Starting phenix.real_space_refine on Sat Oct 24 06:53:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wez_65919/10_2026/9wez_65919_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wez_65919/10_2026/9wez_65919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wez_65919/10_2026/9wez_65919_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wez_65919/10_2026/9wez_65919_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wez_65919/10_2026/9wez_65919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wez_65919/10_2026/9wez_65919.map" } resolution = 2.64 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= 0.003 sd= 0.036 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 8 5.49 5 S 64 5.16 5 C 7756 2.51 5 N 2256 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12424 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3085 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3085 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3087 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 1 Chain: "D" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3087 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'AFP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'AFP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'AFP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'AFP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.08, per 1000 atoms: 0.25 Number of scatterers: 12424 At special positions: 0 Unit cell: (87.55, 117.3, 119, 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 64 16.00 P 8 15.00 O 2340 8.00 N 2256 7.00 C 7756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 525.9 milliseconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 6 sheets defined 52.0% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.886A pdb=" N TYR A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 279 Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.775A pdb=" N VAL A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.805A pdb=" N ILE A 342 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 348 through 364 removed outlier: 3.996A pdb=" N ALA A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.722A pdb=" N ILE A 378 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.521A pdb=" N THR A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.702A pdb=" N ALA A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.754A pdb=" N LEU A 437 " --> pdb=" O TYR A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 467 Processing helix chain 'A' and resid 478 through 487 removed outlier: 4.323A pdb=" N TYR A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 525 through 543 removed outlier: 3.730A pdb=" N VAL A 529 " --> pdb=" O TRP A 525 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 123 through 140 removed outlier: 3.525A pdb=" N HIS B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.748A pdb=" N TYR B 148 " --> pdb=" O PRO B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 4.016A pdb=" N ARG B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 302 removed outlier: 3.730A pdb=" N VAL B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 306 Processing helix chain 'B' and resid 316 through 322 Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 339 through 344 removed outlier: 3.633A pdb=" N ILE B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 344 " --> pdb=" O GLY B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 364 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.662A pdb=" N ILE B 378 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.976A pdb=" N GLY B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.854A pdb=" N ALA B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 430 removed outlier: 3.741A pdb=" N ALA B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 444 removed outlier: 3.684A pdb=" N LEU B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.728A pdb=" N ILE B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 487 removed outlier: 4.301A pdb=" N TYR B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 526 through 543 removed outlier: 3.965A pdb=" N ASP B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG B 532 " --> pdb=" O ASP B 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 123 through 140 removed outlier: 3.540A pdb=" N HIS C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.756A pdb=" N TYR C 148 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 279 removed outlier: 4.230A pdb=" N ARG C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 302 removed outlier: 3.768A pdb=" N VAL C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 306 removed outlier: 3.585A pdb=" N HIS C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 322 through 330 removed outlier: 3.677A pdb=" N ILE C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 364 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.678A pdb=" N ILE C 378 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 379 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 398 removed outlier: 4.009A pdb=" N GLY C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.974A pdb=" N ALA C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.716A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.907A pdb=" N LEU C 437 " --> pdb=" O TYR C 433 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 467 removed outlier: 3.612A pdb=" N VAL C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 487 removed outlier: 4.299A pdb=" N TYR C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 524 through 543 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 123 through 140 removed outlier: 3.525A pdb=" N HIS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.720A