Starting phenix.real_space_refine on Sun Aug 24 12:59:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xem_33156/08_2025/7xem_33156.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xem_33156/08_2025/7xem_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xem_33156/08_2025/7xem_33156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xem_33156/08_2025/7xem_33156.map" model { file = "/net/cci-nas-00/data/ceres_data/7xem_33156/08_2025/7xem_33156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xem_33156/08_2025/7xem_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-2.0-5787/lib/python3.9/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: 5.22, per 1000 atoms: 0.26 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: 1.83 Conformation dependent library (CDL) restraints added in 791.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.66 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: 2.63 Time building geometry restraints manager: 2.29 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 - 21.94: 11246 21.94 - 43.88: 886 43.88 - 65.82: 112 65.82 - 87.76: 24 87.76 - 109.70: 16 Dihedral angle restraints: 12284 sinusoidal: 5116 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 12281 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: 0.640 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.120 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 15.956 109.698 7660 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 aren 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 covalent geometry : bond 0.00393 (20608) covalent geometry : angle 0.73268 (27988) hydrogen bonds : bond 0.14345 ( 1024) hydrogen bonds : angle 5.42996 ( 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 : 0.718 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: 0.1358 time to fit residues: 59.7691 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 : 0.745 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4234 r_free = 0.4234 target = 0.195487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.136121 restraints weight = 27541.255| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.64 r_work: 0.3361 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.0963 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= 0.118 Angle : 0.597 8.252 27988 Z= 0.291 Chirality : 0.039 0.197 3172 Planarity : 0.004 0.043 3432 Dihedral : 6.659 57.210 2980 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 1.65 % Allowed : 9.79 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.17), residues: 2432 helix: 1.40 (0.14), residues: 1436 sheet: -1.44 (0.48), residues: 76 loop : -2.27 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 682 TYR 0.023 0.001 TYR B 466 PHE 0.008 0.001 PHE B 598 TRP 0.010 0.001 TRP C 328 HIS 0.002 0.000 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00262 (20608) covalent geometry : angle 0.59688 (27988) hydrogen bonds : bond 0.04083 ( 1024) hydrogen bonds : angle 4.12445 ( 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 267 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 428 MET cc_start: 0.5142 (tmm) cc_final: 0.4728 (mtm) REVERT: A 619 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8355 (mm) REVERT: B 428 MET cc_start: 0.5204 (tmm) cc_final: 0.4705 (mtm) REVERT: B 682 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.7180 (ttm-80) REVERT: B 684 LEU cc_start: 0.7793 (mm) cc_final: 0.7556 (mm) REVERT: C 619 LEU cc_start: 0.8692 (mm) cc_final: 0.8264 (mm) REVERT: D 619 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8333 (mm) REVERT: D 682 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.7225 (ttm-80) REVERT: D 684 LEU cc_start: 0.7864 (mm) cc_final: 0.7611 (mm) outliers start: 36 outliers final: 24 residues processed: 255 average time/residue: 0.1339 time to fit residues: 53.2071 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 : 0.750 ------------------------------------------------------------------------------- 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: 5.9990 chunk 85 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 183 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN A 658 GLN B 525 GLN C 525 GLN D 525 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.187541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124014 restraints weight = 27682.181| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.49 r_work: 0.3222 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 20608 Z= 0.295 Angle : 0.714 8.163 27988 Z= 0.355 Chirality : 0.044 0.209 3172 Planarity : 0.005 0.061 3432 Dihedral : 5.743 50.310 2960 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 3.31 % Allowed : 11.67 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.17), residues: 2432 helix: 1.18 (0.14), residues: 1444 sheet: -1.38 (0.48), residues: 76 loop : -2.24 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 555 TYR 0.016 0.002 TYR C 407 PHE 0.016 0.002 PHE A 596 TRP 0.011 0.002 TRP A 328 HIS 0.006 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00719 (20608) covalent geometry : angle 0.71433 (27988) hydrogen bonds : bond 0.06110 ( 1024) hydrogen bonds : angle 4.26078 ( 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 293 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 221 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 433 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6704 (t70) REVERT: A 619 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8380 (mm) REVERT: B 433 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.6627 (t70) REVERT: B 619 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8368 (mm) REVERT: C 435 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7722 (mp) REVERT: C 619 LEU cc_start: 0.8850 (mm) cc_final: 0.8470 (mm) REVERT: D 619 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8423 (mm) outliers start: 72 outliers final: 56 residues processed: 275 average time/residue: 0.1457 time to fit residues: 61.0503 Evaluate side-chains 270 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 208 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 676 LYS 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 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 435 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 479 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 456 LEU 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: 2.9990 chunk 32 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 211 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 239 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4225 r_free = 0.4225 target = 0.194655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132545 restraints weight = 27511.698| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.51 r_work: 0.3370 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 20608 Z= 0.107 Angle : 0.540 11.893 27988 Z= 0.266 Chirality : 0.037 0.141 3172 Planarity : 0.003 0.043 3432 Dihedral : 5.131 52.508 2960 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.48 % Allowed : 14.61 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.17), residues: 2432 helix: 1.65 (0.14), residues: 1436 sheet: -1.14 (0.48), residues: 76 loop : -2.21 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 682 TYR 0.015 0.001 TYR D 466 PHE 0.006 0.001 PHE B 598 TRP 0.012 0.001 TRP B 328 HIS 0.003 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00236 (20608) covalent geometry : angle 0.53989 (27988) hydrogen bonds : bond 0.03510 ( 1024) hydrogen bonds : angle 3.79972 ( 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 282 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 428 MET cc_start: 0.5303 (tmm) cc_final: 0.4796 (mtm) REVERT: A 433 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.6768 (t70) REVERT: A 619 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8371 (mm) REVERT: B 428 MET cc_start: 0.5410 (tmm) cc_final: 0.4685 (mtm) REVERT: B 433 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.6741 (t70) REVERT: B 619 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8433 (mm) REVERT: B 682 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7396 (ttm-80) REVERT: B 684 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7681 (mm) REVERT: C 433 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.6807 (t70) REVERT: C 619 LEU cc_start: 0.8704 (mm) cc_final: 0.8307 (mm) REVERT: D 428 MET cc_start: 0.5398 (tmm) cc_final: 0.4696 (mtm) REVERT: D 433 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.6832 (t70) REVERT: D 619 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8362 (mm) REVERT: D 682 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7412 (ttm-80) REVERT: D 684 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7694 (mm) outliers start: 54 outliers final: 26 residues processed: 272 average time/residue: 0.1444 time to fit residues: 60.7534 Evaluate side-chains 248 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 611 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 631 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 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 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: 9.9990 chunk 186 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 258 ASN C 258 ASN D 164 HIS D 258 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.189109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125321 restraints weight = 27472.455| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.64 r_work: 0.3242 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20608 Z= 0.220 Angle : 0.643 12.656 27988 Z= 0.314 Chirality : 0.040 0.165 3172 Planarity : 0.004 0.043 3432 Dihedral : 5.306 52.267 2956 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.51 % Favored : 94.33 % Rotamer: Outliers : 3.54 % Allowed : 16.22 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.17), residues: 2432 helix: 1.55 (0.14), residues: 1440 sheet: -1.09 (0.47), residues: 76 loop : -2.12 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 555 TYR 0.012 0.001 TYR C 407 PHE 0.016 0.002 PHE D 596 TRP 0.015 0.001 TRP C 655 HIS 0.006 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00533 (20608) covalent geometry : angle 0.64317 (27988) hydrogen bonds : bond 0.05234 ( 1024) hydrogen bonds : angle 4.02110 ( 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 292 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 215 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 433 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.6590 (t70) REVERT: A 619 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8382 (mm) REVERT: A 640 MET cc_start: 0.9104 (mtt) cc_final: 0.8891 (mtt) REVERT: B 433 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.6576 (t70) REVERT: B 619 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8368 (mm) REVERT: C 433 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.6586 (t70) REVERT: C 435 