Starting phenix.real_space_refine on Fri May 16 02:55:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uya_42797/05_2025/8uya_42797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uya_42797/05_2025/8uya_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_42797/05_2025/8uya_42797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uya_42797/05_2025/8uya_42797.map" model { file = "/net/cci-nas-00/data/ceres_data/8uya_42797/05_2025/8uya_42797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uya_42797/05_2025/8uya_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.73, 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: 4.12 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: 2.29 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: 5.26 Time building geometry restraints manager: 4.30 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: 2.330 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: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.420 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.840 ------------------------------------------------------------------------------- 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= 0.115 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 Details of bonding type rmsd hydrogen bonds : bond 0.17316 ( 607) hydrogen bonds : angle 5.97803 ( 1776) covalent geometry : bond 0.00237 (14173) covalent geometry : angle 0.54043 (19317) *********************** 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 : 1.505 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: 0.2323 time to fit residues: 64.6240 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 : 1.500 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.090036 restraints weight = 26041.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.090919 restraints weight = 22220.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091784 restraints weight = 18038.139| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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= 0.128 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 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 607) hydrogen bonds : angle 4.33077 ( 1776) covalent geometry : bond 0.00296 (14173) covalent geometry : angle 0.55933 (19317) *********************** 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 : 1.530 Fit side-chains REVERT: A 45 MET cc_start: 0.8935 (mmm) cc_final: 0.8639 (mmt) REVERT: A 144 LYS cc_start: 0.7954 (tmmt) cc_final: 0.7257 (ttpt) REVERT: A 381 ASP cc_start: 0.8092 (t70) cc_final: 0.7784 (t0) REVERT: A 840 MET cc_start: 0.8053 (tpp) cc_final: 0.7565 (mmt) REVERT: B 45 MET cc_start: 0.8688 (mmm) cc_final: 0.8463 (mmm) REVERT: B 144 LYS cc_start: 0.8132 (tmmt) cc_final: 0.7447 (ttpt) REVERT: B 226 ARG cc_start: 0.7405 (ptp90) cc_final: 0.7168 (ptp90) REVERT: B 840 MET cc_start: 0.7771 (mmt) cc_final: 0.7513 (mmt) outliers start: 16 outliers final: 13 residues processed: 138 average time/residue: 0.2302 time to fit residues: 48.8043 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 : 1.496 ------------------------------------------------------------------------------- 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 145 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 6 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090389 restraints weight = 26071.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.091084 restraints weight = 21049.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.091623 restraints weight = 19171.168| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14173 Z= 0.118 Angle : 0.525 7.394 19317 Z= 0.265 Chirality : 0.041 0.133 2280 Planarity : 0.004 0.042 2451 Dihedral : 6.636 60.749 1974 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.08 % Allowed : 10.03 % Favored : 88.88 % 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: -0.97 (0.20), residues: 1792 helix: 0.72 (0.19), residues: 870 sheet: -1.26 (0.42), residues: 160 loop : -2.16 (0.21), residues: 762 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 0.013 0.001 PHE A 364 TYR 0.022 0.001 TYR B 698 ARG 0.003 0.000 ARG A 431 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 607) hydrogen bonds : angle 4.01343 ( 1776) covalent geometry : bond 0.00277 (14173) covalent geometry : angle 0.52536 (19317) *********************** 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 142 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.555 Fit side-chains REVERT: A 144 LYS cc_start: 0.7946 (tmmt) cc_final: 0.7231 (ttpt) REVERT: A 381 ASP cc_start: 0.8080 (t70) cc_final: 0.7858 (t0) REVERT: A 816 LEU cc_start: 0.8723 (mt) cc_final: 0.8502 (mt) REVERT: A 840 MET cc_start: 