pdb=" N TYR D 148 " --> pdb=" O PRO D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 279 removed outlier: 4.159A pdb=" N ARG D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 302 removed outlier: 3.808A pdb=" N VAL D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 306 removed outlier: 3.636A pdb=" N HIS D 306 " --> pdb=" O PRO D 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 306' Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 322 through 330 removed outlier: 3.675A pdb=" N VAL D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 364 Processing helix chain 'D' and resid 374 through 378 removed outlier: 3.529A pdb=" N MET D 377 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 378 " --> pdb=" O GLU D 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 374 through 378' Processing helix chain 'D' and resid 384 through 398 removed outlier: 3.978A pdb=" N GLY D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.961A pdb=" N ALA D 409 " --> pdb=" O SER D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 431 removed outlier: 3.868A pdb=" N ALA D 430 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 444 removed outlier: 3.789A pdb=" N LEU D 437 " --> pdb=" O TYR D 433 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 467 removed outlier: 3.561A pdb=" N VAL D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 486 Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 524 through 543 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 93 removed outlier: 6.738A pdb=" N ILE A 90 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ARG A 116 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA A 92 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 153 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE A 284 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 155 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 310 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N MET A 334 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER A 312 " --> pdb=" O MET A 334 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 401 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 403 " --> pdb=" O CYS A 369 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N SER A 89 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU A 404 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 91 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 516 removed outlier: 6.752A pdb=" N VAL A 493 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU A 515 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA A 495 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 471 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL A 496 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 473 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 470 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL A 555 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 472 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 556 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 567 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN B 566 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 470 " --> pdb=" O ILE B 553 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL B 555 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 472 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N GLY B 557 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LEU B 474 " --> pdb=" O GLY B 557 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 471 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL B 496 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 473 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 493 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 515 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 495 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 93 removed outlier: 6.723A pdb=" N ILE B 90 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG B 116 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 92 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA B 115 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP B 156 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 117 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 153 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N PHE B 284 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU B 155 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 310 " --> pdb=" O GLY B 332 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET B 334 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER B 312 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B 403 " --> pdb=" O CYS B 369 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER B 89 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU B 404 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE B 91 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 89 through 93 removed outlier: 6.701A pdb=" N ILE C 90 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ARG C 116 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 92 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASN C 118 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA C 115 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP C 156 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU C 117 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 153 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE C 284 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 155 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE C 310 " --> pdb=" O GLY C 332 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET C 334 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER C 312 " --> pdb=" O MET C 334 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS C 401 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET C 403 " --> pdb=" O CYS C 369 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER C 89 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU C 404 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE C 91 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 512 through 516 removed outlier: 6.776A pdb=" N VAL C 493 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU C 515 " --> pdb=" O VAL C 493 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA C 495 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C 471 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL C 496 " --> pdb=" O ILE C 471 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL C 473 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA C 470 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY C 557 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASN C 566 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN D 566 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA D 470 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY D 557 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE D 471 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL D 496 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 473 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL D 493 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU D 515 " --> pdb=" O VAL D 493 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA D 495 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 89 through 93 removed outlier: 6.713A pdb=" N ILE D 90 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ARG D 116 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA D 92 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA D 115 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASP D 156 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU D 117 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE D 153 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE D 284 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU D 155 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE D 310 " --> pdb=" O GLY D 332 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N MET D 334 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER D 312 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE D 333 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS D 401 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET D 403 " --> pdb=" O CYS D 369 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER D 89 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU D 404 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE D 91 " --> pdb=" O LEU D 404 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1671 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: 1.95 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4282 1.35 - 1.47: 2517 1.47 - 1.59: 5708 1.59 - 1.71: 13 1.71 - 1.83: 104 Bond restraints: 12624 Sorted by residual: bond pdb=" N GLU A 439 " pdb=" CA GLU A 439 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.08e+00 bond pdb=" N GLN A 505 " pdb=" CA GLN A 505 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.31e-02 5.83e+03 6.02e+00 bond pdb=" N GLN B 505 " pdb=" CA GLN B 505 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.84e+00 bond pdb=" N GLY B 302 " pdb=" CA GLY B 302 " ideal model delta sigma weight residual 1.443 1.476 -0.033 1.37e-02 5.33e+03 5.77e+00 bond pdb=" CB PRO A 303 " pdb=" CG PRO A 303 " ideal model delta sigma weight residual 1.492 1.607 -0.115 5.00e-02 4.00e+02 5.30e+00 ... (remaining 12619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 16766 2.44 - 4.88: 285 4.88 - 7.32: 43 7.32 - 9.76: 5 9.76 - 12.20: 3 Bond angle restraints: 17102 Sorted by residual: angle pdb=" N HIS B 507 " pdb=" CA HIS B 507 " pdb=" C HIS B 507 " ideal model delta sigma weight residual 113.23 107.38 5.85 1.24e+00 6.50e-01 2.23e+01 angle pdb=" N HIS A 507 " pdb=" CA HIS A 507 " pdb=" C HIS A 507 " ideal model delta sigma weight residual 113.38 107.69 5.69 1.23e+00 6.61e-01 2.14e+01 angle pdb=" CA PRO A 303 " pdb=" N PRO A 303 " pdb=" CD PRO A 303 " ideal model delta sigma weight residual 112.00 106.43 5.57 1.40e+00 5.10e-01 1.59e+01 angle pdb=" CB MET B 420 " pdb=" CG MET B 420 " pdb=" SD MET B 420 " ideal model delta sigma weight residual 112.70 124.34 -11.64 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CB GLU B 439 " pdb=" CG GLU B 439 " pdb=" CD GLU B 439 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.70e+00 3.46e-01 1.46e+01 ... (remaining 17097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 6446 17.41 - 34.82: 906 34.82 - 52.23: 342 52.23 - 69.64: 93 69.64 - 87.05: 31 Dihedral angle restraints: 7818 sinusoidal: 3162 harmonic: 4656 Sorted by residual: dihedral pdb=" CA ILE C 342 " pdb=" C ILE C 342 " pdb=" N GLU C 343 " pdb=" CA GLU C 343 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLY B 561 " pdb=" C GLY B 561 " pdb=" N SER B 562 " pdb=" CA SER B 562 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLY A 338 " pdb=" C GLY A 338 " pdb=" N ASP A 339 " pdb=" CA ASP A 339 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 7815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1542 0.056 - 0.111: 352 0.111 - 0.167: 79 0.167 - 0.222: 0 0.222 - 0.278: 1 Chirality restraints: 1974 Sorted by residual: chirality pdb=" CB ILE B 344 " pdb=" CA ILE B 344 " pdb=" CG1 ILE B 344 " pdb=" CG2 ILE B 344 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA PRO A 303 " pdb=" N PRO A 303 " pdb=" C PRO A 303 " pdb=" CB PRO A 303 