Starting phenix.real_space_refine on Sat Aug 23 18:27:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uya_42797/08_2025/8uya_42797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uya_42797/08_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_42797/08_2025/8uya_42797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uya_42797/08_2025/8uya_42797.map" model { file = "/net/cci-nas-00/data/ceres_data/8uya_42797/08_2025/8uya_42797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uya_42797/08_2025/8uya_42797.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'GLN:plan1': 4, 'ASN:plan1': 1, '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, 'GLN:plan1': 4, 'ASN:plan1': 1, '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: 2.84, per 1000 atoms: 0.20 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: 0.76 Conformation dependent library (CDL) restraints added in 401.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 2.25 Time building geometry restraints manager: 1.02 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 1005)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.003 0.000 ARG A 650 TYR 0.024 0.001 TYR B 698 PHE 0.013 0.001 PHE B 295 TRP 0.016 0.001 TRP B 788 HIS 0.004 0.000 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00237 (14173) covalent geometry : angle 0.54043 (19317) hydrogen bonds : bond 0.17316 ( 607) hydrogen bonds : angle 5.97803 ( 1776) *********************** 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 : 0.361 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: 0.0989 time to fit residues: 27.8490 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 : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.0670 chunk 149 optimal weight: 1.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- 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** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.088475 restraints weight = 26222.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.089629 restraints weight = 21271.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.090381 restraints weight = 17598.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090575 restraints weight = 13972.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090801 restraints weight = 13129.343| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14173 Z= 0.166 Angle : 0.594 7.827 19317 Z= 0.301 Chirality : 0.043 0.136 2280 Planarity : 0.004 0.045 2451 Dihedral : 7.283 57.073 1974 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.15 % Allowed : 7.32 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.20), residues: 1792 helix: 0.44 (0.19), residues: 884 sheet: -1.25 (0.44), residues: 154 loop : -2.31 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 650 TYR 0.028 0.001 TYR B 698 PHE 0.017 0.001 PHE A 364 TRP 0.017 0.001 TRP A 54 HIS 0.011 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00399 (14173) covalent geometry : angle 0.59435 (19317) hydrogen bonds : bond 0.04802 ( 607) hydrogen bonds : angle 4.37974 ( 1776) *********************** 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 147 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.573 Fit side-chains REVERT: A 45 MET cc_start: 0.8990 (mmm) cc_final: 0.8673 (mmt) REVERT: A 144 LYS cc_start: 0.8071 (tmmt) cc_final: 0.7332 (ttpt) REVERT: A 335 MET cc_start: 0.7665 (ttt) cc_final: 0.7372 (ttt) REVERT: A 381 ASP cc_start: 0.8098 (t70) cc_final: 0.7800 (t0) REVERT: B 45 MET cc_start: 0.8710 (mmm) cc_final: 0.8496 (mmm) REVERT: B 117 ASP cc_start: 0.6649 (t0) cc_final: 0.6320 (p0) REVERT: B 144 LYS cc_start: 0.8192 (tmmt) cc_final: 0.7512 (ttpt) REVERT: B 226 ARG cc_start: 0.7431 (ptp90) cc_final: 0.7203 (ptp90) REVERT: B 381 ASP cc_start: 0.7869 (t0) cc_final: 0.7551 (t0) REVERT: B 840 MET cc_start: 0.7821 (mmt) cc_final: 0.7581 (mmt) outliers start: 17 outliers final: 12 residues processed: 138 average time/residue: 0.1040 time to fit residues: 21.5880 Evaluate side-chains 131 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 713 VAL 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 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 17 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 41 optimal weight: 0.0370 overall best weight: 1.0862 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.114226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.089620 restraints weight = 26188.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088915 restraints weight = 20231.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089640 restraints weight = 17764.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.090200 restraints weight = 15009.