Starting phenix.real_space_refine on Sun Nov 17 21:26:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/11_2024/6qi9_4553.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/11_2024/6qi9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/11_2024/6qi9_4553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/11_2024/6qi9_4553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/11_2024/6qi9_4553.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/11_2024/6qi9_4553.cif" } resolution = 4.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: 8.94, per 1000 atoms: 0.61 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: 3.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.59 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: 4.14 Time building geometry restraints manager: 4.13 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 452 or resid 501)) selection = (chain 'C' and (resid 2 through 120 or resid 239 through 248 or resid 274 throug \ h 452 or resid 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 453 or resid 501)) selection = (chain 'F' and (resid 8 through 127 or resid 242 through 453 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.810 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.040 ------------------------------------------------------------------------------- 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 14740 Z= 0.448 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 : 10.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.002 TRP D 283 HIS 0.010 0.002 HIS A 18 PHE 0.026 0.003 PHE B 300 TYR 0.025 0.003 TYR B 314 ARG 0.016 0.001 ARG C 333 *********************** 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 : 1.808 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: 0.7745 (m-10) REVERT: A 300 PHE cc_start: 0.8661 (t80) cc_final: 0.8430 (t80) REVERT: A 303 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6470 (tm-30) 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: 0.9307 (mp10) REVERT: B 53 VAL cc_start: 0.9067 (t) cc_final: 0.8847 (t) REVERT: B 61 MET cc_start: 0.9096 (tpp) cc_final: 0.8896 (tpp) REVERT: B 66 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7671 (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: 0.8907 (tp30) REVERT: D 125 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7457 (tpt90) REVERT: D 311 PHE cc_start: 0.9395 (t80) cc_final: 0.8735 (t80) REVERT: D 320 MET cc_start: 0.3982 (mtt) cc_final: 0.2871 (ptt) REVERT: D 326 MET cc_start: 0.7138 (mmp) cc_final: 0.6478 (mmp) REVERT: E 25 HIS cc_start: 0.8544 (m-70) cc_final: 0.8172 (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: 0.8874 (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: 0.9089 (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: 0.8382 (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: 0.3275 time to fit residues: 145.5210 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 : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 385 ASN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14740 Z= 0.174 Angle : 0.680 8.923 19910 Z= 0.339 Chirality : 0.045 0.194 2362 Planarity : 0.005 0.057 2538 Dihedral : 8.989 113.528 2070 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.32 % Allowed : 4.88 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.17), residues: 1847 helix: -2.51 (0.14), residues: 830 sheet: -1.18 (0.37), residues: 189 loop : -2.08 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 283 HIS 0.004 0.001 HIS B 316 PHE 0.019 0.001 PHE D 309 TYR 0.022 0.002 TYR E 442 ARG 0.012 0.001 