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA ILE A 344 " pdb=" N ILE A 344 " pdb=" C ILE A 344 " pdb=" CB ILE A 344 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 1971 not shown) Planarity restraints: 2232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 380 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO C 381 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 381 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 381 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 518 " -0.179 9.50e-02 1.11e+02 8.07e-02 5.00e+00 pdb=" NE ARG B 518 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 518 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 518 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 518 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 439 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" CD GLU B 439 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU B 439 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 439 " -0.012 2.00e-02 2.50e+03 ... (remaining 2229 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 4112 2.86 - 3.37: 10564 3.37 - 3.88: 19434 3.88 - 4.39: 20611 4.39 - 4.90: 37931 Nonbonded interactions: 92652 Sorted by model distance: nonbonded pdb=" N GLU D 407 " pdb=" OE1 GLU D 407 " model vdw 2.344 3.120 nonbonded pdb=" OG SER D 312 " pdb=" OG SER D 330 " model vdw 2.360 3.040 nonbonded pdb=" N GLU B 519 " pdb=" OE1 GLU B 519 " model vdw 2.369 3.120 nonbonded pdb=" NH2 ARG C 498 " pdb=" OD2 ASP C 528 " model vdw 2.388 3.120 nonbonded pdb=" CA GLY A 341 " pdb=" CD1 ILE A 344 " model vdw 2.394 3.860 ... (remaining 92647 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 78 through 505 or (resid 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 601)) selection = (chain 'D' and (resid 78 through 505 or (resid 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.170 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 12624 Z= 0.208 Angle : 0.767 12.205 17102 Z= 0.402 Chirality : 0.048 0.278 1974 Planarity : 0.007 0.081 2232 Dihedral : 19.744 87.046 4810 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 33.88 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1616 helix: 0.68 (0.17), residues: 752 sheet: 1.91 (0.31), residues: 308 loop : -1.69 (0.23), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 518 TYR 0.018 0.002 TYR C 487 PHE 0.020 0.002 PHE D 274 TRP 0.011 0.001 TRP C 525 HIS 0.006 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 (12624) covalent geometry : angle 0.76710 / 0.40 (17102) hydrogen bonds : bond 0.18079 / 12.76 ( 568) hydrogen bonds : angle 5.48205 / 3.87 ( 1671) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 348 LYS cc_start: 0.8355 (mttt) cc_final: 0.8153 (mtmt) REVERT: B 287 PHE cc_start: 0.8276 (t80) cc_final: 0.8046 (t80) REVERT: C 359 ARG cc_start: 0.7349 (mtm180) cc_final: 0.6977 (mtm180) REVERT: C 407 GLU cc_start: 0.7838 (mp0) cc_final: 0.7617 (mp0) REVERT: C 440 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7044 (mp0) outliers start: 0 outliers final: 1 residues processed: 338 average time/residue: 0.8040 time to fit residues: 288.2751 Evaluate side-chains 327 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN B 505 GLN C 113 ASN C 361 ASN C 505 GLN D 113 ASN D 361 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.140525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.119471 restraints weight = 15961.116| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.09 r_work: 0.3444 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12624 Z= 0.142 Angle : 0.539 6.026 17102 Z= 0.275 Chirality : 0.045 0.187 1974 Planarity : 0.004 0.038 2232 Dihedral : 9.112 89.714 1910 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.40 % Allowed : 28.76 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1616 helix: 1.86 (0.19), residues: 760 sheet: 1.84 (0.30), residues: 308 loop : -1.46 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 518 TYR 0.011 0.001 TYR C 487 PHE 0.009 0.001 PHE B 535 TRP 0.007 0.001 TRP C 525 HIS 0.003 0.001 HIS D 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (12624) covalent geometry : angle 0.53869 / 0.28 (17102) hydrogen bonds : bond 0.05291 / 3.70 ( 568) hydrogen bonds : angle 3.59245 / 2.59 ( 1671) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 349 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.8808 (ttt) cc_final: 0.8541 (ttt) REVERT: B 440 GLU cc_start: 0.7682 (mp0) cc_final: 0.7333 (mp0) REVERT: C 359 ARG cc_start: 0.8289 (mtm180) cc_final: 0.7824 (mtm180) REVERT: C 524 ILE cc_start: 0.7987 (mm) cc_final: 0.7607 (mp) REVERT: D 426 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8320 (ttp80) REVERT: D 486 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8232 (ptm160) outliers start: 31 outliers final: 13 residues processed: 360 average time/residue: 0.7843 time to fit residues: 299.6996 Evaluate side-chains 356 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 341 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 538 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [55, 18, 71, 133, 29, 154, 77, 119, 98, 49, 97] chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 10.0000 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 306 HIS A 421 GLN C 113 ASN C 361 ASN C 505 GLN D 113 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.141238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120217 restraints weight = 16131.475| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.10 r_work: 0.3456 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12624 Z= 0.113 Angle : 0.495 5.374 17102 Z= 0.251 Chirality : 0.044 0.170 1974 Planarity : 0.004 0.037 2232 Dihedral : 8.310 82.316 1910 