Starting phenix.real_space_refine on Mon Dec 30 20:13:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uya_42797/12_2024/8uya_42797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uya_42797/12_2024/8uya_42797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uya_42797/12_2024/8uya_42797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uya_42797/12_2024/8uya_42797.map" model { file = "/net/cci-nas-00/data/ceres_data/8uya_42797/12_2024/8uya_42797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uya_42797/12_2024/8uya_42797.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.043 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 8 5.21 5 S 76 5.16 5 C 8874 2.51 5 N 2368 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13902 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6912 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 43, 'TRANS': 854} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 6906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6906 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 43, 'TRANS': 854} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 4, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 4, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 9.78, per 1000 atoms: 0.70 Number of scatterers: 13902 At special positions: 0 Unit cell: (102, 129.2, 134.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 6 15.00 Mg 8 11.99 O 2570 8.00 N 2368 7.00 C 8874 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: 3.67 Conformation dependent library (CDL) restraints added in 2.0 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 15 sheets defined 50.8% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 35 through 46 removed outlier: 4.317A pdb=" N SER A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 removed outlier: 3.789A pdb=" N LEU A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.701A pdb=" N GLN A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 117 through 147 removed outlier: 3.601A pdb=" N ASP A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.514A pdb=" N ASN A 261 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 262 " --> pdb=" O GLY A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 262' Processing helix chain 'A' and resid 280 through 311 removed outlier: 3.588A pdb=" N SER A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Proline residue: A 301 - end of helix removed outlier: 3.618A pdb=" N LYS A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 327 through 331 Proline residue: A 330 - end of helix No H-bonds generated for 'chain 'A' and resid 327 through 331' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.642A pdb=" N THR A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 removed outlier: 3.892A pdb=" N ASN A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 Processing helix chain 'A' and resid 417 through 425 removed outlier: 3.725A pdb=" N THR A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 492 through 506 removed outlier: 3.568A pdb=" N LYS A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP A 503 " --> pdb=" O LYS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 532 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 577 through 583 Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.772A pdb=" N GLU A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 593 through 597' Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.530A pdb=" N ASN A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 629 Processing helix chain 'A' and resid 645 through 652 removed outlier: 3.986A pdb=" N LEU A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 668 removed outlier: 3.550A pdb=" N ALA A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 717 removed outlier: 3.535A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET A 695 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 696 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 705 " --> pdb=" O MET A 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 706 " --> pdb=" O THR A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 741 Processing helix chain 'A' and resid 742 through 747 Proline residue: A 745 - end of helix No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'A' and resid 761 through 763 No H-bonds generated for 'chain 'A' and resid 761 through 763' Processing helix chain 'A' and resid 764 through 772 removed outlier: 4.206A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 790 removed outlier: 3.579A pdb=" N SER A 777 " --> pdb=" O GLY A 773 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 817 Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 854 through 858 removed outlier: 4.024A pdb=" N SER A 858 