ARG F 416 *********************** 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 327 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 322 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.7328 (mtt180) cc_final: 0.6750 (mmm-85) REVERT: A 115 ASN cc_start: 0.9239 (m-40) cc_final: 0.8917 (m-40) REVERT: A 301 VAL cc_start: 0.8738 (t) cc_final: 0.7322 (t) REVERT: A 303 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6806 (tm-30) REVERT: A 369 GLN cc_start: 0.9346 (tt0) cc_final: 0.8697 (tm-30) REVERT: A 373 GLN cc_start: 0.9572 (mp10) cc_final: 0.9335 (mp10) REVERT: B 44 ASN cc_start: 0.8918 (t0) cc_final: 0.8104 (t0) REVERT: B 61 MET cc_start: 0.9027 (tpp) cc_final: 0.8694 (tpp) REVERT: B 85 GLN cc_start: 0.9485 (mm-40) cc_final: 0.8624 (mt0) REVERT: B 357 ARG cc_start: 0.8854 (ptm160) cc_final: 0.8596 (ptm160) REVERT: B 420 ASN cc_start: 0.8825 (m-40) cc_final: 0.8457 (t0) REVERT: C 102 TYR cc_start: 0.7528 (m-80) cc_final: 0.7316 (m-80) REVERT: C 113 MET cc_start: 0.9198 (tpt) cc_final: 0.8529 (tpt) REVERT: C 371 MET cc_start: 0.9132 (ttm) cc_final: 0.8707 (mtm) REVERT: C 384 ILE cc_start: 0.9430 (mt) cc_final: 0.9181 (mm) REVERT: C 410 LEU cc_start: 0.9318 (mt) cc_final: 0.9074 (tt) REVERT: C 428 GLU cc_start: 0.8937 (pt0) cc_final: 0.8634 (pm20) REVERT: D 117 GLU cc_start: 0.9188 (tp30) cc_final: 0.8953 (tp30) REVERT: D 309 PHE cc_start: 0.6066 (m-80) cc_final: 0.5731 (m-10) REVERT: D 320 MET cc_start: 0.4352 (mtt) cc_final: 0.2981 (ptt) REVERT: D 326 MET cc_start: 0.7048 (mmp) cc_final: 0.6601 (mmp) REVERT: D 351 LEU cc_start: 0.7447 (mt) cc_final: 0.6990 (mt) REVERT: D 414 ARG cc_start: 0.9266 (mtp-110) cc_final: 0.8943 (ttp80) REVERT: D 415 LYS cc_start: 0.8223 (tppt) cc_final: 0.7762 (tppt) REVERT: D 446 TYR cc_start: 0.8584 (t80) cc_final: 0.8345 (m-80) REVERT: E 62 MET cc_start: 0.7536 (tpp) cc_final: 0.6921 (tpp) REVERT: E 300 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7444 (mt-10) REVERT: E 324 LEU cc_start: 0.8343 (tp) cc_final: 0.8108 (tp) REVERT: E 374 ARG cc_start: 0.8863 (mmm160) cc_final: 0.8536 (mmm160) REVERT: E 404 GLN cc_start: 0.8637 (tt0) cc_final: 0.8110 (tm-30) REVERT: E 405 LEU cc_start: 0.9382 (mt) cc_final: 0.9162 (mm) REVERT: F 25 HIS cc_start: 0.7519 (m-70) cc_final: 0.7287 (m-70) REVERT: F 58 VAL cc_start: 0.9416 (t) cc_final: 0.9200 (p) REVERT: F 61 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8142 (mm-30) REVERT: F 62 MET cc_start: 0.9138 (mtp) cc_final: 0.8684 (mtp) REVERT: F 65 GLU cc_start: 0.8511 (mp0) cc_final: 0.8309 (mp0) REVERT: F 73 VAL cc_start: 0.9354 (t) cc_final: 0.9053 (t) REVERT: F 74 LEU cc_start: 0.9141 (tp) cc_final: 0.8643 (tp) REVERT: F 90 MET cc_start: 0.9055 (ttt) cc_final: 0.8719 (tpp) REVERT: F 119 LEU cc_start: 0.9230 (mt) cc_final: 0.8932 (mt) REVERT: F 317 GLU cc_start: 0.8779 (tp30) cc_final: 0.8424 (tp30) outliers start: 5 outliers final: 0 residues processed: 326 average time/residue: 0.2819 time to fit residues: 131.8080 Evaluate side-chains 225 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 114 optimal weight: 0.0980 chunk 46 optimal weight: 7.9990 chunk 168 optimal weight: 0.0060 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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** F 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14740 Z= 0.163 Angle : 0.646 9.529 19910 Z= 0.318 Chirality : 0.045 0.272 2362 Planarity : 0.005 0.090 2538 Dihedral : 8.535 112.190 2070 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.13 % Allowed : 4.24 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.18), residues: 