8065 (p0) cc_final: 0.7595 (t70) REVERT: D 113 MET cc_start: 0.5607 (ptt) cc_final: 0.4164 (mmm) REVERT: D 277 ASN cc_start: 0.7778 (p0) cc_final: 0.7563 (p0) REVERT: D 299 ASP cc_start: 0.7788 (m-30) cc_final: 0.7066 (t0) REVERT: D 311 PHE cc_start: 0.9299 (t80) cc_final: 0.8787 (t80) REVERT: D 320 MET cc_start: 0.4604 (mtt) cc_final: 0.3095 (ptt) REVERT: D 349 ASP cc_start: 0.9061 (p0) cc_final: 0.8735 (p0) REVERT: D 351 LEU cc_start: 0.7436 (mt) cc_final: 0.6941 (mt) REVERT: E 58 VAL cc_start: 0.9575 (t) cc_final: 0.9365 (t) REVERT: E 61 GLU cc_start: 0.8370 (pt0) cc_final: 0.7220 (tt0) REVERT: E 62 MET cc_start: 0.7480 (tpp) cc_final: 0.6417 (tpp) REVERT: E 68 ILE cc_start: 0.9157 (tp) cc_final: 0.8906 (tp) REVERT: E 90 MET cc_start: 0.9001 (mmm) cc_final: 0.8635 (mmm) REVERT: E 113 MET cc_start: 0.8816 (ppp) cc_final: 0.7697 (ppp) REVERT: E 297 PHE cc_start: 0.9089 (t80) cc_final: 0.8685 (t80) REVERT: E 299 ASP cc_start: 0.7561 (t70) cc_final: 0.7138 (t0) REVERT: E 300 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7428 (mt-10) REVERT: E 324 LEU cc_start: 0.8448 (tp) cc_final: 0.8153 (tp) REVERT: E 351 LEU cc_start: 0.8961 (tp) cc_final: 0.8685 (tp) REVERT: E 374 ARG cc_start: 0.8908 (mmm160) cc_final: 0.8459 (mmm160) REVERT: E 404 GLN cc_start: 0.8773 (tt0) cc_final: 0.8203 (tm-30) REVERT: E 405 LEU cc_start: 0.9471 (mt) cc_final: 0.9208 (mm) REVERT: E 427 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8548 (mmtm) REVERT: E 443 MET cc_start: 0.8975 (mmt) cc_final: 0.8539 (mmm) REVERT: E 452 PHE cc_start: 0.7096 (m-80) cc_final: 0.6684 (m-80) REVERT: F 49 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7540 (mm110) REVERT: F 74 LEU cc_start: 0.9127 (tp) cc_final: 0.8616 (tp) REVERT: F 305 ASP cc_start: 0.9168 (p0) cc_final: 0.8775 (p0) REVERT: F 397 THR cc_start: 0.7100 (p) cc_final: 0.6869 (p) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.1045 time to fit residues: 44.3412 Evaluate side-chains 213 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 109 optimal weight: 0.0980 chunk 89 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 167 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 284 ASN A 305 HIS ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 420 ASN D 245 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS F 49 GLN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.104984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082003 restraints weight = 48306.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.084609 restraints weight = 31072.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.086448 restraints weight = 22536.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087699 restraints weight = 17785.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088662 restraints weight = 14989.801| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14746 Z= 0.109 Angle : 0.651 8.371 19910 Z= 0.314 Chirality : 0.044 0.177 2362 Planarity : 0.006 0.231 2538 Dihedral : 8.124 114.951 2070 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.06 % Allowed : 1.41 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1847 helix: -0.61 (0.18), residues: 845 sheet: -0.63 (0.40), residues: 176 loop : -1.42 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 428 