0.8045 (tpp) cc_final: 0.7560 (mmt) REVERT: B 45 MET cc_start: 0.8708 (mmm) cc_final: 0.8482 (mmm) REVERT: B 144 LYS cc_start: 0.8158 (tmmt) cc_final: 0.7488 (ttpt) REVERT: B 226 ARG cc_start: 0.7401 (ptp90) cc_final: 0.7177 (ptp90) REVERT: B 381 ASP cc_start: 0.7783 (t0) cc_final: 0.7465 (t0) REVERT: B 728 LEU cc_start: 0.8924 (mm) cc_final: 0.8676 (mt) REVERT: B 840 MET cc_start: 0.7766 (mmt) cc_final: 0.7531 (mmt) outliers start: 16 outliers final: 12 residues processed: 136 average time/residue: 0.2372 time to fit residues: 49.4039 Evaluate side-chains 130 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.541 ------------------------------------------------------------------------------- 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 324 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 713 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 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 114 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 152 optimal weight: 0.0970 chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 0.0020 chunk 167 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.115758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089930 restraints weight = 25888.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.091429 restraints weight = 20118.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.092086 restraints weight = 15137.756| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14173 Z= 0.106 Angle : 0.506 7.177 19317 Z= 0.256 Chirality : 0.040 0.131 2280 Planarity : 0.004 0.042 2451 Dihedral : 6.265 64.880 1974 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.07 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: -0.82 (0.20), residues: 1792 helix: 0.88 (0.19), residues: 860 sheet: -1.29 (0.44), residues: 140 loop : -2.07 (0.21), residues: 792 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 0.011 0.001 PHE B 364 TYR 0.019 0.001 TYR B 698 ARG 0.005 0.000 ARG B 824 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 607) hydrogen bonds : angle 3.88202 ( 1776) covalent geometry : bond 0.00245 (14173) covalent geometry : angle 0.50633 (19317) *********************** 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 162 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.549 Fit side-chains REVERT: A 144 LYS cc_start: 0.7897 (tmmt) cc_final: 0.7188 (ttpt) REVERT: A 381 ASP cc_start: 0.8093 (t70) cc_final: 0.7770 (t0) REVERT: A 816 LEU cc_start: 0.8747 (mt) cc_final: 0.8486 (mt) REVERT: A 840 MET cc_start: 0.8022 (tpp) cc_final: 0.7531 (mmt) REVERT: B 144 LYS cc_start: 0.8136 (tmmt) cc_final: 0.7453 (ttpt) REVERT: B 226 ARG cc_start: 0.7429 (ptp90) cc_final: 0.7219 (ptp90) REVERT: B 381 ASP cc_start: 0.7821 (t0) cc_final: 0.7473 (t0) REVERT: B 474 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8547 (mm) REVERT: B 728 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8615 (mt) REVERT: B 840 MET cc_start: 0.7740 (mmt) cc_final: 0.7487 (mmt) outliers start: 26 outliers final: 14 residues processed: 154 average time/residue: 0.2311 time to fit residues: 54.4499 Evaluate side-chains 136 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 324 VAL Chi-restraints excluded: chain A residue 326 VAL 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 70 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 170 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.113793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.088613 restraints weight = 26227.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.089497 restraints weight = 21330.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.090358 restraints weight = 17726.788| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14173 Z= 0.155 Angle : 0.554 7.375 19317 Z= 0.279 Chirality : 0.042 0.134 2280 Planarity : 0.004 0.041 2451 Dihedral : 6.288 69.934 1974 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.17 % Allowed : 11.53 % Favored : 86.31 % 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: -0.90 (0.20), residues: 1792 helix: 0.80 (0.19), residues: 868 sheet: -1.12 (0.43), residues: 160 loop : -2.18 (0.21), residues: 764 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 0.016 0.001 PHE B 364 TYR 0.026 0.001 TYR A 698 ARG 0.004 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 607) hydrogen bonds : angle 3.97670 ( 1776) covalent geometry : bond 0.00378 (14173) covalent geometry : angle 0.55399 (19317) *********************** 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 153 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.581 Fit side-chains REVERT: A 144 LYS cc_start: 0.8039 (tmmt) cc_final: 0.7321 (ttpt) REVERT: A 381 ASP cc_start: 0.8048 (t70) cc_final: 0.7758 (t0) REVERT: A 816 LEU cc_start: 0.8796 (mt) cc_final: 0.8538 (mt) REVERT: A 840 MET cc_start: 0.8086 (tpp) cc_final: 0.7562 (mmt) REVERT: B 144 LYS cc_start: 0.8199 (tmmt) cc_final: 0.7539 (ttpt) REVERT: B 226 ARG cc_start: 0.7378 (ptp90) cc_final: 0.7157 (ptp90) REVERT: B 381 ASP cc_start: 0.7796 (t0) cc_final: 0.7472 (t0) REVERT: B 728 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8641 (mt) REVERT: B 840 MET cc_start: 0.7756 (mmt) cc_final: 0.7524 (mmt) outliers start: 32 outliers final: 23 residues processed: 145 average time/residue: 0.2295 time to fit residues: 52.3758 Evaluate side-chains 141 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 326 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 844 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 324 VAL Chi-restraints excluded: chain B residue 326 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 15 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.090479 restraints weight = 26159.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091307 restraints weight = 21395.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.092002 restraints weight = 18767.895| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1621 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= 0.105 Angle : 0.513 7.213 19317 Z= 0.257 Chirality : 0.040 0.130 2280 Planarity : 0.004 0.041 2451 Dihedral : 6.054 75.644 1974 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.69 % Allowed : 12.14 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.20), residues: 1792 helix: 0.97 (0.19), residues: 860 sheet: -1.14 (0.44), residues: 140 loop : -2.06 (0.21), residues: 792 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 0.011 0.001 PHE A 779 TYR 0.018 0.001 TYR A 698 ARG 0.002 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 607) hydrogen bonds : angle 3.79730 ( 1776) covalent geometry : bond 0.00241 (14173) covalent geometry : angle 0.51259 (19317) *********************** 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 155 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.655 Fit side-chains REVERT: A 144 LYS cc_start: 0.7931 (tmmt) cc_final: 0.7230 (ttpt) REVERT: A 381 ASP cc_start: 0.8051 (t70) cc_final: 0.7820 (t0) REVERT: A 816 LEU cc_start: 0.8751 (mt) cc_final: 0.8486 (mt) REVERT: A 840 MET cc_start: 0.8002 (tpp) cc_final: 0.7504 (mmt) REVERT: B 144 LYS cc_start: 0.8133 (tmmt) cc_final: 0.7474 (ttpt) REVERT: B 226 ARG cc_start: 0.7342 (ptp90) cc_final: 0.7132 (ptp90) REVERT: B 381 ASP cc_start: 0.7782 (t0) cc_final: 0.7469 (t0) REVERT: B 474 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8577 (mm) REVERT: B 728 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8658 (mt) REVERT: B 840 MET cc_start: 0.7674 (mmt) cc_final: 0.7468 (mmt) outliers start: 25 outliers final: 15 residues processed: 149 average time/residue: 0.2301 time to fit residues: 53.0911 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 : 1.484 ------------------------------------------------------------------------------- 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 460 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 LEU 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 326 VAL Chi-restraints excluded: chain B residue 466 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 16 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.114740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090154 restraints weight = 26086.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090363 restraints weight = 20605.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.091044 restraints weight = 20721.712| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 0.042 14173 Z= 0.123 Angle : 0.523 8.591 19317 Z= 0.263 Chirality : 0.041 0.131 2280 Planarity : 0.004 0.040 2451 Dihedral : 6.006 79.414 1974 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.24 % Allowed : 11.80 % Favored : 85.97 % 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: -0.72 (0.20), residues: 1792 helix: 0.97 (0.19), residues: 862 sheet: -1.12 (0.44), residues: 140 loop : -2.08 (0.21), residues: 790 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 0.012 0.001 PHE B 364 TYR 0.022 0.001 TYR A 698 ARG 0.003 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 607) hydrogen bonds : angle 3.82461 ( 1776) covalent geometry : bond 0.00293 (14173) covalent geometry : angle 0.52304 (19317) *********************** 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 162 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.800 Fit side-chains REVERT: A 144 LYS cc_start: 0.7932 (tmmt) cc_final: 0.7227 (ttpt) REVERT: A 381 ASP cc_start: 0.8126 (t70) cc_final: 