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7649 (mp) REVERT: C 619 LEU cc_start: 0.8782 (mm) cc_final: 0.8363 (mm) REVERT: D 433 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6473 (t70) REVERT: D 619 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8354 (mm) outliers start: 77 outliers final: 56 residues processed: 270 average time/residue: 0.1540 time to fit residues: 62.8721 Evaluate side-chains 268 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 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 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 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 599 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain B residue 684 LEU 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 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 684 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 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 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 599 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 684 LEU 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: 0.0980 chunk 230 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 153 optimal weight: 0.0040 chunk 50 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 238 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.194781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130773 restraints weight = 27491.432| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.65 r_work: 0.3355 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 20608 Z= 0.101 Angle : 0.546 13.627 27988 Z= 0.264 Chirality : 0.037 0.134 3172 Planarity : 0.003 0.042 3432 Dihedral : 4.962 52.766 2956 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.67 % Allowed : 17.14 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.17), residues: 2432 helix: 1.78 (0.14), residues: 1436 sheet: -0.62 (0.50), residues: 76 loop : -2.12 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 682 TYR 0.012 0.001 TYR A 466 PHE 0.007 0.001 PHE D 700 TRP 0.012 0.001 TRP B 328 HIS 0.003 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00220 (20608) covalent geometry : angle 0.54628 (27988) hydrogen bonds : bond 0.03379 ( 1024) hydrogen bonds : angle 3.70957 ( 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 280 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 379 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7923 (mm-30) REVERT: A 428 MET cc_start: 0.5328 (tmm) cc_final: 0.4739 (mtm) REVERT: A 433 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.6765 (t70) REVERT: A 619 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8290 (mm) REVERT: B 428 MET cc_start: 0.5316 (tmm) cc_final: 0.4634 (mtm) REVERT: B 433 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.6736 (t70) REVERT: B 619 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8368 (mm) REVERT: B 702 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8227 (m) REVERT: C 433 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.6775 (t70) REVERT: C 619 LEU cc_start: 0.8727 (mm) cc_final: 0.8304 (mm) REVERT: C 702 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8198 (m) REVERT: D 379 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7935 (mm-30) REVERT: D 428 MET cc_start: 0.5237 (tmm) cc_final: 0.4549 (mtm) REVERT: D 433 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.6694 (t70) REVERT: D 619 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8334 (mm) outliers start: 58 outliers final: 41 residues processed: 268 average time/residue: 0.1331 time to fit residues: 55.6275 Evaluate side-chains 260 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 265 MET 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 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 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 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 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 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR 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 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 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 686 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 174 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 172 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** D 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.194296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130047 restraints weight = 27558.129| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.69 r_work: 0.3345 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 20608 Z= 0.108 Angle : 0.545 14.164 27988 Z= 0.262 Chirality : 0.037 0.133 3172 Planarity : 0.003 0.041 3432 Dihedral : 4.847 52.247 2956 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.71 % Allowed : 17.69 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.17), residues: 2432 helix: 1.90 (0.14), residues: 1436 sheet: -0.46 (0.50), residues: 76 loop : -2.05 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 682 TYR 0.011 0.001 TYR D 466 PHE 0.008 0.001 PHE D 700 TRP 0.011 0.001 TRP D 328 HIS 0.004 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00246 (20608) covalent geometry : angle 0.54543 (27988) hydrogen bonds : bond 0.03540 ( 1024) hydrogen bonds : angle 3.67585 ( 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 277 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8015 (mt) REVERT: A 428 MET cc_start: 0.5321 (tmm) cc_final: 0.4827 (mtm) REVERT: A 433 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.6613 (t70) REVERT: A 619 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8300 (mm) REVERT: A 702 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8094 (m) REVERT: B 248 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8033 (mt) REVERT: B 433 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6588 (t70) REVERT: B 619 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8214 (mm) REVERT: C 433 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.6678 (t70) REVERT: C 619 LEU cc_start: 0.8710 (mm) cc_final: 0.8303 (mm) REVERT: C 702 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.8047 (m) REVERT: D 428 MET cc_start: 0.5251 (tmm) cc_final: 0.4662 (mtm) REVERT: D 433 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.6566 (t70) REVERT: D 619 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8267 (mm) outliers start: 59 outliers final: 40 residues processed: 261 average time/residue: 0.1425 time to fit residues: 58.2213 Evaluate side-chains 256 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 456 LEU Chi-restraints excluded: chain A residue 467 PHE 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 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 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 686 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 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR 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 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 511 THR Chi-restraints excluded: chain D residue 517 THR 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 686 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: 6.9990 chunk 135 optimal weight: 0.0030 chunk 122 optimal weight: 30.0000 chunk 233 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 50 optimal weight: 0.0370 chunk 204 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 overall best weight: 3.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.190144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124866 restraints weight = 27201.871| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.34 r_work: 0.3307 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20608 Z= 0.181 Angle : 0.612 14.419 27988 Z= 0.296 Chirality : 0.039 0.148 3172 Planarity : 0.004 0.043 3432 Dihedral : 5.069 51.833 2956 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.22 % Allowed : 17.83 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.17), residues: 2432 helix: 1.80 (0.14), residues: 1440 sheet: -0.46 (0.49), residues: 76 loop : -1.97 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 512 TYR 0.010 0.001 TYR C 407 PHE 0.012 0.001 PHE A 596 TRP 0.011 0.001 TRP C 655 HIS 0.006 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00440 (20608) covalent geometry : angle 0.61168 (27988) hydrogen bonds : bond 0.04607 ( 1024) hydrogen bonds : angle 3.81991 ( 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 282 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.6711 (t70) REVERT: A 619 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 640 MET cc_start: 0.9171 (mtt) cc_final: 0.8958 (mtt) REVERT: B 433 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.6610 (t70) REVERT: B 619 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8408 (mm) REVERT: C 433 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.6712 (t70) REVERT: C 619 LEU cc_start: 0.8796 (mm) cc_final: 0.8417 (mm) REVERT: C 640 MET cc_start: 0.9183 (mtt) cc_final: 0.8973 (mtt) REVERT: D 433 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.6560 (t70) REVERT: D 619 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8409 (mm) outliers start: 70 outliers final: 58 residues processed: 271 average time/residue: 0.1440 time to fit residues: 61.4516 Evaluate side-chains 275 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 210 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 631 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 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 686 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 479 VAL 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 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 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 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 chunk 169 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.192496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.128097 restraints weight = 27166.495| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.49 r_work: 0.3332 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20608 Z= 0.123 Angle : 0.570 14.628 27988 Z= 0.275 Chirality : 0.037 0.135 3172 Planarity : 0.003 0.042 3432 Dihedral : 4.969 52.122 2956 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.22 % Allowed : 18.38 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.17), residues: 2432 helix: 1.86 (0.14), residues: 1436 sheet: -0.31 (0.50), residues: 76 loop : -1.96 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 512 TYR 0.011 0.001 TYR A 466 PHE 0.007 0.001 PHE A 596 TRP 0.015 0.001 TRP D 655 HIS 0.004 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00291 (20608) covalent geometry : angle 0.56969 (27988) hydrogen bonds : bond 0.03836 ( 1024) hydrogen bonds : angle 3.71140 ( 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 285 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 215 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7985 (mm-30) REVERT: A 433 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.6782 (t70) REVERT: A 619 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8325 (mm) REVERT: A 702 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8198 (m) REVERT: B 379 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7981 (mm-30) REVERT: B 433 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.6663 (t70) REVERT: B 619 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8375 (mm) REVERT: C 433 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.6688 (t70) REVERT: C 619 LEU cc_start: 0.8765 (mm) cc_final: 0.8329 (mm) REVERT: D 379 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7984 (mm-30) REVERT: D 433 HIS cc_start: 0.7578 (OUTLIER) cc_final: 0.6660 (t70) REVERT: D 619 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8397 (mm) outliers start: 70 outliers final: 55 residues processed: 273 average time/residue: 0.1376 time to fit residues: 58.7207 Evaluate side-chains 271 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 631 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 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 113 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 69 optimal weight: 0.0020 chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 132 optimal weight: 0.0870 chunk 239 optimal weight: 4.9990 chunk 111 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 overall best weight: 0.4366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 525 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.197521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.134278 restraints weight = 27818.368| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.73 r_work: 0.3396 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20608 Z= 0.094 Angle : 0.544 15.057 27988 Z= 0.260 Chirality : 0.036 0.132 3172 Planarity : 0.003 0.041 3432 Dihedral : 4.752 52.023 2956 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.16 % Allowed : 19.35 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.17), residues: 2432 helix: 2.03 (0.14), residues: 1412 sheet: 0.03 (0.51), residues: 76 loop : -1.85 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 682 TYR 0.012 0.001 TYR A 466 PHE 0.006 0.001 PHE C 700 TRP 0.015 0.001 TRP A 655 HIS 0.003 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00203 (20608) covalent geometry : angle 0.54382 (27988) hydrogen bonds : bond 0.02979 ( 1024) hydrogen bonds : angle 3.59902 ( 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 277 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.5273 (tmm) cc_final: 0.4792 (mtm) REVERT: A 433 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.6668 (t70) REVERT: A 619 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 702 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8081 (m) REVERT: B 428 MET cc_start: 0.5314 (tmm) cc_final: 0.4727 (mtm) REVERT: B 433 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6647 (t70) REVERT: B 619 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8256 (mm) REVERT: C 428 MET cc_start: 0.5220 (ttt) cc_final: 0.4967 (tmm) REVERT: C 433 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.6708 (t70) REVERT: C 619 LEU cc_start: 0.8655 (mm) cc_final: 0.8234 (mm) REVERT: D 428 MET cc_start: 0.5328 (tmm) cc_final: 0.4707 (mtm) REVERT: D 433 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.6495 (t70) REVERT: D 619 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8166 (mm) outliers start: 47 outliers final: 29 residues processed: 270 average time/residue: 0.1331 time to fit residues: 56.4246 Evaluate side-chains 243 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 467 PHE 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 619 LEU Chi-restraints excluded: chain A residue 625 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 249 VAL Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 483 VAL 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 625 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 107 THR 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 467 PHE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 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 467 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 135 optimal weight: 0.0020 chunk 132 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4232 r_free = 0.4232 target = 0.195328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131878 restraints weight = 27658.246| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.69 r_work: 0.3358 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20608 Z= 0.113 Angle : 0.557 14.946 27988 Z= 0.265 Chirality : 0.036 0.132 3172 Planarity : 0.003 0.041 3432 Dihedral : 4.746 51.357 2956 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.39 % Allowed : 19.44 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.17), residues: 2432 helix: 2.03 (0.15), residues: 1412 sheet: 0.17 (0.50), residues: 76 loop : -1.78 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 682 TYR 0.010 0.001 TYR D 466 PHE 0.008 0.001 PHE C 700 TRP 0.015 0.001 TRP D 655 HIS 0.005 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00267 (20608) covalent geometry : angle 0.55651 (27988) hydrogen bonds : bond 0.03434 ( 1024) hydrogen bonds : angle 3.61866 ( 3012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5294.23 seconds wall clock time: 91 minutes 11.97 seconds (5471.97 seconds total)