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 893 removed outlier: 4.767A pdb=" N TRP A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 884 " --> pdb=" O TYR A 880 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN A 885 " --> pdb=" O MET A 881 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N PHE A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 891 " --> pdb=" O VAL A 887 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 removed outlier: 3.910A pdb=" N VAL B 18 " --> pdb=" O PRO B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 46 removed outlier: 3.535A pdb=" N ALA B 46 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.829A pdb=" N LYS B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 77 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.840A pdb=" N GLN B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 117 through 147 removed outlier: 4.010A pdb=" N ALA B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.636A pdb=" N ASN B 261 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 262 " --> pdb=" O GLY B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' Processing helix chain 'B' and resid 280 through 311 removed outlier: 3.736A pdb=" N SER B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.582A pdb=" N LYS B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 327 through 331 Proline residue: B 330 - end of helix No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 332 through 350 removed outlier: 3.601A pdb=" N THR B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.893A pdb=" N ASN B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 removed outlier: 3.934A pdb=" N ASN B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 424 removed outlier: 3.504A pdb=" N THR B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 471 through 476 Processing helix chain 'B' and resid 492 through 506 removed outlier: 3.601A pdb=" N ILE B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG B 500 " --> pdb=" O ARG B 496 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.889A pdb=" N GLU B 532 " --> pdb=" O ARG B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 577 through 583 Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 618 through 628 Processing helix chain 'B' and resid 645 through 652 removed outlier: 3.896A pdb=" N LEU B 649 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 668 Processing helix chain 'B' and resid 679 through 717 removed outlier: 3.579A pdb=" N ILE B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR B 702 " --> pdb=" O TYR B 698 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 704 " --> pdb=" O LYS B 700 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER B 705 " --> pdb=" O MET B 701 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 706 " --> pdb=" O THR B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 742 Processing helix chain 'B' and resid 743 through 747 Processing helix chain 'B' and resid 761 through 763 No H-bonds generated for 'chain 'B' and resid 761 through 763' Processing helix chain 'B' and resid 764 through 772 removed outlier: 4.487A pdb=" N ILE B 770 " --> pdb=" O GLY B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 776 through 791 Processing helix chain 'B' and resid 799 through 817 Processing helix chain 'B' and resid 834 through 851 Processing helix chain 'B' and resid 854 through 858 removed outlier: 3.906A pdb=" N SER B 858 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 888 removed outlier: 3.763A pdb=" N THR B 884 " --> pdb=" O TYR B 880 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN B 885 " --> pdb=" O MET B 881 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 886 " --> pdb=" O THR B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 removed outlier: 4.078A pdb=" N SER B 892 " --> pdb=" O LYS B 888 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 893 " --> pdb=" O GLY B 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 888 through 893' Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 187 removed outlier: 6.940A pdb=" N GLN A 252 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS A 240 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 221 removed outlier: 3.903A pdb=" N LEU A 205 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 206 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.233A pdb=" N VAL A 591 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N PHE A 614 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 567 " --> pdb=" O PHE A 614 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 387 removed outlier: 3.875A pdb=" N LEU A 385 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL A 515 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR A 540 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 513 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 542 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG A 511 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 469 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET A 452 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N SER A 453 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU A 442 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 455 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 385 through 387 removed outlier: 3.875A pdb=" N LEU A 385 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN A 480 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLY A 539 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG A 482 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 13.220A pdb=" N ILE A 541 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 462 through 464 Processing sheet with id=AA8, first strand: chain 'A' and resid 657 through 658 removed outlier: 6.683A pdb=" N SER A 657 " --> pdb=" O LEU A 673 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 159 Processing sheet with id=AB1, first strand: chain 'B' and resid 184 through 187 removed outlier: 4.700A pdb=" N VAL B 246 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE B 206 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N SER B 248 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 204 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR B 250 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA B 202 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN B 252 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 205 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 187 removed outlier: 4.700A pdb=" N VAL B 246 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE B 206 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N SER B 248 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 204 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR B 250 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA B 202 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN B 252 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS B 240 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 591 through 592 removed outlier: 6.318A pdb=" N VAL B 591 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N PHE B 614 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 567 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 370 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 568 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR B 372 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 654 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 671 " --> pdb=" O GLY B 655 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 385 through 387 removed outlier: 3.999A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 515 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR B 540 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 513 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 542 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG B 511 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 469 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER B 453 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLU B 442 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 455 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 385 through 387 removed outlier: 3.999A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN B 480 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLY B 539 " --> pdb=" O GLN B 480 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ARG B 482 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 13.127A pdb=" N ILE B 541 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 462 through 464 620 hydrogen bonds defined for protein. 1776 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: 5.51 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4555 1.34 - 1.46: 2565 1.46 - 1.58: 6911 1.58 - 1.69: 10 1.69 - 1.81: 132 Bond restraints: 14173 Sorted by residual: bond pdb=" C ALA B 646 " pdb=" N PRO B 647 " ideal model delta sigma weight residual 1.337 1.352 -0.015 1.24e-02 6.50e+03 1.51e+00 bond pdb=" N ASP A 381 " pdb=" CA ASP A 381 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.97e-01 bond pdb=" CA ILE A 744 " pdb=" CB ILE A 744 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.89e-01 bond pdb=" CA ALA B 300 " pdb=" C ALA B 300 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.33e-01 bond pdb=" C ILE A 744 " pdb=" N PRO A 745 " ideal model delta sigma weight residual 1.334 1.352 -0.019 2.34e-02 1.83e+03 6.31e-01 ... (remaining 