TYR 0.022 0.001 TYR B 314 PHE 0.021 0.001 PHE D 309 TRP 0.005 0.001 TRP D 283 HIS 0.006 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00241 (14740) covalent geometry : angle 0.65068 (19910) hydrogen bonds : bond 0.02980 ( 439) hydrogen bonds : angle 4.31741 ( 1221) Misc. bond : bond 0.00216 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 PHE cc_start: 0.8731 (t80) cc_final: 0.8425 (t80) REVERT: A 369 GLN cc_start: 0.9261 (tt0) cc_final: 0.8888 (tm-30) REVERT: A 408 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8551 (tp-100) REVERT: B 44 ASN cc_start: 0.9072 (t0) cc_final: 0.8591 (t0) REVERT: B 364 MET cc_start: 0.7589 (mmp) cc_final: 0.7255 (mmp) REVERT: B 420 ASN cc_start: 0.8741 (m-40) cc_final: 0.8359 (t0) REVERT: C 102 TYR cc_start: 0.7675 (m-80) cc_final: 0.7373 (m-80) REVERT: C 113 MET cc_start: 0.8845 (tpt) cc_final: 0.8049 (tpt) REVERT: C 436 LEU cc_start: 0.9023 (mm) cc_final: 0.8560 (tp) REVERT: D 68 ILE cc_start: 0.7325 (tp) cc_final: 0.7026 (tp) REVERT: D 74 LEU cc_start: 0.8752 (mm) cc_final: 0.8404 (mm) REVERT: D 90 MET cc_start: 0.8693 (tmm) cc_final: 0.8075 (mmp) REVERT: D 92 GLN cc_start: 0.6996 (tm-30) cc_final: 0.6725 (tm-30) REVERT: D 97 ASP cc_start: 0.8056 (p0) cc_final: 0.7600 (t70) REVERT: D 113 MET cc_start: 0.5672 (ptt) cc_final: 0.4368 (mmm) REVERT: D 277 ASN cc_start: 0.7808 (p0) cc_final: 0.7605 (p0) REVERT: D 311 PHE cc_start: 0.9264 (t80) cc_final: 0.8837 (t80) REVERT: D 320 MET cc_start: 0.4593 (mtt) cc_final: 0.3049 (ptt) REVERT: D 349 ASP cc_start: 0.9019 (p0) cc_final: 0.8770 (p0) REVERT: D 351 LEU cc_start: 0.7506 (mt) cc_final: 0.6860 (mt) REVERT: E 58 VAL cc_start: 0.9607 (t) cc_final: 0.9373 (t) REVERT: E 61 GLU cc_start: 0.8362 (pt0) cc_final: 0.7211 (tt0) REVERT: E 62 MET cc_start: 0.7594 (tpp) cc_final: 0.6523 (tpp) REVERT: E 68 ILE cc_start: 0.9162 (tp) cc_final: 0.8920 (tp) REVERT: E 90 MET cc_start: 0.8974 (mmm) cc_final: 0.8597 (mmm) REVERT: E 113 MET cc_start: 0.8804 (ppp) cc_final: 0.7949 (ppp) REVERT: E 115 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8160 (tttt) REVERT: E 297 PHE cc_start: 0.9050 (t80) cc_final: 0.8693 (t80) REVERT: E 299 ASP cc_start: 0.7415 (t70) cc_final: 0.7089 (t0) REVERT: E 300 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7461 (mt-10) REVERT: E 324 LEU cc_start: 0.8495 (tp) cc_final: 0.8284 (tp) REVERT: E 374 ARG cc_start: 0.8955 (mmm160) cc_final: 0.8505 (mmm160) REVERT: E 404 GLN cc_start: 0.8734 (tt0) cc_final: 0.8170 (tm-30) REVERT: E 405 LEU cc_start: 0.9466 (mt) cc_final: 0.9218 (mm) REVERT: E 427 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8514 (mmtm) REVERT: E 435 ASP cc_start: 0.6493 (p0) cc_final: 0.6228 (p0) REVERT: E 443 MET cc_start: 0.8992 (mmt) cc_final: 0.8560 (mmm) REVERT: E 452 PHE cc_start: 0.7048 (m-80) cc_final: 0.6663 (m-80) REVERT: F 74 LEU cc_start: 0.9088 (tp) cc_final: 0.8629 (tp) REVERT: F 305 ASP cc_start: 0.9062 (p0) cc_final: 0.8724 (p0) outliers start: 1 outliers final: 0 residues processed: 296 average time/residue: 0.1056 time to fit residues: 46.6316 Evaluate side-chains 222 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 184 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 420 ASN D 245 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.104345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081327 restraints weight = 48634.