0.7817 (t0) REVERT: A 499 LYS cc_start: 0.8673 (mttp) cc_final: 0.8366 (mttp) REVERT: A 816 LEU cc_start: 0.8767 (mt) cc_final: 0.8530 (mt) REVERT: A 840 MET cc_start: 0.8047 (tpp) cc_final: 0.7520 (mmt) REVERT: B 144 LYS cc_start: 0.8177 (tmmt) cc_final: 0.7535 (ttpt) REVERT: B 381 ASP cc_start: 0.7822 (t0) cc_final: 0.7506 (t0) REVERT: B 728 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8673 (mt) REVERT: B 840 MET cc_start: 0.7692 (mmt) cc_final: 0.7485 (mmt) outliers start: 33 outliers final: 28 residues processed: 151 average time/residue: 0.2282 time to fit residues: 53.8312 Evaluate side-chains 149 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 324 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 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 A residue 844 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 250 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 460 THR Chi-restraints excluded: chain B residue 466 VAL 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 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 104 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 120 optimal weight: 0.0870 chunk 22 optimal weight: 0.0870 chunk 173 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.116135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091257 restraints weight = 25971.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.092421 restraints weight = 21170.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.093125 restraints weight = 17474.138| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 0.028 14173 Z= 0.099 Angle : 0.505 9.291 19317 Z= 0.253 Chirality : 0.040 0.130 2280 Planarity : 0.004 0.040 2451 Dihedral : 5.864 82.980 1974 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.69 % Allowed : 12.68 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1792 helix: 1.07 (0.19), residues: 858 sheet: -1.04 (0.45), residues: 140 loop : -1.99 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.005 0.000 HIS B 729 PHE 0.014 0.001 PHE A 779 TYR 0.017 0.001 TYR A 698 ARG 0.003 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 607) hydrogen bonds : angle 3.71148 ( 1776) covalent geometry : bond 0.00222 (14173) covalent geometry : angle 0.50517 (19317) *********************** 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 153 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.773 Fit side-chains REVERT: A 144 LYS cc_start: 0.7857 (tmmt) cc_final: 0.7167 (ttpt) REVERT: A 381 ASP cc_start: 0.8087 (t70) cc_final: 0.7783 (t0) REVERT: A 816 LEU cc_start: 0.8740 (mt) cc_final: 0.8478 (mt) REVERT: A 840 MET cc_start: 0.7983 (tpp) cc_final: 0.7487 (mmt) REVERT: B 144 LYS cc_start: 0.8096 (tmmt) cc_final: 0.7401 (ttpt) REVERT: B 226 ARG cc_start: 0.7120 (ptp90) cc_final: 0.6804 (ptp90) REVERT: B 381 ASP cc_start: 0.7735 (t0) cc_final: 0.7430 (t0) REVERT: B 728 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8646 (mt) REVERT: B 840 MET cc_start: 0.7661 (mmt) cc_final: 0.7421 (mmt) outliers start: 25 outliers final: 22 residues processed: 147 average time/residue: 0.2475 time to fit residues: 55.3129 Evaluate side-chains 146 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 460 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 720 LEU 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 460 THR Chi-restraints excluded: chain B residue 466 VAL 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 728 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 101 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 153 optimal weight: 0.3980 chunk 133 optimal weight: 0.0970 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.092165 restraints weight = 25965.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.093168 restraints weight = 20691.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093688 restraints weight = 18512.698| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1860 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= 0.096 Angle : 0.503 7.937 19317 Z= 0.251 Chirality : 0.040 0.129 2280 Planarity : 0.004 0.040 2451 Dihedral : 5.749 85.570 1974 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.69 % Allowed : 12.81 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.54 (0.21), residues: 1792 helix: 1.10 (0.19), residues: 866 sheet: -0.94 (0.45), residues: 140 loop : -1.98 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 54 HIS 0.005 0.000 HIS B 729 PHE 0.013 0.001 PHE A 779 TYR 0.016 0.001 TYR A 698 ARG 0.002 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 607) hydrogen bonds : angle 3.65628 ( 1776) covalent geometry : bond 0.00215 (14173) covalent geometry : angle 0.50290 (19317) *********************** 