14168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 18670 1.26 - 2.52: 498 2.52 - 3.78: 119 3.78 - 5.04: 22 5.04 - 6.29: 8 Bond angle restraints: 19317 Sorted by residual: angle pdb=" N ILE B 821 " pdb=" CA ILE B 821 " pdb=" C ILE B 821 " ideal model delta sigma weight residual 111.91 108.77 3.14 8.90e-01 1.26e+00 1.24e+01 angle pdb=" N PRO B 24 " pdb=" CA PRO B 24 " pdb=" C PRO B 24 " ideal model delta sigma weight residual 114.68 111.47 3.21 1.04e+00 9.25e-01 9.51e+00 angle pdb=" C GLN A 380 " pdb=" N ASP A 381 " pdb=" CA ASP A 381 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.92e+00 angle pdb=" N GLY B 469 " pdb=" CA GLY B 469 " pdb=" C GLY B 469 " ideal model delta sigma weight residual 110.38 114.42 -4.04 1.42e+00 4.96e-01 8.09e+00 angle pdb=" N GLU B 116 " pdb=" CA GLU B 116 " pdb=" C GLU B 116 " ideal model delta sigma weight residual 114.56 111.05 3.51 1.27e+00 6.20e-01 7.65e+00 ... (remaining 19312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 7694 16.90 - 33.79: 675 33.79 - 50.69: 134 50.69 - 67.59: 34 67.59 - 84.49: 13 Dihedral angle restraints: 8550 sinusoidal: 3344 harmonic: 5206 Sorted by residual: dihedral pdb=" CA ILE A 163 " pdb=" C ILE A 163 " pdb=" N ASN A 164 " pdb=" CA ASN A 164 " ideal model delta harmonic sigma weight residual 180.00 -163.86 -16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CG ARG A 496 " pdb=" CD ARG A 496 " pdb=" NE ARG A 496 " pdb=" CZ ARG A 496 " ideal model delta sinusoidal sigma weight residual 90.00 133.83 -43.83 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CB GLU B 215 " pdb=" CG GLU B 215 " pdb=" CD GLU B 215 " pdb=" OE1 GLU B 215 " ideal model delta sinusoidal sigma weight residual 0.00 84.49 -84.49 1 3.00e+01 1.11e-03 9.64e+00 ... (remaining 8547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1626 0.039 - 0.078: 486 0.078 - 0.116: 147 0.116 - 0.155: 20 0.155 - 0.194: 1 Chirality restraints: 2280 Sorted by residual: chirality pdb=" CB ILE A 163 " pdb=" CA ILE A 163 " pdb=" CG1 ILE A 163 " pdb=" CG2 ILE A 163 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA VAL B 575 " pdb=" N VAL B 575 " pdb=" C VAL B 575 " pdb=" CB VAL B 575 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE B 443 " pdb=" N ILE B 443 " pdb=" C ILE B 443 " pdb=" CB ILE B 443 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 2277 not shown) Planarity restraints: 2451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 773 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 774 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 774 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 774 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 756 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 757 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 757 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 757 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 698 " -0.013 2.00e-02 2.50e+03 9.98e-03 1.99e+00 pdb=" CG TYR B 698 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 698 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 698 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 698 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 698 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 698 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 698 " -0.001 2.00e-02 2.50e+03 ... (remaining 2448 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 71 2.56 - 3.14: 10899 3.14 - 3.73: 20506 3.73 - 4.31: 26707 4.31 - 4.90: 45990 Nonbonded interactions: 104173 Sorted by model distance: nonbonded pdb=" OD1 ASN B 709 " pdb="MG MG B1001 " model vdw 1.970 2.170 nonbonded pdb=" OD1 ASN A 709 " pdb="MG MG A1001 " model vdw 1.994 2.170 nonbonded pdb=" OD1 ASP B 663 " pdb="MG MG B1002 " model vdw 2.070 2.170 nonbonded pdb=" OD1 ASP A 663 " pdb="MG MG A1002 " model vdw 2.091 2.170 nonbonded pdb="MG MG A1004 " pdb=" O2B ATP A1005 " model vdw 2.104 2.170 ... (remaining 104168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 898 or resid 1001 through 1005)) selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.490 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 : 0.002 0.027 14173 Z= 0.160 Angle : 0.540 6.295 19317 Z= 0.292 Chirality : 0.041 0.194 2280 Planarity : 0.004 0.040 2451 Dihedral : 13.960 84.487 5166 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1792 helix: 0.33 (0.19), residues: 868 sheet: -1.59 (0.41), residues: 170 loop : -2.23 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 788 HIS 0.004 0.000 HIS B 357 PHE 0.013 0.001 PHE B 295 TYR 0.024 0.001 TYR B 698 ARG 0.003 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.584 Fit side-chains REVERT: A 45 MET cc_start: 0.8859 (mmm) cc_final: 0.8638 (mmt) REVERT: A 144 LYS cc_start: 0.7955 (tmmt) cc_final: 0.7276 (ttpt) REVERT: A 381 ASP cc_start: 0.8128 (t70) cc_final: 0.7843 (t0) REVERT: A 499 LYS cc_start: 0.8560 (mttp) cc_final: 0.8293 (mttp) REVERT: A 840 MET cc_start: 0.7903 (tpp) cc_final: 0.7425 (mmt) REVERT: A 881 MET cc_start: 0.7851 (ttp) cc_final: 0.7598 (ttm) REVERT: B 45 MET cc_start: 0.8748 (mmm) cc_final: 0.7871 (mmm) REVERT: B 144 LYS cc_start: 0.8071 (tmmt) cc_final: 0.7402 (ttpt) REVERT: B 840 MET cc_start: 0.7642 (mmt) cc_final: 0.7418 (mmt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2565 time to fit residues: 71.8721 Evaluate side-chains 126 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.0870 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14173 Z= 0.199 Angle : 0.559 7.536 19317 Z= 0.283 Chirality : 0.042 0.135 2280 Planarity : 0.004 0.042 2451 Dihedral : 7.213 57.755 1974 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 1.08 % Allowed : 7.12 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.20), residues: 1792 helix: 0.52 (0.19), residues: 880 sheet: -1.46 (0.45), residues: 140 loop : -2.22 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 54 HIS 0.011 0.001 HIS B 729 PHE 0.012 0.001 PHE B 614 TYR 0.021 0.001 TYR B 698 ARG 0.003 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.544 Fit side-chains REVERT: A 45 MET cc_start: 0.8993 (mmm) cc_final: 0.8707 (mmt) REVERT: A 144 LYS cc_start: 0.7948 (tmmt) cc_final: 0.7233 (ttpt) REVERT: A 381 ASP cc_start: 0.8147 (t70) cc_final: 0.7842 (t0) REVERT: A 840 MET cc_start: 0.8052 (tpp) cc_final: 0.7551 (mmt) REVERT: B 45 MET cc_start: 0.8739 (mmm) cc_final: 0.8536 (mmm) REVERT: B 144 LYS cc_start: 0.8112 (tmmt) cc_final: 0.7414 (ttpt) REVERT: B 226 ARG cc_start: 0.7456 (ptp90) cc_final: 0.7213 (ptp90) REVERT: B 840 MET cc_start: 0.7773 (mmt) cc_final: 0.7493 (mmt) outliers start: 16 outliers final: 13 residues processed: 138 average time/residue: 0.2408 time to fit residues: 51.3402 Evaluate side-chains 131 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 887 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14173 Z= 0.295 Angle : 0.582 7.638 19317 Z= 0.295 Chirality : 0.042 0.136 2280 Planarity : 0.004 0.042 2451 Dihedral : 6.921 63.113 1974 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 1.36 % Allowed : 10.10 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.20), residues: 1792 helix: 0.51 (0.18), residues: 884 sheet: -1.35 (0.43), residues: 160 loop : -2.26 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 54 HIS 0.006 0.001 HIS B 729 PHE 0.020 0.002 PHE B 364 TYR 0.031 0.001 TYR B 698 ARG 0.005 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.676 Fit side-chains REVERT: A 144 LYS cc_start: 0.8058 (tmmt) cc_final: 0.7332 (ttpt) REVERT: A 381 ASP cc_start: 0.8154 (t70) cc_final: 0.7852 (t0) REVERT: B 144 LYS cc_start: 0.8221 (tmmt) cc_final: 0.7544 (ttpt) REVERT: B 226 ARG cc_start: 0.7481 (ptp90) cc_final: 0.7267 (ptp90) REVERT: B 381 ASP cc_start: 0.7867 (t0) cc_final: 0.7532 (t0) REVERT: B 840 MET cc_start: 0.7815 (mmt) cc_final: 0.7570 (mmt) outliers start: 20 outliers final: 18 residues processed: 131 average time/residue: 0.2438 time to fit residues: 48.8842 Evaluate side-chains 132 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14173 Z= 0.167 Angle : 0.516 7.521 19317 Z= 0.261 Chirality : 0.040 0.132 2280 Planarity : 0.004 0.042 2451 Dihedral : 6.417 73.043 1974 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.76 % Allowed : 10.92 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1792 helix: 0.73 (0.19), residues: 876 sheet: -1.34 (0.44), residues: 140 loop : -2.16 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.006 0.001 HIS B 729 PHE 0.011 0.001 PHE A 807 TYR 0.019 0.001 TYR B 698 ARG 0.002 0.000 ARG A 431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.676 Fit side-chains REVERT: A 144 LYS cc_start: 0.7964 (tmmt) cc_final: 0.7240 (ttpt) REVERT: A 381 ASP cc_start: 0.8116 (t70) cc_final: 0.7885 (t0) REVERT: A 840 MET cc_start: 0.8034 (tpp) cc_final: 0.7524 (mmt) REVERT: B 144 LYS cc_start: 0.8146 (tmmt) cc_final: 0.7458 (ttpt) REVERT: B 226 ARG cc_start: 0.7473 (ptp90) cc_final: 0.7250 (ptp90) REVERT: B 381 ASP cc_start: 0.7830 (t0) cc_final: 0.7490 (t0) REVERT: B 728 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8607 (mt) REVERT: B 840 MET cc_start: 0.7752 (mmt) cc_final: 0.7494 (mmt) outliers start: 26 outliers final: 16 residues processed: 146 average time/residue: 0.2477 time to fit residues: 55.5662 Evaluate side-chains 132 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 128 optimal weight: 0.0040 chunk 70 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14173 Z= 0.159 Angle : 0.510 7.346 19317 Z= 0.256 Chirality : 0.040 0.131 2280 Planarity : 0.004 0.041 2451 Dihedral : 6.153 79.131 1974 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.56 % Allowed : 11.66 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1792 helix: 0.92 (0.19), residues: 866 sheet: -1.25 (0.44), residues: 140 loop : -2.12 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 54 HIS 0.006 0.001 HIS B 729 PHE 0.010 0.001 PHE A 807 TYR 0.018 0.001 TYR A 698 ARG 0.002 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.700 Fit side-chains REVERT: A 144 LYS cc_start: 0.7912 (tmmt) cc_final: 0.7191 (ttpt) REVERT: A 381 ASP cc_start: 0.8154 (t70) cc_final: 0.7833 (t0) REVERT: A 840 MET cc_start: 0.7997 (tpp) cc_final: 0.7494 (mmt) REVERT: A 887 VAL cc_start: 0.9092 (t) cc_final: 0.8735 (p) REVERT: B 144 LYS cc_start: 0.8110 (tmmt) cc_final: 0.7422 (ttpt) REVERT: B 226 ARG cc_start: 0.7469 (ptp90) cc_final: 0.7263 (ptp90) REVERT: B 381 ASP cc_start: 0.7817 (t0) cc_final: 0.7489 (t0) REVERT: B 474 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8495 (mm) REVERT: B 728 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8547 (mt) REVERT: B 840 MET cc_start: 0.7732 (mmt) cc_final: 0.7491 (mmt) outliers start: 23 outliers final: 15 residues processed: 150 average time/residue: 0.2335 time to fit residues: 54.7553 Evaluate side-chains 136 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 14173 Z= 0.446 Angle : 0.655 7.835 19317 Z= 0.334 Chirality : 0.045 0.139 2280 Planarity : 0.005 0.040 2451 Dihedral : 6.684 85.479 1974 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 2.31 % Allowed : 11.80 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.20), residues: 1792 helix: 0.56 (0.18), residues: 878 sheet: -1.27 (0.42), residues: 160 loop : -2.38 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 54 HIS 0.007 0.001 HIS A 357 PHE 0.022 0.002 PHE B 364 TYR 0.036 0.002 TYR A 698 ARG 0.006 0.001 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.668 Fit side-chains REVERT: A 144 LYS cc_start: 0.8151 (tmmt) cc_final: 0.7438 (ttpt) REVERT: A 381 ASP cc_start: 0.8133 (t70) cc_final: 0.7782 (t0) REVERT: A 499 LYS cc_start: 0.8687 (mttp) cc_final: 0.8471 (mttp) REVERT: B 144 LYS cc_start: 0.8277 (tmmt) cc_final: 0.7607 (ttpt) REVERT: B 226 ARG cc_start: 0.7478 (ptp90) cc_final: 0.7271 (ptp90) REVERT: B 381 ASP cc_start: 0.7873 (t0) cc_final: 0.7516 (t0) REVERT: B 840 MET cc_start: 0.7841 (mmt) cc_final: 0.7598 (mmt) outliers start: 34 outliers final: 27 residues processed: 138 average time/residue: 0.2404 time to fit residues: 52.0203 Evaluate side-chains 137 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14173 Z= 0.169 Angle : 0.537 7.368 19317 Z= 0.270 Chirality : 0.041 0.132 2280 Planarity : 0.004 0.044 2451 Dihedral : 6.283 88.399 1974 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.56 % Allowed : 13.22 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1792 helix: 0.82 (0.19), residues: 880 sheet: -1.30 (0.44), residues: 140 loop : -2.19 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 54 HIS 0.006 0.001 HIS B 729 PHE 0.013 0.001 PHE A 807 TYR 0.019 0.001 TYR A 698 ARG 0.001 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.740 Fit side-chains REVERT: A 144 LYS cc_start: 0.8002 (tmmt) cc_final: 0.7283 (ttpt) REVERT: A 381 ASP cc_start: 0.8038 (t70) cc_final: 0.7732 (t0) REVERT: A 840 MET cc_start: 0.8013 (tpp) cc_final: 0.7487 (mmt) REVERT: B 144 LYS cc_start: 0.8167 (tmmt) cc_final: 0.7483 (ttpt) REVERT: B 226 ARG cc_start: 0.7435 (ptp90) cc_final: 0.7220 (ptp90) REVERT: B 381 ASP cc_start: 0.7855 (t0) cc_final: 0.7535 (t0) REVERT: B 728 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8659 (mt) REVERT: B 840 MET cc_start: 0.7684 (mmt) cc_final: 0.7475 (mmt) outliers start: 23 outliers final: 18 residues processed: 137 average time/residue: 0.2450 time to fit residues: 51.9724 Evaluate side-chains 133 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 164 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14173 Z= 0.168 Angle : 0.527 7.396 19317 Z= 0.266 Chirality : 0.040 0.130 2280 Planarity : 0.004 0.042 2451 Dihedral : 6.055 87.384 1974 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.56 % Allowed : 13.36 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1792 helix: 0.91 (0.19), residues: 868 sheet: -1.19 (0.44), residues: 140 loop : -2.09 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 54 HIS 0.005 0.001 HIS B 729 PHE 0.012 0.001 PHE A 807 TYR 0.019 0.001 TYR A 698 ARG 0.011 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.722 Fit side-chains REVERT: A 144 LYS cc_start: 0.7908 (tmmt) cc_final: 0.7200 (ttpt) REVERT: A 226 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.7164 (mtt90) REVERT: A 381 ASP cc_start: 0.8124 (t70) cc_final: 0.7801 (t0) REVERT: A 499 LYS cc_start: 0.8688 (mttp) cc_final: 0.8472 (mttp) REVERT: A 840 MET cc_start: 0.8013 (tpp) cc_final: 0.7476 (mmt) REVERT: B 144 LYS cc_start: 0.8149 (tmmt) cc_final: 0.7435 (ttpt) REVERT: B 226 ARG cc_start: 0.7418 (ptp90) cc_final: 0.7210 (ptp90) REVERT: B 381 ASP cc_start: 0.7820 (t0) cc_final: 0.7554 (t0) REVERT: B 728 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8698 (mt) REVERT: B 840 MET cc_start: 0.7682 (mmt) cc_final: 0.7433 (mmt) outliers start: 23 outliers final: 21 residues processed: 143 average time/residue: 0.2445 time to fit residues: 53.4093 Evaluate side-chains 140 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 0.0070 chunk 159 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 125 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 144 optimal weight: 0.4980 chunk 151 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14173 Z= 0.146 Angle : 0.511 8.107 19317 Z= 0.257 Chirality : 0.040 0.129 2280 Planarity : 0.004 0.042 2451 Dihedral : 5.836 86.725 1974 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.76 % Allowed : 13.36 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1792 helix: 1.06 (0.19), residues: 860 sheet: -1.07 (0.44), residues: 140 loop : -2.00 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.006 0.001 HIS B 729 PHE 0.013 0.001 PHE A 807 TYR 0.015 0.001 TYR A 698 ARG 0.001 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.570 Fit side-chains REVERT: A 144 LYS cc_start: 0.7866 (tmmt) cc_final: 0.7148 (ttpt) REVERT: A 381 ASP cc_start: 0.8084 (t70) cc_final: 0.7788 (t0) REVERT: A 499 LYS cc_start: 0.8682 (mttp) cc_final: 0.8434 (mttp) REVERT: A 840 MET cc_start: 0.7924 (tpp) cc_final: 0.7430 (mmt) REVERT: B 144 LYS cc_start: 0.8071 (tmmt) cc_final: 0.7357 (ttpt) REVERT: B 226 ARG cc_start: 0.7350 (ptp90) cc_final: 0.7139 (ptp90) REVERT: B 381 ASP cc_start: 0.7771 (t0) cc_final: 0.7539 (t0) REVERT: B 840 MET cc_start: 0.7649 (mmt) cc_final: 0.7407 (mmt) outliers start: 26 outliers final: 21 residues processed: 154 average time/residue: 0.2460 time to fit residues: 57.8626 Evaluate side-chains 145 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 177 optimal weight: 0.0770 chunk 163 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14173 Z= 0.156 Angle : 0.515 7.932 19317 Z= 0.259 Chirality : 0.040 0.130 2280 Planarity : 0.004 0.041 2451 Dihedral : 5.755 86.898 1974 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.63 % Allowed : 13.83 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1792 helix: 1.11 (0.19), residues: 856 sheet: -0.99 (0.45), residues: 140 loop : -1.92 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.006 0.001 HIS B 729 PHE 0.015 0.001 PHE A 779 TYR 0.017 0.001 TYR A 698 ARG 0.003 0.000 ARG B 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.701 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.7849 (tmmt) cc_final: 0.7137 (ttpt) REVERT: A 381 ASP cc_start: 0.8055 (t70) cc_final: 0.7751 (t0) REVERT: A 499 LYS cc_start: 0.8676 (mttp) cc_final: 0.8428 (mttp) REVERT: A 840 MET cc_start: 0.7956 (tpp) cc_final: 0.7446 (mmt) REVERT: B 144 LYS cc_start: 0.8074 (tmmt) cc_final: 0.7352 (ttpt) REVERT: B 381 ASP cc_start: 0.7769 (t0) cc_final: 0.7547 (t0) REVERT: B 431 ARG cc_start: 0.8426 (ttp-110) cc_final: 0.7920 (mtm110) REVERT: B 840 MET cc_start: 0.7653 (mmt) cc_final: 0.7377 (mmt) outliers start: 24 outliers final: 23 residues processed: 151 average time/residue: 0.2529 time to fit residues: 58.1854 Evaluate side-chains 155 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 141 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 26 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 729 HIS ** 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 = 0.3521 r_free = 0.3521 target = 0.116592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.091524 restraints weight = 25828.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.092761 restraints weight = 20477.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093675 restraints weight = 16570.045| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14173 Z= 0.148 Angle : 0.509 7.735 19317 Z= 0.255 Chirality : 0.040 0.129 2280 Planarity : 0.004 0.042 2451 Dihedral : 5.647 86.676 1974 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.56 % Allowed : 13.90 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1792 helix: 1.14 (0.19), residues: 866 sheet: -0.89 (0.45), residues: 140 loop : -1.94 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 806 HIS 0.006 0.000 HIS B 729 PHE 0.016 0.001 PHE A 779 TYR 0.016 0.001 TYR A 698 ARG 0.004 0.000 ARG B 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.51 seconds wall clock time: 46 minutes 25.42 seconds (2785.42 seconds total)