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.49 % Allowed : 28.14 % Favored : 68.37 % 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: 1.54 (0.21), residues: 1616 helix: 2.25 (0.19), residues: 764 sheet: 1.63 (0.30), residues: 316 loop : -1.29 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 531 TYR 0.009 0.001 TYR C 487 PHE 0.008 0.001 PHE D 274 TRP 0.008 0.001 TRP C 525 HIS 0.003 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (12624) covalent geometry : angle 0.49474 / 0.25 (17102) hydrogen bonds : bond 0.04374 / 3.07 ( 568) hydrogen bonds : angle 3.42749 / 2.46 ( 1671) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 VAL cc_start: 0.8139 (t) cc_final: 0.7826 (p) REVERT: A 334 MET cc_start: 0.8805 (ttt) cc_final: 0.8582 (ttt) REVERT: A 355 MET cc_start: 0.7916 (ttp) cc_final: 0.7652 (ttp) REVERT: B 373 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8178 (mmm) REVERT: B 440 GLU cc_start: 0.7749 (mp0) cc_final: 0.7433 (mp0) REVERT: C 376 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8312 (p) REVERT: C 518 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.8254 (mmt180) REVERT: D 139 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: D 426 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8281 (ttp80) REVERT: D 486 ARG cc_start: 0.8445 (ptm-80) cc_final: 0.8222 (ptm160) outliers start: 45 outliers final: 24 residues processed: 362 average time/residue: 0.7424 time to fit residues: 285.9201 Evaluate side-chains 362 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 334 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain D residue 571 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [114, 148, 112, 18, 145, 75, 123, 109, 14, 108, 45] chunk 114 optimal weight: 0.5980 chunk 148 optimal weight: 0.0970 chunk 112 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 421 GLN C 113 ASN C 361 ASN D 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.141991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.120860 restraints weight = 15924.245| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.10 r_work: 0.3467 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12624 Z= 0.096 Angle : 0.471 5.997 17102 Z= 0.238 Chirality : 0.043 0.168 1974 Planarity : 0.003 0.036 2232 Dihedral : 7.784 74.177 1910 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.10 % Allowed : 28.60 % Favored : 68.29 % 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: 1.70 (0.22), residues: 1616 helix: 2.43 (0.19), residues: 764 sheet: 1.62 (0.30), residues: 316 loop : -1.20 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 531 TYR 0.008 0.001 TYR B 126 PHE 0.007 0.001 PHE D 274 TRP 0.008 0.001 TRP C 525 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (12624) covalent geometry : angle 0.47139 / 0.24 (17102) hydrogen bonds : bond 0.03709 / 2.60 ( 568) hydrogen bonds : angle 3.32983 / 2.39 ( 1671) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 337 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8293 (ttpp) REVERT: A 329 VAL cc_start: 0.8070 (t) cc_final: 0.7773 (p) REVERT: A 334 MET cc_start: 0.8806 (ttt) cc_final: 0.8605 (ttt) REVERT: A 440 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7523 (mt-10) REVERT: B 99 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7710 (mtp-110) REVERT: B 139 GLU cc_start: 0.8039 (tp30) cc_final: 0.7820 (tp30) REVERT: B 373 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8164 (mmm) REVERT: B 440 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: C 376 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8313 (p) REVERT: D 139 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: D 426 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8251 (ttp80) REVERT: D 486 ARG cc_start: 0.8451 (ptm-80) cc_final: 0.8226 (ptm160) outliers start: 40 outliers final: 23 residues processed: 356 average time/residue: 0.7578 time to fit residues: 286.8079 Evaluate side-chains 357 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 328 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 397 ASP Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain D residue 571 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [71, 159, 29, 156, 93, 48, 58, 30, 26, 32, 144] chunk 71 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 421 GLN B 412 ASN C 113 ASN C 361 ASN D 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.138260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117098 restraints weight = 16013.917| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.10 r_work: 0.3408 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12624 Z= 0.197 Angle : 0.564 6.843 17102 Z= 0.289 Chirality : 0.046 0.192 1974 Planarity : 0.004 0.047 2232 Dihedral : 8.102 74.241 1908 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.10 % Allowed : 28.29 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.21), residues: 1616 helix: 2.55 (0.19), residues: 736 sheet: 1.54 (0.29), residues: 328 loop : -1.46 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 531 TYR 0.014 0.002 TYR A 564 PHE 0.009 0.002 PHE B 535 TRP 0.006 0.001 TRP D 558 HIS 0.004 0.001 HIS D 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.20 (12624) covalent geometry : angle 0.56423 / 0.29 (17102) hydrogen bonds : bond 0.06243 / 4.39 ( 568) hydrogen bonds : angle 3.53789 / 2.55 ( 1671) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 346 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8778 (m-80) cc_final: 0.8354 (m-80) REVERT: A 158 LYS cc_start: 0.8619 (ttpp) cc_final: 0.8363 (ttpp) REVERT: A 329 VAL cc_start: 0.8260 (t) cc_final: 0.7962 (p) REVERT: A 335 VAL cc_start: 0.8555 (m) cc_final: 0.8354 (t) REVERT: A 355 MET cc_start: 0.7973 (ttp) cc_final: 0.7625 (ttp) REVERT: A 359 