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 160 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.7810 (tmmt) cc_final: 0.7136 (ttpt) REVERT: A 381 ASP cc_start: 0.8050 (t70) cc_final: 0.7743 (t0) REVERT: A 816 LEU cc_start: 0.8700 (mt) cc_final: 0.8442 (mt) REVERT: A 840 MET cc_start: 0.7984 (tpp) cc_final: 0.7494 (mmt) REVERT: B 144 LYS cc_start: 0.8051 (tmmt) cc_final: 0.7365 (ttpt) REVERT: B 226 ARG cc_start: 0.7117 (ptp90) cc_final: 0.6788 (ptp90) REVERT: B 381 ASP cc_start: 0.7722 (t0) cc_final: 0.7472 (t0) REVERT: B 728 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8668 (mt) REVERT: B 840 MET cc_start: 0.7638 (mmt) cc_final: 0.7430 (mmt) outliers start: 25 outliers final: 22 residues processed: 153 average time/residue: 0.2344 time to fit residues: 55.0113 Evaluate side-chains 152 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 460 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 VAL 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 728 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 143 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091850 restraints weight = 26000.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092611 restraints weight = 20330.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093288 restraints weight = 18606.992| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14173 Z= 0.102 Angle : 0.507 8.031 19317 Z= 0.253 Chirality : 0.040 0.129 2280 Planarity : 0.004 0.039 2451 Dihedral : 5.684 87.932 1974 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.76 % Allowed : 13.08 % Favored : 85.15 % 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: -0.45 (0.21), residues: 1792 helix: 1.16 (0.19), residues: 858 sheet: -0.86 (0.45), residues: 140 loop : -1.89 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.005 0.001 HIS B 729 PHE 0.013 0.001 PHE A 779 TYR 0.018 0.001 TYR A 698 ARG 0.007 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 607) hydrogen bonds : angle 3.65090 ( 1776) covalent geometry : bond 0.00234 (14173) covalent geometry : angle 0.50707 (19317) ********************** 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: 26 poor density : 132 time to evaluate : 1.682 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.7826 (tmmt) cc_final: 0.7145 (ttpt) REVERT: A 226 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7123 (mtt90) REVERT: A 381 ASP cc_start: 0.8042 (t70) cc_final: 0.7727 (t0) REVERT: A 499 LYS cc_start: 0.8585 (mttp) cc_final: 0.8264 (mppt) REVERT: A 816 LEU cc_start: 0.8707 (mt) cc_final: 0.8446 (mt) REVERT: A 840 MET cc_start: 0.7998 (tpp) cc_final: 0.7498 (mmt) REVERT: B 144 LYS cc_start: 0.8063 (tmmt) cc_final: 0.7379 (ttpt) REVERT: B 381 ASP cc_start: 0.7689 (t0) cc_final: 0.7440 (t0) REVERT: B 728 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8682 (mt) REVERT: B 840 MET cc_start: 0.7639 (mmt) cc_final: 0.7404 (mmt) outliers start: 26 outliers final: 25 residues processed: 151 average time/residue: 0.2385 time to fit residues: 55.1611 Evaluate side-chains 155 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 460 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 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 A residue 844 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 139 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 44 optimal weight: 0.0000 chunk 112 optimal weight: 0.0980 chunk 106 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.117696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093329 restraints weight = 26143.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094506 restraints weight = 20315.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095138 restraints weight = 17612.487| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2029 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= 0.090 Angle : 0.491 8.346 19317 Z= 0.245 Chirality : 0.040 0.130 2280 Planarity : 0.004 0.040 2451 Dihedral : 5.518 89.985 1974 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.49 % Allowed : 13.15 % Favored : 85.36 % 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: -0.34 (0.21), residues: 1792 helix: 1.22 (0.19), residues: 868 sheet: -0.70 (0.42), residues: 168 loop : -1.89 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 54 HIS 0.005 0.000 HIS B 729 PHE 0.012 0.001 PHE A 779 TYR 0.014 0.001 TYR A 698 ARG 0.004 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 607) hydrogen bonds : angle 3.57546 ( 1776) covalent geometry : bond 0.00196 (14173) covalent geometry : angle 0.49100 (19317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3663.52 seconds wall clock time: 65 minutes 26.24 seconds (3926.24 seconds total)