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083901 restraints weight = 31407.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.085730 restraints weight = 22845.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086871 restraints weight = 18115.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087797 restraints weight = 15430.970| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14746 Z= 0.124 Angle : 0.669 10.238 19910 Z= 0.323 Chirality : 0.045 0.297 2362 Planarity : 0.006 0.197 2538 Dihedral : 8.136 114.456 2070 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.20), residues: 1847 helix: -0.58 (0.18), residues: 838 sheet: -0.58 (0.40), residues: 174 loop : -1.39 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 404 TYR 0.016 0.001 TYR E 442 PHE 0.022 0.001 PHE D 309 TRP 0.015 0.002 TRP D 283 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00275 (14740) covalent geometry : angle 0.66927 (19910) hydrogen bonds : bond 0.03028 ( 439) hydrogen bonds : angle 4.33538 ( 1221) Misc. bond : bond 0.00160 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7600 (pmm) cc_final: 0.7047 (pmm) REVERT: A 113 MET cc_start: 0.8758 (mtm) cc_final: 0.8509 (mpp) REVERT: A 300 PHE cc_start: 0.8766 (t80) cc_final: 0.8410 (t80) REVERT: A 369 GLN cc_start: 0.9238 (tt0) cc_final: 0.8620 (tm-30) REVERT: A 373 GLN cc_start: 0.9522 (mp10) cc_final: 0.8987 (mp10) REVERT: A 408 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8524 (tp-100) REVERT: B 44 ASN cc_start: 0.9064 (t0) cc_final: 0.8563 (t0) REVERT: B 87 LEU cc_start: 0.8955 (mt) cc_final: 0.8560 (mp) REVERT: B 364 MET cc_start: 0.7480 (mmp) cc_final: 0.7112 (mmp) REVERT: B 420 ASN cc_start: 0.8775 (m-40) cc_final: 0.8398 (t0) REVERT: C 102 TYR cc_start: 0.7811 (m-80) cc_final: 0.7398 (m-80) REVERT: C 113 MET cc_start: 0.8858 (tpt) cc_final: 0.8067 (tpt) REVERT: C 436 LEU cc_start: 0.8984 (mm) cc_final: 0.8709 (tp) REVERT: D 68 ILE cc_start: 0.7461 (tp) cc_final: 0.7235 (tp) REVERT: D 74 LEU cc_start: 0.8846 (mm) cc_final: 0.8508 (mm) REVERT: D 90 MET cc_start: 0.8609 (tmm) cc_final: 0.8034 (mmp) REVERT: D 92 GLN cc_start: 0.7006 (tm-30) cc_final: 0.6636 (tm-30) REVERT: D 97 ASP cc_start: 0.8070 (p0) cc_final: 0.7614 (t70) REVERT: D 113 MET cc_start: 0.5740 (ptt) cc_final: 0.4437 (mmm) REVERT: D 299 ASP cc_start: 0.7672 (m-30) cc_final: 0.7047 (t0) REVERT: D 311 PHE cc_start: 0.9297 (t80) cc_final: 0.8820 (t80) REVERT: D 320 MET cc_start: 0.4612 (mtt) cc_final: 0.3129 (ptt) REVERT: D 351 LEU cc_start: 0.7773 (mt) cc_final: 0.7099 (mt) REVERT: E 61 GLU cc_start: 0.8361 (pt0) cc_final: 0.7234 (tt0) REVERT: E 62 MET cc_start: 0.7560 (tpp) cc_final: 0.6523 (tpp) REVERT: E 68 ILE cc_start: 0.9158 (tp) cc_final: 0.8895 (tp) REVERT: E 113 MET cc_start: 0.8792 (ppp) cc_final: 0.7659 (ppp) REVERT: E 115 LYS cc_start: 0.8426 (ttpp) cc_final: 0.8224 (tttt) REVERT: E 297 PHE cc_start: 0.9037 (t80) cc_final: 0.8638 (t80) REVERT: E 299 ASP cc_start: 0.7438 (t70) cc_final: 0.7098 (t0) REVERT: E 300 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7393 (mt-10) REVERT: E 324 LEU cc_start: 0.8332 (tp) cc_final: 0.8073 (tp) REVERT: E 404 GLN cc_start: 0.8738 (tt0) cc_final: 0.8219 (tm-30) REVERT: E 405 LEU cc_start: 0.9480 (mt) cc_final: 0.9196 (mm) REVERT: E 427 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8465 (mmtm) REVERT: E 443 MET cc_start: 0.8984 (mmt) cc_final: 0.8554 (mmm) REVERT: E 452 PHE cc_start: 0.7088 (m-80) cc_final: 0.6678 (m-80) REVERT: F 312 LEU cc_start: 0.9062 (pp) cc_final: 0.8837 (mt) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.0940 time to fit residues: 42.0567 Evaluate side-chains 219 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.0000 chunk 136 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 174 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN D 245 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.105705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082610 restraints weight = 47912.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.085227 restraints weight = 30800.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.087072 restraints weight = 22392.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088196 restraints weight = 17661.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089158 restraints weight = 15077.741| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 14746 Z= 0.113 Angle : 0.675 10.719 19910 Z= 0.328 Chirality : 0.045 0.176 2362 Planarity : 0.005 0.175 2538 Dihedral : 8.028 117.781 2070 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.20), residues: 1847 helix: -0.49 (0.18), residues: 836 sheet: -0.48 (0.40), residues: 178 loop : -1.32 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 64 TYR 0.016 0.001 TYR E 442 PHE 0.025 0.001 PHE E 450 TRP 0.010 0.001 TRP D 283 HIS 0.006 0.001 HIS F 302 Details of bonding type rmsd covalent geometry : bond 0.00250 (14740) covalent geometry : angle 0.67538 (19910) hydrogen bonds : bond 0.03091 ( 439) hydrogen bonds : angle 4.21837 ( 1221) Misc. bond : bond 0.00139 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7434 (pmm) cc_final: 0.6699 (pmm) REVERT: A 102 TYR cc_start: 0.8984 (m-10) cc_final: 0.8775 (m-10) REVERT: A 110 GLU cc_start: 0.8991 (pm20) cc_final: 0.8751 (pm20) REVERT: A 300 PHE cc_start: 0.8774 (t80) cc_final: 0.8411 (t80) REVERT: A 369 GLN cc_start: 0.9230 (tt0) cc_final: 0.8631 (tm-30) REVERT: A 373 GLN cc_start: 0.9539 (mp10) cc_final: 0.9002 (mp10) REVERT: A 408 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8570 (tp-100) REVERT: B 44 ASN cc_start: 0.9043 (t0) cc_final: 0.8520 (t0) REVERT: B 87 LEU cc_start: 0.8895 (mt) cc_final: 0.8472 (mp) REVERT: B 112 LEU cc_start: 0.9194 (mm) cc_final: 0.8817 (pp) REVERT: B 113 MET cc_start: 0.8527 (mmp) cc_final: 0.8030 (mmp) REVERT: B 420 ASN cc_start: 0.8753 (m-40) cc_final: 0.8377 (t0) REVERT: C 102 TYR cc_start: 0.7722 (m-80) cc_final: 0.7333 (m-80) REVERT: C 113 MET cc_start: 0.8905 (tpt) cc_final: 0.8126 (tpt) REVERT: C 436 LEU cc_start: 0.8947 (mm) cc_final: 0.8540 (tp) REVERT: D 74 LEU cc_start: 0.8811 (mm) cc_final: 0.8456 (mm) REVERT: D 90 MET cc_start: 0.8640 (tmm) cc_final: 0.8082 (mmp) REVERT: D 92 GLN cc_start: 0.7023 (tm-30) cc_final: 0.6657 (tm-30) REVERT: D 97 ASP cc_start: 0.8131 (p0) cc_final: 0.7590 (t70) REVERT: D 113 MET cc_start: 0.5871 (ptt) cc_final: 0.4537 (mmm) REVERT: D 283 TRP cc_start: 0.7538 (m-10) cc_final: 0.7251 (m-10) REVERT: D 299 ASP cc_start: 