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7891 (mtm-85) REVERT: A 440 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7452 (mt-10) REVERT: B 99 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7617 (mtp-110) REVERT: B 139 GLU cc_start: 0.8124 (tp30) cc_final: 0.7867 (tp30) REVERT: B 373 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8317 (mmm) REVERT: B 421 GLN cc_start: 0.8759 (mt0) cc_final: 0.8450 (mt0) REVERT: B 440 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: B 528 ASP cc_start: 0.8147 (t0) cc_final: 0.7865 (t70) REVERT: C 330 SER cc_start: 0.7692 (OUTLIER) cc_final: 0.7411 (p) REVERT: C 359 ARG cc_start: 0.8308 (mtm180) cc_final: 0.8037 (mtm180) REVERT: C 376 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8293 (p) REVERT: D 139 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: D 426 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8321 (ttp80) REVERT: D 486 ARG cc_start: 0.8477 (ptm-80) cc_final: 0.8259 (ptm160) outliers start: 40 outliers final: 22 residues processed: 365 average time/residue: 0.7529 time to fit residues: 292.1608 Evaluate side-chains 372 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 342 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain D residue 571 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [145, 92, 77, 158, 65, 47, 133, 26, 152, 118, 78] chunk 145 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 152 optimal weight: 0.0370 chunk 118 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 421 GLN C 113 ASN C 361 ASN D 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.140329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.119248 restraints weight = 15941.794| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.10 r_work: 0.3446 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12624 Z= 0.115 Angle : 0.500 7.183 17102 Z= 0.254 Chirality : 0.043 0.168 1974 Planarity : 0.004 0.043 2232 Dihedral : 6.650 73.484 1908 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.33 % Allowed : 28.14 % Favored : 68.53 % 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: 1.67 (0.21), residues: 1616 helix: 2.61 (0.19), residues: 740 sheet: 1.37 (0.28), residues: 336 loop : -1.34 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 531 TYR 0.008 0.001 TYR C 126 PHE 0.008 0.001 PHE B 535 TRP 0.007 0.001 TRP C 525 HIS 0.003 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (12624) covalent geometry : angle 0.49976 / 0.25 (17102) hydrogen bonds : bond 0.04249 / 2.98 ( 568) hydrogen bonds : angle 3.41602 / 2.45 ( 1671) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 341 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8355 (ttpp) REVERT: A 316 ASN cc_start: 0.7113 (OUTLIER) cc_final: 0.6856 (p0) REVERT: A 329 VAL cc_start: 0.8183 (t) cc_final: 0.7878 (p) REVERT: A 344 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7100 (mt) REVERT: A 440 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7408 (mt-10) REVERT: B 99 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7611 (mtp-110) REVERT: B 139 GLU cc_start: 0.8105 (tp30) cc_final: 0.7824 (tp30) REVERT: B 373 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8291 (mmm) REVERT: B 440 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: B 453 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7148 (tm-30) REVERT: B 528 ASP cc_start: 0.8113 (t0) cc_final: 0.7850 (t70) REVERT: C 330 SER cc_start: 0.7606 (OUTLIER) cc_final: 0.7341 (p) REVERT: C 359 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8035 (mtm180) REVERT: C 376 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8309 (p) REVERT: C 518 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8325 (mtt180) REVERT: D 139 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: D 486 ARG cc_start: 0.8464 (ptm-80) cc_final: 0.8240 (ptm160) outliers start: 43 outliers final: 25 residues processed: 364 average time/residue: 0.7386 time to fit residues: 286.2508 Evaluate side-chains 371 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 337 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 571 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [100, 58, 96, 68, 141, 13, 140, 148, 19, 107, 53] chunk 100 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 118 ASN B 412 ASN C 113 ASN C 361 ASN D 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117301 restraints weight = 15887.284| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.10 r_work: 0.3411 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12624 Z= 0.177 Angle : 0.551 8.036 17102 Z= 0.282 Chirality : 0.046 0.181 1974 Planarity : 0.004 0.049 2232 Dihedral : 7.024 73.499 1908 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.57 % Allowed : 27.98 % Favored : 68.45 % 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: 1.53 (0.21), residues: 1616 helix: 2.54 (0.19), residues: 736 sheet: 1.31 (0.28), residues: 336 loop : -1.45 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 531 TYR 0.012 0.002 TYR A 564 PHE 0.009 0.001 PHE B 535 TRP 0.006 0.001 TRP A 558 HIS 0.004 0.001 HIS D 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (12624) covalent geometry : angle 0.55091 / 0.28 (17102) hydrogen bonds : bond 0.05803 / 4.08 ( 568) hydrogen bonds : angle 3.51007 / 2.52 ( 1671) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 356 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8811 (m-80) cc_final: 0.8433 (m-80) REVERT: A 158 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8381 (ttpp) REVERT: A 316 ASN cc_start: 0.7205 (OUTLIER) cc_final: 0.6975 (p0) REVERT: A 329 VAL cc_start: 0.8282 (t) cc_final: 0.7987 (p) REVERT: A 344 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7143 (mt) REVERT: A 373 