1847 helix: -1.85 (0.16), residues: 837 sheet: -1.01 (0.38), residues: 191 loop : -1.76 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 283 HIS 0.003 0.001 HIS F 302 PHE 0.017 0.001 PHE D 309 TYR 0.017 0.001 TYR B 405 ARG 0.007 0.000 ARG E 438 *********************** 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 309 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 1.589 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 64 ARG cc_start: 0.7347 (mtt180) cc_final: 0.6677 (mmm-85) REVERT: A 301 VAL cc_start: 0.8501 (t) cc_final: 0.7944 (t) REVERT: A 369 GLN cc_start: 0.9331 (tt0) cc_final: 0.8533 (tm-30) REVERT: A 373 GLN cc_start: 0.9580 (mp10) cc_final: 0.9093 (mp10) REVERT: B 42 GLN cc_start: 0.8629 (mm110) cc_final: 0.8411 (mp10) REVERT: B 44 ASN cc_start: 0.8903 (t0) cc_final: 0.8666 (t0) REVERT: B 306 MET cc_start: 0.8683 (mtm) cc_final: 0.8455 (mtm) REVERT: B 364 MET cc_start: 0.8113 (mmp) cc_final: 0.7671 (mmp) REVERT: B 420 ASN cc_start: 0.8888 (m-40) cc_final: 0.8495 (t0) REVERT: C 86 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8504 (mp0) REVERT: C 102 TYR cc_start: 0.7534 (m-80) cc_final: 0.7311 (m-80) REVERT: C 113 MET cc_start: 0.9204 (tpt) cc_final: 0.8496 (tpt) REVERT: C 371 MET cc_start: 0.9016 (ttm) cc_final: 0.8351 (mtp) REVERT: C 428 GLU cc_start: 0.9308 (pt0) cc_final: 0.8955 (pm20) REVERT: C 436 LEU cc_start: 0.8746 (mm) cc_final: 0.8466 (tp) REVERT: D 68 ILE cc_start: 0.7202 (tp) cc_final: 0.6823 (tp) REVERT: D 90 MET cc_start: 0.8731 (tmm) cc_final: 0.7883 (mmp) REVERT: D 97 ASP cc_start: 0.7936 (p0) cc_final: 0.7476 (t70) REVERT: D 113 MET cc_start: 0.6076 (ptt) cc_final: 0.4398 (mmt) REVERT: D 277 ASN cc_start: 0.7643 (p0) cc_final: 0.7418 (p0) REVERT: D 311 PHE cc_start: 0.9337 (t80) cc_final: 0.8768 (t80) REVERT: D 320 MET cc_start: 0.4206 (mtt) cc_final: 0.2896 (ptt) REVERT: D 326 MET cc_start: 0.7312 (mmp) cc_final: 0.6420 (mmp) REVERT: D 338 THR cc_start: 0.8496 (t) cc_final: 0.8206 (m) REVERT: D 414 ARG cc_start: 0.9157 (mtp-110) cc_final: 0.8895 (ttp80) REVERT: D 446 TYR cc_start: 0.8582 (t80) cc_final: 0.8339 (m-80) REVERT: E 62 MET cc_start: 0.7621 (tpp) cc_final: 0.6550 (tpp) REVERT: E 68 ILE cc_start: 0.9235 (tp) cc_final: 0.9015 (tp) REVERT: E 90 MET cc_start: 0.9134 (mmm) cc_final: 0.8725 (mmt) REVERT: E 113 MET cc_start: 0.9022 (ttp) cc_final: 0.8669 (ppp) REVERT: E 297 PHE cc_start: 0.9122 (t80) cc_final: 0.8658 (t80) REVERT: E 324 LEU cc_start: 0.8533 (tp) cc_final: 0.8314 (tp) REVERT: E 374 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8526 (mmm160) REVERT: E 404 GLN cc_start: 0.8590 (tt0) cc_final: 0.8159 (tm-30) REVERT: E 405 LEU cc_start: 0.9393 (mt) cc_final: 0.9173 (mm) REVERT: E 427 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8523 (mmtm) REVERT: E 435 ASP cc_start: 0.7707 (p0) cc_final: 0.5861 (p0) REVERT: E 452 PHE cc_start: 0.7262 (m-80) cc_final: 0.6760 (m-80) REVERT: F 88 MET cc_start: 0.8194 (ptm) cc_final: 0.7952 (ptm) REVERT: F 90 MET cc_start: 0.9155 (ttt) cc_final: 0.8858 (tpp) REVERT: F 305 ASP cc_start: 0.8985 (p0) cc_final: 0.8671 (p0) REVERT: F 317 GLU cc_start: 0.8857 (tp30) cc_final: 0.8541 (tp30) outliers start: 2 outliers final: 0 residues processed: 309 average time/residue: 0.3113 time to fit residues: 138.7912 Evaluate side-chains 224 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** B 348 HIS B 450 GLN C 247 ASN C 332 ASN C 380 GLN D 245 HIS 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3477 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: