Starting phenix.real_space_refine on Sat Jul 4 09:48:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xem_33156/07_2026/7xem_33156.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xem_33156/07_2026/7xem_33156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xem_33156/07_2026/7xem_33156.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xem_33156/07_2026/7xem_33156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xem_33156/07_2026/7xem_33156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xem_33156/07_2026/7xem_33156.map" model { file = "/net/cci-nas-00/data/ceres_data/7xem_33156/07_2026/7xem_33156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xem_33156/07_2026/7xem_33156.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 13172 2.51 5 N 3372 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20096 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.70, per 1000 atoms: 0.23 Number of scatterers: 20096 At special positions: 0 Unit cell: (153.114, 153.114, 116.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3444 8.00 N 3372 7.00 C 13172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 755.4 milliseconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 62.1% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.555A pdb=" N ARG A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.872A pdb=" N THR A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.506A pdb=" N ARG A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.516A pdb=" N LEU A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.529A pdb=" N VAL A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 255 through 277 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.780A pdb=" N ARG A 366 " --> pdb=" O HIS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 384 removed outlier: 3.535A pdb=" N GLN A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 408 Processing helix chain 'A' and resid 424 through 454 Processing helix chain 'A' and resid 456 through 461 removed outlier: 4.003A pdb=" N ILE A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 removed outlier: 3.986A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 4.174A pdb=" N LEU A 495 " --> pdb=" O TRP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 512 removed outlier: 4.243A pdb=" N ARG A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 531 removed outlier: 3.506A pdb=" N GLY A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 553 removed outlier: 3.934A pdb=" N VAL A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 601 Processing helix chain 'A' and resid 613 through 629 Processing helix chain 'A' and resid 631 through 647 Processing helix chain 'A' and resid 647 through 668 removed outlier: 4.292A pdb=" N TRP A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 removed outlier: 3.568A pdb=" N THR A 713 " --> pdb=" O TRP A 710 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 714 " --> pdb=" O GLU A 711 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 710 through 714' Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.555A pdb=" N ARG B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.872A pdb=" N THR B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.506A pdb=" N ARG B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 97 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 130 through 142 removed outlier: 3.516A pdb=" N LEU B 134 " --> pdb=" O CYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.529A pdb=" N VAL B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.780A pdb=" N ARG B 366 " --> pdb=" O HIS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 384 removed outlier: 3.535A pdb=" N GLN B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 408 Processing helix chain 'B' and resid 424 through 454 Processing helix chain 'B' and resid 456 through 461 removed outlier: 4.003A pdb=" N ILE B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 487 removed outlier: 3.986A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 506 removed outlier: 4.173A pdb=" N LEU B 495 " --> pdb=" O TRP B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 512 removed outlier: 4.243A pdb=" N ARG B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 531 removed outlier: 3.506A pdb=" N GLY B 518 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.934A pdb=" N VAL B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 601 Processing helix chain 'B' and resid 613 through 629 Processing helix chain 'B' and resid 631 through 647 Processing helix chain 'B' and resid 647 through 668 removed outlier: 4.291A pdb=" N TRP B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER B 653 " --> pdb=" O THR B 649 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 714 removed outlier: 3.567A pdb=" N THR B 713 " --> pdb=" O TRP B 710 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 714 " --> pdb=" O GLU B 711 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 710 through 714' Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.555A pdb=" N ARG C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.873A pdb=" N THR C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 removed outlier: 3.507A pdb=" N ARG C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 130 through 142 removed outlier: 3.516A pdb=" N LEU C 134 " --> pdb=" O CYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 171 through 181 removed outlier: 3.529A pdb=" N VAL C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 255 through 277 Processing helix chain 'C' and resid 292 through 300 Processing helix chain 'C' and resid 303 through 311 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.780A pdb=" N ARG C 366 " --> pdb=" O HIS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 384 removed outlier: 3.536A pdb=" N GLN C 378 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 408 Processing helix chain 'C' and resid 424 through 454 Processing helix chain 'C' and resid 456 through 461 removed outlier: 4.003A pdb=" N ILE C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 487 removed outlier: 3.986A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 506 removed outlier: 4.173A pdb=" N LEU C 495 " --> pdb=" O TRP C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 512 removed outlier: 4.244A pdb=" N ARG C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 531 removed outlier: 3.506A pdb=" N GLY C 518 " --> pdb=" O PHE C 514 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 553 removed outlier: 3.934A pdb=" N VAL C 548 " --> pdb=" O PHE C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 601 Processing helix chain 'C' and resid 613 through 629 Processing helix chain 'C' and resid 631 through 647 Processing helix chain 'C' and resid 647 through 668 removed outlier: 4.291A pdb=" N TRP C 652 " --> pdb=" O ALA C 648 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER C 653 " --> pdb=" O THR C 649 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 714 removed outlier: 3.569A pdb=" N THR C 713 " --> pdb=" O TRP C 710 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU C 714 " --> pdb=" O GLU C 711 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 710 through 714' Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.554A pdb=" N ARG D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.872A pdb=" N THR D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 removed outlier: 3.507A pdb=" N ARG D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 97 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.517A pdb=" N LEU D 134 " --> pdb=" O CYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.529A pdb=" N VAL D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 255 through 277 Processing helix chain 'D' and resid 292 through 300 Processing helix chain 'D' and resid 303 through 311 Processing helix chain 'D' and resid 350 through 358 Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.780A pdb=" N ARG D 366 " --> pdb=" O HIS D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 384 removed outlier: 3.535A pdb=" N GLN D 378 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 408 Processing helix chain 'D' and resid 424 through 454 Processing helix chain 'D' and resid 456 through 461 removed outlier: 4.003A pdb=" N ILE D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 487 removed outlier: 3.987A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 506 removed outlier: 4.174A pdb=" N LEU D 495 " --> pdb=" O TRP D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 512 removed outlier: 4.243A pdb=" N ARG D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 531 removed outlier: 3.506A pdb=" N GLY D 518 " --> pdb=" O PHE D 514 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE D 519 " --> pdb=" O GLN D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 553 removed outlier: 3.933A pdb=" N VAL D 548 " --> pdb=" O PHE D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 601 Processing helix chain 'D' and resid 613 through 629 Processing helix chain 'D' and resid 631 through 647 Processing helix chain 'D' and resid 647 through 668 removed outlier: 4.291A pdb=" N TRP D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER D 653 " --> pdb=" O THR D 649 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 714 removed outlier: 3.568A pdb=" N THR D 713 " --> pdb=" O TRP D 710 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 714 " --> pdb=" O GLU D 711 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 710 through 714' Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 326 removed outlier: 7.289A pdb=" N ASP A 695 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A 686 " --> pdb=" O ASP A 695 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG A 697 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 684 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 324 through 326 removed outlier: 7.289A pdb=" N ASP B 695 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 686 " --> pdb=" O ASP B 695 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG B 697 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 684 " --> pdb=" O ARG B 697 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.290A pdb=" N ASP C 695 " --> pdb=" O VAL C 686 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL C 686 " --> pdb=" O ASP C 695 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG C 697 " --> pdb=" O LEU C 684 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 684 " --> pdb=" O ARG C 697 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 324 through 326 removed outlier: 7.290A pdb=" N ASP D 695 " --> pdb=" O VAL D 686 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL D 686 " --> pdb=" O ASP D 695 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG D 697 " --> pdb=" O LEU D 684 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 684 " --> pdb=" O ARG D 697 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 3012 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: 3.23 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6166 1.34 - 1.46: 3301 1.46 - 1.57: 10981 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 20608 Sorted by residual: bond pdb=" C13 CLR B1001 " pdb=" C17 CLR B1001 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C13 CLR D1001 " pdb=" C17 CLR D1001 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C13 CLR C1001 " pdb=" C17 CLR C1001 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C13 CLR A1001 " pdb=" C17 CLR A1001 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" CG1 ILE D 436 " pdb=" CD1 ILE D 436 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.66e+00 ... (remaining 20603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 27290 2.01 - 4.02: 550 4.02 - 6.03: 112 6.03 - 8.04: 24 8.04 - 10.06: 12 Bond angle restraints: 27988 Sorted by residual: angle pdb=" N PHE C 467 " pdb=" CA PHE C 467 " pdb=" C PHE C 467 " ideal model delta sigma weight residual 114.75 107.03 7.72 1.26e+00 6.30e-01 3.76e+01 angle pdb=" N PHE B 467 " pdb=" CA PHE B 467 " pdb=" C PHE B 467 " ideal model delta sigma weight residual 114.75 107.03 7.72 1.26e+00 6.30e-01 3.75e+01 angle pdb=" N PHE D 467 " pdb=" CA PHE D 467 " pdb=" C PHE D 467 " ideal model delta sigma weight residual 114.75 107.05 7.70 1.26e+00 6.30e-01 3.74e+01 angle pdb=" N PHE A 467 " pdb=" CA PHE A 467 " pdb=" C PHE A 467 " ideal model delta sigma weight residual 114.75 107.08 7.67 1.26e+00 6.30e-01 3.71e+01 angle pdb=" N ASN A 143 " pdb=" CA ASN A 143 " pdb=" C ASN A 143 " ideal model delta sigma weight residual 110.24 102.34 7.90 1.46e+00 4.69e-01 2.93e+01 ... (remaining 27983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.71: 10794 18.71 - 37.42: 978 37.42 - 56.13: 224 56.13 - 74.84: 44 74.84 - 93.55: 20 Dihedral angle restraints: 12060 sinusoidal: 4892 harmonic: 7168 Sorted by residual: dihedral pdb=" CA LEU B 631 " pdb=" C LEU B 631 " pdb=" N LEU B 632 " pdb=" CA LEU B 632 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LEU A 631 " pdb=" C LEU A 631 " pdb=" N LEU A 632 " pdb=" CA LEU A 632 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LEU C 631 " pdb=" C LEU C 631 " pdb=" N LEU C 632 " pdb=" CA LEU C 632 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 12057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2829 0.067 - 0.134: 296 0.134 - 0.201: 27 0.201 - 0.269: 8 0.269 - 0.336: 12 Chirality restraints: 3172 Sorted by residual: chirality pdb=" CA TYR C 466 " pdb=" N TYR C 466 " pdb=" C TYR C 466 " pdb=" CB TYR C 466 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA TYR D 466 " pdb=" N TYR D 466 " pdb=" C TYR D 466 " pdb=" CB TYR D 466 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA TYR A 466 " pdb=" N TYR A 466 " pdb=" C TYR A 466 " pdb=" CB TYR A 466 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 3169 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 465 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C SER B 465 " -0.034 2.00e-02 2.50e+03 pdb=" O SER B 465 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR B 466 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 465 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C SER D 465 " 0.034 2.00e-02 2.50e+03 pdb=" O SER D 465 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR D 466 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 465 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C SER A 465 " 0.034 2.00e-02 2.50e+03 pdb=" O SER A 465 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR A 466 " -0.011 2.00e-02 2.50e+03 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6459 2.84 - 3.35: 19485 3.35 - 3.87: 32679 3.87 - 4.38: 36011 4.38 - 4.90: 62760 Nonbonded interactions: 157394 Sorted by model distance: nonbonded pdb=" NZ LYS B 299 " pdb=" OE2 GLU B 300 " model vdw 2.324 3.120 nonbonded pdb=" NZ LYS A 299 " pdb=" OE2 GLU A 300 " model vdw 2.325 3.120 nonbonded pdb=" NZ LYS D 299 " pdb=" OE2 GLU D 300 " model vdw 2.325 3.120 nonbonded pdb=" NZ LYS C 299 " pdb=" OE2 GLU C 300 " model vdw 2.325 3.120 nonbonded pdb=" O PHE C 76 " pdb=" OG SER C 80 " model vdw 2.325 3.040 ... (remaining 157389 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.020 Process input model: 18.190 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 0.064 20608 Z= 0.177 Angle : 0.733 10.055 27988 Z= 0.391 Chirality : 0.046 0.336 3172 Planarity : 0.004 0.048 3432 Dihedral : 15.435 93.551 7436 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.59 % Favored : 94.08 % Rotamer: Outliers : 0.74 % Allowed : 0.74 % Favored : 98.53 % 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: -0.39 (0.17), residues: 2432 helix: 1.07 (0.14), residues: 1432 sheet: -1.75 (0.47), residues: 76 loop : -2.34 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 682 TYR 0.010 0.001 TYR D 510 PHE 0.016 0.001 PHE D 462 TRP 0.021 0.001 TRP C 655 HIS 0.003 0.001 HIS D 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (20608) covalent geometry : angle 0.73268 / 0.39 (27988) hydrogen bonds : bond 0.14345 / 10.08 ( 1024) hydrogen bonds : angle 5.42996 / 3.92 ( 3012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 274 time to evaluate : 0.743 Fit side-chains REVERT: B 263 ILE cc_start: 0.8684 (mp) cc_final: 0.8088 (mp) REVERT: B 272 MET cc_start: 0.8022 (tpp) cc_final: 0.7632 (tpp) REVERT: B 684 LEU cc_start: 0.7750 (mm) cc_final: 0.7445 (mm) REVERT: C 272 MET cc_start: 0.8059 (tpp) cc_final: 0.7859 (tpt) REVERT: C 619 LEU cc_start: 0.8785 (mm) cc_final: 0.8577 (mm) REVERT: D 684 LEU cc_start: 0.7778 (mm) cc_final: 0.7469 (mm) outliers start: 16 outliers final: 12 residues processed: 286 average time/residue: 0.1490 time to fit residues: 65.0098 Evaluate side-chains 239 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 370 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 525 GLN B 525 GLN B 658 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 GLN C 658 GLN D 525 GLN D 658 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.195625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131910 restraints weight = 27475.290| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.47 r_work: 0.3379 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20608 Z= 0.117 Angle : 0.584 8.269 27988 Z= 0.287 Chirality : 0.039 0.206 3172 Planarity : 0.004 0.042 3432 Dihedral : 5.832 51.390 2756 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.65 % Allowed : 10.06 % Favored : 88.28 % 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: -0.05 (0.17), residues: 2432 helix: 1.38 (0.14), residues: 1436 sheet: -1.40 (0.48), residues: 76 loop : -2.30 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 682 TYR 0.025 0.001 TYR B 466 PHE 0.008 0.001 PHE D 306 TRP 0.010 0.001 TRP C 328 HIS 0.002 0.000 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (20608) covalent geometry : angle 0.58423 / 0.29 (27988) hydrogen bonds : bond 0.04029 / 2.73 ( 1024) hydrogen bonds : angle 4.10996 / 2.97 ( 3012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.5163 (tmm) cc_final: 0.4702 (mtm) REVERT: A 619 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8420 (mm) REVERT: B 272 MET cc_start: 0.8410 (tpp) cc_final: 0.8187 (mmt) REVERT: B 682 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7200 (ttm-80) REVERT: B 684 LEU cc_start: 0.7834 (mm) cc_final: 0.7578 (mm) REVERT: C 556 GLU cc_start: 0.5821 (tm-30) cc_final: 0.5582 (tm-30) REVERT: C 619 LEU cc_start: 0.8622 (mm) cc_final: 0.8209 (mm) REVERT: D 619 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8458 (mm) REVERT: D 682 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.7198 (ttm-80) REVERT: D 684 LEU cc_start: 0.7891 (mm) cc_final: 0.7628 (mm) outliers start: 36 outliers final: 24 residues processed: 259 average time/residue: 0.1463 time to fit residues: 58.5641 Evaluate side-chains 237 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 619 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 149 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 183 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN A 658 GLN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 GLN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.186473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123835 restraints weight = 27765.241| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.57 r_work: 0.3205 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 20608 Z= 0.324 Angle : 0.758 7.961 27988 Z= 0.377 Chirality : 0.046 0.228 3172 Planarity : 0.005 0.057 3432 Dihedral : 6.077 54.051 2736 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.55 % Favored : 94.28 % Rotamer: Outliers : 3.91 % Allowed : 12.13 % Favored : 83.96 % 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: -0.30 (0.17), residues: 2432 helix: 1.08 (0.14), residues: 1444 sheet: -1.49 (0.48), residues: 76 loop : -2.25 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 555 TYR 0.018 0.002 TYR C 407 PHE 0.015 0.002 PHE A 596 TRP 0.014 0.002 TRP D 655 HIS 0.007 0.002 HIS D 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00784 / 0.32 (20608) covalent geometry : angle 0.75827 / 0.38 (27988) hydrogen bonds : bond 0.06558 / 4.32 ( 1024) hydrogen bonds : angle 4.34966 / 3.13 ( 3012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 224 time to evaluate : 0.755 Fit side-chains REVERT: A 433 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.6730 (t70) REVERT: A 619 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8482 (mm) REVERT: B 433 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.6672 (t70) REVERT: B 619 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8445 (mm) REVERT: C 433 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.6794 (t70) REVERT: C 435 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7897 (mp) REVERT: C 619 LEU cc_start: 0.8820 (mm) cc_final: 0.8397 (mm) REVERT: D 433 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.6701 (t70) REVERT: D 619 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8502 (mm) outliers start: 85 outliers final: 60 residues processed: 285 average time/residue: 0.1529 time to fit residues: 66.8018 Evaluate side-chains 281 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 466 TYR Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 201 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 211 optimal weight: 0.2980 chunk 175 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 225 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 239 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.194431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133125 restraints weight = 27498.238| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.54 r_work: 0.3353 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 20608 Z= 0.111 Angle : 0.555 8.658 27988 Z= 0.272 Chirality : 0.037 0.156 3172 Planarity : 0.004 0.043 3432 Dihedral : 5.729 57.380 2736 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.21 % Allowed : 15.67 % Favored : 82.12 % 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 (0.17), residues: 2432 helix: 1.58 (0.14), residues: 1436 sheet: -1.26 (0.47), residues: 76 loop : -2.21 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 275 TYR 0.021 0.001 TYR D 466 PHE 0.007 0.001 PHE D 598 TRP 0.013 0.001 TRP B 328 HIS 0.003 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (20608) covalent geometry : angle 0.55454 / 0.27 (27988) hydrogen bonds : bond 0.03626 / 2.45 ( 1024) hydrogen bonds : angle 3.81287 / 2.75 ( 3012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 428 MET cc_start: 0.5324 (tmm) cc_final: 0.4800 (mtm) REVERT: A 433 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.6667 (t70) REVERT: A 463 MET cc_start: 0.7958 (mmp) cc_final: 0.7756 (tpp) REVERT: A 619 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8408 (mm) REVERT: B 428 MET cc_start: 0.5394 (tmm) cc_final: 0.4712 (mtm) REVERT: B 433 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.6731 (t70) REVERT: B 463 MET cc_start: 0.7971 (mmp) cc_final: 0.7766 (tpp) REVERT: B 619 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8485 (mm) REVERT: B 682 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7452 (ttm-80) REVERT: B 684 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7871 (mm) REVERT: C 433 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.6779 (t70) REVERT: C 463 MET cc_start: 0.7987 (mmp) cc_final: 0.7759 (tpp) REVERT: C 619 LEU cc_start: 0.8742 (mm) cc_final: 0.8337 (mm) REVERT: D 339 ASP cc_start: 0.8738 (t0) cc_final: 0.8536 (t0) REVERT: D 428 MET cc_start: 0.5456 (tmm) cc_final: 0.4713 (mtm) REVERT: D 433 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.6806 (t70) REVERT: D 463 MET cc_start: 0.8000 (mmp) cc_final: 0.7797 (tpp) REVERT: D 619 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8376 (mm) REVERT: D 682 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7450 (ttm-80) REVERT: D 684 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7878 (mm) outliers start: 48 outliers final: 24 residues processed: 267 average time/residue: 0.1560 time to fit residues: 63.2759 Evaluate side-chains 243 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 684 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 239 optimal weight: 6.9990 chunk 69 optimal weight: 0.0000 chunk 4 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN B 258 ASN C 258 ASN D 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.187266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125796 restraints weight = 27490.894| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.33 r_work: 0.3234 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 20608 Z= 0.259 Angle : 0.690 12.839 27988 Z= 0.337 Chirality : 0.042 0.143 3172 Planarity : 0.005 0.044 3432 Dihedral : 5.713 55.661 2732 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.59 % Favored : 94.24 % Rotamer: Outliers : 4.14 % Allowed : 16.73 % Favored : 79.14 % 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: 0.23 (0.18), residues: 2432 helix: 1.53 (0.14), residues: 1416 sheet: -1.33 (0.47), residues: 76 loop : -1.97 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 682 TYR 0.024 0.002 TYR C 466 PHE 0.017 0.002 PHE B 596 TRP 0.014 0.002 TRP C 655 HIS 0.006 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.26 (20608) covalent geometry : angle 0.69039 / 0.34 (27988) hydrogen bonds : bond 0.05737 / 3.79 ( 1024) hydrogen bonds : angle 4.12792 / 2.98 ( 3012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 218 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 379 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8077 (tp30) REVERT: A 433 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.6726 (t70) REVERT: A 619 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8468 (mm) REVERT: B 379 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8091 (tp30) REVERT: B 433 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6718 (t70) REVERT: B 536 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8608 (mt) REVERT: B 619 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8468 (mm) REVERT: B 640 MET cc_start: 0.9206 (mtt) cc_final: 0.8950 (mtt) REVERT: C 379 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8144 (tp30) REVERT: C 433 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.6744 (t70) REVERT: C 435 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7794 (mp) REVERT: C 619 LEU cc_start: 0.8855 (mm) cc_final: 0.8413 (mm) REVERT: D 433 HIS cc_start: 0.7514 (OUTLIER) cc_final: 0.6671 (t70) REVERT: D 536 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8605 (mt) REVERT: D 619 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8457 (mm) outliers start: 90 outliers final: 68 residues processed: 282 average time/residue: 0.1555 time to fit residues: 67.2432 Evaluate side-chains 292 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 214 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 466 TYR Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 74 optimal weight: 0.7980 chunk 230 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.193150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129820 restraints weight = 27534.522| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.56 r_work: 0.3340 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.002 0.058 20608 Z= 0.106 Angle : 0.561 13.139 27988 Z= 0.271 Chirality : 0.037 0.135 3172 Planarity : 0.004 0.043 3432 Dihedral : 5.594 56.427 2732 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.08 % Allowed : 17.92 % Favored : 79.00 % 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: 0.37 (0.17), residues: 2432 helix: 1.72 (0.14), residues: 1436 sheet: -1.00 (0.47), residues: 76 loop : -2.16 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 275 TYR 0.025 0.001 TYR C 466 PHE 0.006 0.001 PHE D 700 TRP 0.013 0.001 TRP A 328 HIS 0.004 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (20608) covalent geometry : angle 0.56050 / 0.27 (27988) hydrogen bonds : bond 0.03650 / 2.46 ( 1024) hydrogen bonds : angle 3.78392 / 2.73 ( 3012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 219 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.5279 (tmm) cc_final: 0.4694 (mtm) REVERT: A 433 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.6670 (t70) REVERT: A 463 MET cc_start: 0.8017 (mmp) cc_final: 0.7762 (tpp) REVERT: A 619 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8374 (mm) REVERT: B 428 MET cc_start: 0.5301 (tmm) cc_final: 0.4669 (mtm) REVERT: B 433 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.6643 (t70) REVERT: B 463 MET cc_start: 0.7988 (mmp) cc_final: 0.7730 (tpp) REVERT: B 619 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8410 (mm) REVERT: B 702 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8218 (m) REVERT: C 433 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.6844 (t70) REVERT: C 463 MET cc_start: 0.8004 (mmp) cc_final: 0.7755 (tpp) REVERT: C 619 LEU cc_start: 0.8754 (mm) cc_final: 0.8314 (mm) REVERT: D 433 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.6738 (t70) REVERT: D 463 MET cc_start: 0.8027 (mmp) cc_final: 0.7776 (tpp) REVERT: D 619 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8406 (mm) REVERT: D 702 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8237 (m) outliers start: 67 outliers final: 49 residues processed: 270 average time/residue: 0.1487 time to fit residues: 62.2206 Evaluate side-chains 263 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 174 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.193527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130237 restraints weight = 27512.096| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.59 r_work: 0.3340 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 20608 Z= 0.106 Angle : 0.550 13.994 27988 Z= 0.264 Chirality : 0.037 0.134 3172 Planarity : 0.004 0.041 3432 Dihedral : 5.447 55.796 2732 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.22 % Allowed : 18.84 % Favored : 77.94 % 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: 0.53 (0.17), residues: 2432 helix: 1.84 (0.14), residues: 1436 sheet: -0.85 (0.49), residues: 76 loop : -2.07 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 275 TYR 0.027 0.001 TYR D 466 PHE 0.008 0.001 PHE A 596 TRP 0.012 0.001 TRP C 328 HIS 0.004 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (20608) covalent geometry : angle 0.55009 / 0.26 (27988) hydrogen bonds : bond 0.03580 / 2.40 ( 1024) hydrogen bonds : angle 3.69705 / 2.66 ( 3012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 222 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8188 (mt) REVERT: A 428 MET cc_start: 0.5394 (tmm) cc_final: 0.4798 (mtm) REVERT: A 433 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.6676 (t70) REVERT: A 463 MET cc_start: 0.8006 (mmp) cc_final: 0.7769 (tpp) REVERT: A 619 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8337 (mm) REVERT: B 248 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 433 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.6673 (t70) REVERT: B 463 MET cc_start: 0.7970 (mmp) cc_final: 0.7735 (tpp) REVERT: B 619 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8330 (mm) REVERT: B 702 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8186 (m) REVERT: C 433 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.6691 (t70) REVERT: C 463 MET cc_start: 0.7985 (mmp) cc_final: 0.7742 (tpp) REVERT: C 619 LEU cc_start: 0.8770 (mm) cc_final: 0.8329 (mm) REVERT: C 640 MET cc_start: 0.9125 (mtt) cc_final: 0.8901 (mtt) REVERT: C 682 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7488 (ttm-80) REVERT: C 702 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8192 (m) REVERT: D 433 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.6728 (t70) REVERT: D 463 MET cc_start: 0.8026 (mmp) cc_final: 0.7794 (tpp) REVERT: D 619 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8369 (mm) REVERT: D 702 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8213 (m) outliers start: 70 outliers final: 50 residues processed: 279 average time/residue: 0.1453 time to fit residues: 63.7356 Evaluate side-chains 268 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 117 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 chunk 233 optimal weight: 0.7980 chunk 201 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 204 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.191066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126339 restraints weight = 27405.350| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.63 r_work: 0.3287 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20608 Z= 0.152 Angle : 0.592 14.462 27988 Z= 0.286 Chirality : 0.038 0.135 3172 Planarity : 0.004 0.042 3432 Dihedral : 5.456 55.464 2732 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.09 % Allowed : 18.29 % Favored : 77.62 % 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: 0.53 (0.17), residues: 2432 helix: 1.83 (0.14), residues: 1436 sheet: -0.93 (0.49), residues: 76 loop : -2.04 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 275 TYR 0.025 0.001 TYR D 466 PHE 0.012 0.001 PHE B 596 TRP 0.010 0.001 TRP C 328 HIS 0.005 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (20608) covalent geometry : angle 0.59186 / 0.29 (27988) hydrogen bonds : bond 0.04302 / 2.86 ( 1024) hydrogen bonds : angle 3.80192 / 2.74 ( 3012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 206 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.6626 (t70) REVERT: A 463 MET cc_start: 0.7940 (mmp) cc_final: 0.7715 (tpp) REVERT: A 619 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8336 (mm) REVERT: B 433 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.6585 (t70) REVERT: B 463 MET cc_start: 0.7903 (mmp) cc_final: 0.7685 (tpp) REVERT: B 619 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8316 (mm) REVERT: C 433 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.6738 (t70) REVERT: C 463 MET cc_start: 0.7913 (mmp) cc_final: 0.7678 (tpp) REVERT: C 619 LEU cc_start: 0.8752 (mm) cc_final: 0.8312 (mm) REVERT: C 682 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7366 (ttm-80) REVERT: D 433 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.6563 (t70) REVERT: D 463 MET cc_start: 0.7942 (mmp) cc_final: 0.7723 (tpp) REVERT: D 619 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8346 (mm) outliers start: 89 outliers final: 67 residues processed: 280 average time/residue: 0.1342 time to fit residues: 59.7133 Evaluate side-chains 277 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 203 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 102 optimal weight: 0.0980 chunk 63 optimal weight: 0.2980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.193273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128785 restraints weight = 27376.096| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.73 r_work: 0.3320 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20608 Z= 0.117 Angle : 0.572 14.820 27988 Z= 0.276 Chirality : 0.037 0.134 3172 Planarity : 0.004 0.042 3432 Dihedral : 5.476 57.101 2732 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.58 % Allowed : 18.43 % Favored : 77.99 % 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: 0.63 (0.17), residues: 2432 helix: 1.89 (0.14), residues: 1436 sheet: -0.72 (0.49), residues: 76 loop : -2.01 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 275 TYR 0.025 0.001 TYR D 466 PHE 0.007 0.001 PHE A 596 TRP 0.015 0.001 TRP C 655 HIS 0.004 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (20608) covalent geometry : angle 0.57246 / 0.28 (27988) hydrogen bonds : bond 0.03766 / 2.53 ( 1024) hydrogen bonds : angle 3.70941 / 2.67 ( 3012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 204 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.6584 (t70) REVERT: A 619 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8253 (mm) REVERT: B 433 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.6571 (t70) REVERT: B 619 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8321 (mm) REVERT: B 702 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8037 (m) REVERT: C 433 HIS cc_start: 0.7679 (OUTLIER) cc_final: 0.6687 (t70) REVERT: C 619 LEU cc_start: 0.8723 (mm) cc_final: 0.8292 (mm) REVERT: D 433 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.6655 (t70) REVERT: D 619 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8267 (mm) REVERT: D 702 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.8050 (m) outliers start: 78 outliers final: 63 residues processed: 268 average time/residue: 0.1231 time to fit residues: 52.0772 Evaluate side-chains 271 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 199 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 113 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.196221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131941 restraints weight = 27670.648| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.37 r_work: 0.3394 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20608 Z= 0.097 Angle : 0.553 15.460 27988 Z= 0.262 Chirality : 0.036 0.133 3172 Planarity : 0.003 0.040 3432 Dihedral : 5.468 58.215 2732 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.12 % Allowed : 18.66 % Favored : 78.22 % 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: 0.78 (0.17), residues: 2432 helix: 1.99 (0.14), residues: 1436 sheet: -0.44 (0.50), residues: 76 loop : -1.93 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 275 TYR 0.027 0.001 TYR D 466 PHE 0.005 0.001 PHE B 462 TRP 0.017 0.001 TRP C 655 HIS 0.004 0.000 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (20608) covalent geometry : angle 0.55283 / 0.26 (27988) hydrogen bonds : bond 0.03163 / 2.13 ( 1024) hydrogen bonds : angle 3.61363 / 2.59 ( 3012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 428 MET cc_start: 0.5344 (tmm) cc_final: 0.4800 (mtm) REVERT: A 433 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.6755 (t70) REVERT: A 619 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8296 (mm) REVERT: B 248 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8184 (mt) REVERT: B 428 MET cc_start: 0.5399 (tmm) cc_final: 0.4825 (mtm) REVERT: B 433 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.6673 (t70) REVERT: B 619 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8319 (mm) REVERT: B 702 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8225 (m) REVERT: C 248 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8145 (mt) REVERT: C 428 MET cc_start: 0.5317 (ttt) cc_final: 0.5027 (tmm) REVERT: C 619 LEU cc_start: 0.8684 (mm) cc_final: 0.8324 (mm) REVERT: C 702 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8254 (m) REVERT: D 248 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8183 (mt) REVERT: D 428 MET cc_start: 0.5392 (tmm) cc_final: 0.4793 (mtm) REVERT: D 433 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.6793 (t70) REVERT: D 619 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8297 (mm) REVERT: D 702 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8223 (m) outliers start: 68 outliers final: 49 residues processed: 285 average time/residue: 0.1431 time to fit residues: 63.9790 Evaluate side-chains 264 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 202 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 115 optimal weight: 0.3980 chunk 126 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 132 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.192904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129176 restraints weight = 27611.425| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.75 r_work: 0.3309 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20608 Z= 0.138 Angle : 0.584 16.371 27988 Z= 0.279 Chirality : 0.037 0.133 3172 Planarity : 0.004 0.042 3432 Dihedral : 5.448 59.093 2732 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.22 % Allowed : 19.07 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2432 helix: 1.95 (0.14), residues: 1436 sheet: -0.41 (0.51), residues: 76 loop : -1.90 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 275 TYR 0.025 0.001 TYR A 466 PHE 0.010 0.001 PHE C 700 TRP 0.017 0.001 TRP C 655 HIS 0.005 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (20608) covalent geometry : angle 0.58391 / 0.28 (27988) hydrogen bonds : bond 0.04009 / 2.67 ( 1024) hydrogen bonds : angle 3.70743 / 2.66 ( 3012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5819.81 seconds wall clock time: 100 minutes 8.77 seconds (6008.77 seconds total)