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8289 (mmm) REVERT: A 387 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: A 407 GLU cc_start: 0.7907 (mp0) cc_final: 0.7500 (mp0) REVERT: A 439 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 440 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 139 GLU cc_start: 0.8156 (tp30) cc_final: 0.7870 (tp30) REVERT: B 373 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: B 440 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: B 453 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: B 528 ASP cc_start: 0.8141 (t0) cc_final: 0.7872 (t70) REVERT: C 359 ARG cc_start: 0.8313 (mtm180) cc_final: 0.8086 (mtm180) REVERT: C 373 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8384 (mmm) REVERT: C 376 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8300 (p) REVERT: C 518 ARG cc_start: 0.8554 (mtt-85) cc_final: 0.8340 (mtt180) REVERT: D 139 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: D 426 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8146 (ttp80) REVERT: D 486 ARG cc_start: 0.8462 (ptm-80) cc_final: 0.8247 (ptm160) outliers start: 46 outliers final: 23 residues processed: 379 average time/residue: 0.7400 time to fit residues: 298.5549 Evaluate side-chains 382 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 349 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 571 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [45, 16, 121, 152, 83, 50, 113, 157, 58, 25, 130] chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 152 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 118 ASN A 421 GLN B 118 ASN C 113 ASN C 361 ASN C 412 ASN D 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.139856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118703 restraints weight = 15938.570| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.11 r_work: 0.3436 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12624 Z= 0.123 Angle : 0.514 8.721 17102 Z= 0.262 Chirality : 0.044 0.170 1974 Planarity : 0.004 0.044 2232 Dihedral : 6.571 72.557 1908 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.26 % Allowed : 28.76 % Favored : 67.98 % 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: 1.64 (0.21), residues: 1616 helix: 2.64 (0.19), residues: 736 sheet: 1.30 (0.28), residues: 336 loop : -1.36 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 531 TYR 0.011 0.001 TYR C 517 PHE 0.008 0.001 PHE B 535 TRP 0.007 0.001 TRP C 525 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 (12624) covalent geometry : angle 0.51448 / 0.26 (17102) hydrogen bonds : bond 0.04481 / 3.15 ( 568) hydrogen bonds : angle 3.43054 / 2.46 ( 1671) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 341 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8370 (ttpp) REVERT: A 316 ASN cc_start: 0.7122 (OUTLIER) cc_final: 0.6872 (p0) REVERT: A 329 VAL cc_start: 0.8230 (t) cc_final: 0.7934 (p) REVERT: A 359 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7907 (mtm-85) REVERT: A 373 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8244 (mmm) REVERT: A 387 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: A 407 GLU cc_start: 0.7880 (mp0) cc_final: 0.7477 (mp0) REVERT: A 439 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 440 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7409 (mt-10) REVERT: B 139 GLU cc_start: 0.8123 (tp30) cc_final: 0.7821 (tp30) REVERT: B 373 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8305 (mmm) REVERT: B 440 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: B 453 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7154 (tm-30) REVERT: B 528 ASP cc_start: 0.8129 (t0) cc_final: 0.7852 (t70) REVERT: C 334 MET cc_start: 0.8582 (ttt) cc_final: 0.8296 (ttt) REVERT: C 359 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8019 (mtm180) REVERT: C 373 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8333 (mmm) REVERT: C 376 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8296 (p) REVERT: D 139 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: D 426 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8095 (ttp80) REVERT: D 486 ARG cc_start: 0.8471 (ptm-80) cc_final: 0.8250 (ptm160) outliers start: 42 outliers final: 23 residues processed: 359 average time/residue: 0.7422 time to fit residues: 283.2993 Evaluate side-chains 372 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 340 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 571 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [46, 111, 81, 154, 0, 45, 62, 131, 139, 27, 118] chunk 46 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 154 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 118 ASN A 353 GLN B 412 ASN C 113 ASN C 361 ASN D 113 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116403 restraints weight = 15911.333| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.07 r_work: 0.3409 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12624 Z= 0.166 Angle : 0.557 9.514 17102 Z= 0.285 Chirality : 0.045 0.176 1974 Planarity : 0.004 0.037 2232 Dihedral : 6.869 72.678 1908 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.56 % Allowed : 29.30 % Favored : 68.14 % 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: 1.53 (0.21), residues: 1616 helix: 2.55 (0.19), residues: 736 sheet: 1.28 (0.28), residues: 336 loop : -1.44 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 531 TYR 0.012 0.002 TYR C 517 PHE 0.010 0.001 PHE B 535 TRP 0.006 0.001 TRP A 558 HIS 0.003 0.001 HIS D 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (12624) covalent geometry : angle 0.55686 / 0.28 (17102) hydrogen bonds : bond 0.05551 / 3.90 ( 568) hydrogen bonds : angle 3.49803 / 2.51 ( 