0.7713 (m-30) cc_final: 0.7071 (t0) REVERT: D 311 PHE cc_start: 0.9229 (t80) cc_final: 0.8822 (t80) REVERT: D 320 MET cc_start: 0.4588 (mtt) cc_final: 0.3091 (ptt) REVERT: D 349 ASP cc_start: 0.8999 (p0) cc_final: 0.8781 (p0) REVERT: D 351 LEU cc_start: 0.7939 (mt) cc_final: 0.7176 (mt) REVERT: E 58 VAL cc_start: 0.9607 (t) cc_final: 0.9381 (t) REVERT: E 61 GLU cc_start: 0.8337 (pt0) cc_final: 0.7239 (tt0) REVERT: E 62 MET cc_start: 0.7535 (tpp) cc_final: 0.6547 (tpp) REVERT: E 68 ILE cc_start: 0.9115 (tp) cc_final: 0.8888 (tp) REVERT: E 90 MET cc_start: 0.8997 (mmm) cc_final: 0.8639 (mmt) REVERT: E 108 ILE cc_start: 0.8941 (pt) cc_final: 0.8727 (mt) REVERT: E 113 MET cc_start: 0.8704 (ppp) cc_final: 0.7941 (ppp) REVERT: E 115 LYS cc_start: 0.8378 (ttpp) cc_final: 0.7818 (tttt) REVERT: E 297 PHE cc_start: 0.9009 (t80) cc_final: 0.8644 (t80) REVERT: E 300 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7394 (mt-10) REVERT: E 325 ILE cc_start: 0.8125 (mt) cc_final: 0.7868 (mt) REVERT: E 326 MET cc_start: 0.8801 (mpp) cc_final: 0.8549 (mpp) REVERT: E 404 GLN cc_start: 0.8761 (tt0) cc_final: 0.8225 (tm-30) REVERT: E 405 LEU cc_start: 0.9460 (mt) cc_final: 0.9224 (mm) REVERT: E 427 LYS cc_start: 0.8682 (mmtt) cc_final: 0.7474 (pttm) REVERT: E 443 MET cc_start: 0.8988 (mmt) cc_final: 0.8556 (mmm) REVERT: E 452 PHE cc_start: 0.7039 (m-80) cc_final: 0.6688 (m-80) REVERT: F 74 LEU cc_start: 0.9105 (tp) cc_final: 0.8436 (tp) REVERT: F 300 GLU cc_start: 0.8038 (tt0) cc_final: 0.7697 (tt0) REVERT: F 303 MET cc_start: 0.8439 (mpp) cc_final: 0.7360 (mpp) REVERT: F 354 LEU cc_start: 0.9242 (tp) cc_final: 0.8885 (tp) REVERT: F 387 TYR cc_start: 0.9170 (m-80) cc_final: 0.8416 (m-80) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.0956 time to fit residues: 43.0323 Evaluate side-chains 223 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 162 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS C 420 ASN D 245 HIS ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.098913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076495 restraints weight = 50567.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078827 restraints weight = 33170.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.080507 restraints weight = 24378.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081691 restraints weight = 19557.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082502 restraints weight = 16667.756| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14746 Z= 0.251 Angle : 0.799 10.174 19910 Z= 0.398 Chirality : 0.049 0.189 2362 Planarity : 0.006 0.204 2538 Dihedral : 8.536 110.461 2070 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.19), residues: 1847 helix: -0.99 (0.17), residues: 834 sheet: -0.86 (0.38), residues: 187 loop : -1.29 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 64 TYR 0.031 0.002 TYR E 387 PHE 0.028 0.002 PHE F 109 TRP 0.032 0.004 TRP D 283 HIS 0.007 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00534 (14740) covalent geometry : angle 0.79905 (19910) hydrogen bonds : bond 0.03842 ( 439) hydrogen bonds : angle 4.91982 ( 1221) Misc. bond : bond 0.00206 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.61 seconds wall clock time: 35 minutes 48.97 seconds (2148.97 seconds total)