1671) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 348 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8800 (m-80) cc_final: 0.8423 (m-80) REVERT: A 158 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8391 (ttpp) REVERT: A 316 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6951 (p0) REVERT: A 329 VAL cc_start: 0.8319 (t) cc_final: 0.8030 (p) REVERT: A 359 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.8016 (mtm-85) REVERT: A 373 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8298 (mmm) REVERT: A 440 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 139 GLU cc_start: 0.8137 (tp30) cc_final: 0.7856 (tp30) REVERT: B 373 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8302 (mmm) REVERT: B 440 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: B 453 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: B 528 ASP cc_start: 0.8141 (t0) cc_final: 0.7874 (t70) REVERT: C 334 MET cc_start: 0.8590 (ttt) cc_final: 0.8304 (ttt) REVERT: C 359 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8068 (mtm180) REVERT: C 376 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8326 (p) REVERT: D 139 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: D 426 ARG cc_start: 0.8389 (ttm110) cc_final: 0.8108 (ttp80) REVERT: D 486 ARG cc_start: 0.8456 (ptm-80) cc_final: 0.8236 (ptm160) outliers start: 33 outliers final: 24 residues processed: 362 average time/residue: 0.7502 time to fit residues: 288.8472 Evaluate side-chains 378 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 346 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 571 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [130, 71, 159, 11, 93, 152, 66, 147, 156, 155, 73] chunk 130 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 353 GLN A 421 GLN B 118 ASN B 412 ASN C 113 ASN C 361 ASN D 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117840 restraints weight = 16036.105| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.08 r_work: 0.3443 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12624 Z= 0.123 Angle : 0.531 9.590 17102 Z= 0.268 Chirality : 0.044 0.170 1974 Planarity : 0.004 0.038 2232 Dihedral : 6.488 70.899 1908 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.71 % Allowed : 29.46 % Favored : 67.83 % 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: 1.64 (0.21), residues: 1616 helix: 2.64 (0.19), residues: 736 sheet: 1.30 (0.28), residues: 336 loop : -1.35 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 385 TYR 0.012 0.001 TYR C 517 PHE 0.009 0.001 PHE B 535 TRP 0.007 0.001 TRP C 525 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 (12624) covalent geometry : angle 0.53080 / 0.27 (17102) hydrogen bonds : bond 0.04362 / 3.06 ( 568) hydrogen bonds : angle 3.43424 / 2.46 ( 1671) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 340 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8375 (ttpp) REVERT: A 316 ASN cc_start: 0.7076 (OUTLIER) cc_final: 0.6825 (p0) REVERT: A 329 VAL cc_start: 0.8252 (t) cc_final: 0.7961 (p) REVERT: A 359 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: A 373 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8262 (mmm) REVERT: A 387 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: A 439 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 440 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7388 (mt-10) REVERT: B 139 GLU cc_start: 0.8118 (tp30) cc_final: 0.7826 (tp30) REVERT: B 373 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8298 (mmm) REVERT: B 440 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: B 453 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: B 528 ASP cc_start: 0.8114 (t0) cc_final: 0.7827 (t70) REVERT: B 539 SER cc_start: 0.8428 (t) cc_final: 0.8168 (m) REVERT: C 334 MET cc_start: 0.8584 (ttt) cc_final: 0.8290 (ttt) REVERT: C 376 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8263 (p) REVERT: D 139 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: D 426 ARG cc_start: 0.8333 (ttm110) cc_final: 0.8066 (ttp80) REVERT: D 486 ARG cc_start: 0.8468 (ptm-80) cc_final: 0.8245 (ptm160) outliers start: 35 outliers final: 24 residues processed: 354 average time/residue: 0.7575 time to fit residues: 285.1041 Evaluate side-chains 370 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 338 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 571 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [28, 81, 149, 97, 143, 108, 25, 88, 76, 133, 130] chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 97 optimal weight: 0.0040 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 118 ASN A 421 GLN B 118 ASN B 412 ASN C 113 ASN C 361 ASN D 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120156 restraints weight = 15929.025| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.12 r_work: 0.3454 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12624 Z= 0.101 Angle : 0.514 10.148 17102 Z= 0.258 Chirality : 0.043 0.167 1974 Planarity : 0.004 0.037 2232 Dihedral : 6.178 67.743 1908 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.56 % Allowed : 29.69 % Favored : 67.75 % 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: 1.75 (0.21), residues: 1616 helix: 2.68 (0.19), residues: 740 sheet: 1.38 (0.28), residues: 336 loop : -1.28 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 486 TYR 0.012 0.001 TYR C 517 PHE 0.008 0.001 PHE B 535 TRP 0.008 0.001 TRP C 525 HIS 0.003 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (12624) covalent geometry : angle 0.51366 / 0.26 (17102) hydrogen bonds : bond 0.03741 / 2.63 ( 568) hydrogen bonds : angle 3.38720 / 2.42 ( 1671) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5996.81 seconds wall clock time: 102 minutes 15.44 seconds (6135.44 seconds total)