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090250 restraints weight = 14179.026| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14173 Z= 0.131 Angle : 0.542 7.415 19317 Z= 0.274 Chirality : 0.041 0.133 2280 Planarity : 0.004 0.044 2451 Dihedral : 6.833 65.315 1974 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.22 % Allowed : 10.58 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.20), residues: 1792 helix: 0.57 (0.19), residues: 884 sheet: -1.33 (0.42), residues: 160 loop : -2.25 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 650 TYR 0.024 0.001 TYR B 698 PHE 0.014 0.001 PHE A 364 TRP 0.010 0.001 TRP A 54 HIS 0.006 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00311 (14173) covalent geometry : angle 0.54198 (19317) hydrogen bonds : bond 0.04296 ( 607) hydrogen bonds : angle 4.10763 ( 1776) *********************** 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 140 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.365 Fit side-chains REVERT: A 144 LYS cc_start: 0.8023 (tmmt) cc_final: 0.7293 (ttpt) REVERT: A 381 ASP cc_start: 0.8114 (t70) cc_final: 0.7830 (t0) REVERT: A 840 MET cc_start: 0.8083 (tpp) cc_final: 0.7552 (mmt) REVERT: B 45 MET cc_start: 0.8743 (mmm) cc_final: 0.8534 (mmm) REVERT: B 144 LYS cc_start: 0.8176 (tmmt) cc_final: 0.7499 (ttpt) REVERT: B 226 ARG cc_start: 0.7467 (ptp90) cc_final: 0.7246 (ptp90) REVERT: B 381 ASP cc_start: 0.7833 (t0) cc_final: 0.7497 (t0) REVERT: B 499 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8463 (mtmt) REVERT: B 728 LEU cc_start: 0.8929 (mm) cc_final: 0.8674 (mt) REVERT: B 840 MET cc_start: 0.7780 (mmt) cc_final: 0.7525 (mmt) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.1023 time to fit residues: 20.9689 Evaluate side-chains 129 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 326 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 104 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 128 optimal weight: 0.0370 chunk 158 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.085149 restraints weight = 26439.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.085744 restraints weight = 19958.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.086263 restraints weight = 18625.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.086710 restraints weight = 15393.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.086794 restraints weight = 14268.754| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14173 Z= 0.237 Angle : 0.639 7.815 19317 Z= 0.325 Chirality : 0.044 0.137 2280 Planarity : 0.005 0.042 2451 Dihedral : 7.057 81.508 1974 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 2.24 % Allowed : 10.78 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.20), residues: 1792 helix: 0.41 (0.18), residues: 878 sheet: -1.35 (0.44), residues: 154 loop : -2.29 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.035 0.002 TYR B 698 PHE 0.022 0.002 PHE B 364 TRP 0.015 0.002 TRP A 54 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00582 (14173) covalent geometry : angle 0.63894 (19317) hydrogen bonds : bond 0.05397 ( 607) hydrogen bonds : angle 4.33573 ( 1776) *********************** 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 154 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.427 Fit side-chains REVERT: A 144 LYS cc_start: 0.8178 (tmmt) cc_final: 0.7466 (ttpt) REVERT: A 381 ASP cc_start: 0.8141 (t70) cc_final: 0.7822 (t0) REVERT: A 499 LYS cc_start: 0.8671 (mttp) cc_final: 0.8420 (mttp) REVERT: B 144 LYS cc_start: 0.8329 (tmmt) cc_final: 0.7665 (ttpt) REVERT: B 226 ARG cc_start: 0.7458 (ptp90) cc_final: 0.7254 (ptp90) REVERT: B 381 ASP cc_start: 0.7825 (t0) cc_final: 0.7467 (t0) REVERT: B 840 MET cc_start: 0.7841 (mmt) cc_final: 0.7606 (mmt) outliers start: 33 outliers final: 26 residues processed: 143 average time/residue: 0.0963 time to fit residues: 20.6220 Evaluate side-chains 140 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 544 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 176 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 0.0570 chunk 121 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.113610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.088497 restraints weight = 26234.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089490 restraints weight = 21212.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.090378 restraints weight = 17350.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090501 restraints weight = 14105.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.090562 restraints weight = 13130.660| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14173 Z= 0.124 Angle : 0.539 7.469 19317 Z= 0.273 Chirality : 0.041 0.134 2280 Planarity : 0.004 0.044 2451 Dihedral : 6.711 85.934 1974 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.90 % Allowed : 12.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.20), residues: 1792 helix: 0.66 (0.19), residues: 880 sheet: -1.44 (0.44), residues: 140 loop : -2.24 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 431 TYR 0.022 0.001 TYR A 698 PHE 0.013 0.001 PHE A 807 TRP 0.012 0.001 TRP A 54 HIS 0.006 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00293 (14173) covalent geometry : angle 0.53949 (19317) hydrogen bonds : bond 0.04126 ( 607) hydrogen bonds : angle 3.98208 ( 1776) *********************** 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 149 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.375 Fit side-chains REVERT: A 144 LYS cc_start: 0.8052 (tmmt) cc_final: 0.7338 (ttpt) REVERT: A 381 ASP cc_start: 0.8012 (t70) cc_final: 0.7734 (t0) REVERT: A 840 MET cc_start: 0.8070 (tpp) cc_final: 0.7554 (mmt) REVERT: B 144 LYS cc_start: 0.8199 (tmmt) cc_final: 0.7548 (ttpt) REVERT: B 226 ARG cc_start: 0.7445 (ptp90) cc_final: 0.7230 (ptp90) REVERT: B 381 ASP cc_start: 0.7805 (t0) cc_final: 0.7477 (t0) REVERT: B 728 LEU cc_start: 0.8889 (mm) cc_final: 0.8685 (mt) REVERT: B 840 MET cc_start: 0.7717 (mmt) cc_final: 0.7496 (mmt) outliers start: 28 outliers final: 20 residues processed: 143 average time/residue: 0.0916 time to fit residues: 20.2944 Evaluate side-chains 137 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 535 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 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 329 THR 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 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 115 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 148 optimal weight: 0.0170 chunk 4 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.115080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.089490 restraints weight = 26013.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.090635 restraints weight = 20145.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091628 restraints weight = 15963.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.091833 restraints weight = 13321.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.092131 restraints weight = 12791.262| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14173 Z= 0.101 Angle : 0.516 7.341 19317 Z= 0.259 Chirality : 0.040 0.131 2280 Planarity : 0.004 0.042 2451 Dihedral : 6.373 82.106 1974 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.76 % Allowed : 12.81 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.20), residues: 1792 helix: 0.92 (0.19), residues: 858 sheet: -1.29 (0.44), residues: 140 loop : -2.08 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 650 TYR 0.017 0.001 TYR A 698 PHE 0.013 0.001 PHE A 807 TRP 0.010 0.001 TRP A 54 HIS 0.005 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00226 (14173) covalent geometry : angle 0.51616 (19317) hydrogen bonds : bond 0.03570 ( 607) hydrogen bonds : angle 3.80039 ( 1776) *********************** 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 159 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.518 Fit side-chains REVERT: A 144 LYS cc_start: 0.7918 (tmmt) cc_final: 0.7216 (ttpt) REVERT: A 381 ASP cc_start: 0.8071 (t70) cc_final: 0.7778 (t0) REVERT: A 840 MET cc_start: 0.8012 (tpp) cc_final: 0.7506 (mmt) REVERT: B 144 LYS cc_start: 0.8127 (tmmt) cc_final: 0.7452 (ttpt) REVERT: B 226 ARG cc_start: 0.7431 (ptp90) cc_final: 0.7222 (ptp90) REVERT: B 381 ASP cc_start: 0.7779 (t0) cc_final: 0.7480 (t0) REVERT: B 499 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8410 (mttp) REVERT: B 728 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8615 (mt) REVERT: B 840 MET cc_start: 0.7675 (mmt) cc_final: 0.7439 (mmt) outliers start: 26 outliers final: 16 residues processed: 153 average time/residue: 0.0931 time to fit residues: 21.6092 Evaluate side-chains 138 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 460 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 156 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN ** 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 = 0.3487 r_free = 0.3487 target = 0.114364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.089814 restraints weight = 26054.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089406 restraints weight = 20595.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.090203 restraints weight = 18066.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.091020 restraints weight = 14549.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.091131 restraints weight = 13130.183| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14173 Z= 0.121 Angle : 0.534 7.266 19317 Z= 0.268 Chirality : 0.041 0.131 2280 Planarity : 0.004 0.042 2451 Dihedral : 6.318 81.193 1974 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.90 % Allowed : 13.02 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.20), residues: 1792 helix: 0.94 (0.19), residues: 856 sheet: -1.23 (0.44), residues: 140 loop : -2.11 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 650 TYR 0.020 0.001 TYR A 698 PHE 0.011 0.001 PHE A 807 TRP 0.011 0.001 TRP A 54 HIS 0.005 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00287 (14173) covalent geometry : angle 0.53420 (19317) hydrogen bonds : bond 0.03764 ( 607) hydrogen bonds : angle 3.83490 ( 1776) *********************** 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 153 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.411 Fit side-chains REVERT: A 144 LYS cc_start: 0.7923 (tmmt) cc_final: 0.7231 (ttpt) REVERT: A 381 ASP cc_start: 0.8093 (t70) cc_final: 0.7793 (t0) REVERT: A 840 MET cc_start: 0.8023 (tpp) cc_final: 0.7505 (mmt) REVERT: B 144 LYS cc_start: 0.8139 (tmmt) cc_final: 0.7432 (ttpt) REVERT: B 220 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 226 ARG cc_start: 0.7448 (ptp90) cc_final: 0.7234 (ptp90) REVERT: B 381 ASP cc_start: 0.7775 (t0) cc_final: 0.7520 (t0) REVERT: B 499 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8390 (mttp) REVERT: B 728 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8646 (mt) REVERT: B 840 MET cc_start: 0.7674 (mmt) cc_final: 0.7461 (mmt) outliers start: 28 outliers final: 25 residues processed: 147 average time/residue: 0.0857 time to fit residues: 19.6434 Evaluate side-chains 147 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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 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 329 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 VAL 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 544 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 53 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 33 optimal weight: 0.0170 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 93 optimal weight: 0.0060 chunk 41 optimal weight: 2.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.116946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.091981 restraints weight = 25847.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.093101 restraints weight = 21239.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.094074 restraints weight = 16614.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.094308 restraints weight = 13548.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.094566 restraints weight = 12854.587| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14173 Z= 0.094 Angle : 0.508 7.652 19317 Z= 0.254 Chirality : 0.040 0.130 2280 Planarity : 0.004 0.042 2451 Dihedral : 5.998 80.205 1974 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.49 % Allowed : 13.69 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.20), residues: 1792 helix: 1.06 (0.19), residues: 858 sheet: -1.14 (0.43), residues: 142 loop : -2.03 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 226 TYR 0.012 0.001 TYR A 698 PHE 0.013 0.001 PHE A 807 TRP 0.009 0.001 TRP A 54 HIS 0.005 0.000 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00202 (14173) covalent geometry : angle 0.50756 (19317) hydrogen bonds : bond 0.03112 ( 607) hydrogen bonds : angle 3.66412 ( 1776) *********************** 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 158 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.527 Fit side-chains REVERT: A 144 LYS cc_start: 0.7822 (tmmt) cc_final: 0.7117 (ttpt) REVERT: A 381 ASP cc_start: 0.8018 (t70) cc_final: 0.7730 (t0) REVERT: A 840 MET cc_start: 0.7893 (tpp) cc_final: 0.7430 (mmt) REVERT: B 144 LYS cc_start: 0.8076 (tmmt) cc_final: 0.7404 (ttpt) REVERT: B 226 ARG cc_start: 0.7313 (ptp90) cc_final: 0.7108 (ptp90) REVERT: B 381 ASP cc_start: 0.7697 (t0) cc_final: 0.7476 (t0) REVERT: B 431 ARG cc_start: 0.8298 (ttp-110) cc_final: 0.7995 (ttm110) REVERT: B 499 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8386 (mttp) REVERT: B 728 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8616 (mt) REVERT: B 820 MET cc_start: 0.8588 (mtp) cc_final: 0.8374 (mtp) REVERT: B 840 MET cc_start: 0.7631 (mmt) cc_final: 0.7429 (mmt) REVERT: B 881 MET cc_start: 0.7276 (ttm) cc_final: 0.6977 (ttm) outliers start: 22 outliers final: 16 residues processed: 154 average time/residue: 0.0925 time to fit residues: 21.9601 Evaluate side-chains 142 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 156 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.113185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.088509 restraints weight = 26246.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.088948 restraints weight = 20377.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.089805 restraints weight = 18493.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090066 restraints weight = 15689.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.090430 restraints weight = 15337.694| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14173 Z= 0.163 Angle : 0.573 9.324 19317 Z= 0.290 Chirality : 0.042 0.133 2280 Planarity : 0.004 0.039 2451 Dihedral : 6.232 81.411 1974 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.76 % Allowed : 13.83 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.20), residues: 1792 helix: 0.91 (0.19), residues: 858 sheet: -0.96 (0.42), residues: 160 loop : -2.06 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 650 TYR 0.027 0.001 TYR A 698 PHE 0.014 0.001 PHE B 364 TRP 0.013 0.001 TRP A 54 HIS 0.007 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00396 (14173) covalent geometry : angle 0.57314 (19317) hydrogen bonds : bond 0.04302 ( 607) hydrogen bonds : angle 3.93043 ( 1776) *********************** 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 150 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8003 (tmmt) cc_final: 0.7288 (ttpt) REVERT: A 381 ASP cc_start: 0.8072 (t70) cc_final: 0.7737 (t0) REVERT: B 144 LYS cc_start: 0.8214 (tmmt) cc_final: 0.7518 (ttpt) REVERT: B 226 ARG cc_start: 0.7348 (ptp90) cc_final: 0.7140 (ptp90) REVERT: B 381 ASP cc_start: 0.7767 (t0) cc_final: 0.7502 (t0) REVERT: B 431 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.7980 (ttm110) REVERT: B 728 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8719 (mt) REVERT: B 840 MET cc_start: 0.7739 (mmt) cc_final: 0.7492 (mmt) outliers start: 26 outliers final: 21 residues processed: 146 average time/residue: 0.0976 time to fit residues: 21.8878 Evaluate side-chains 145 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 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 329 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 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 171 optimal weight: 0.0980 chunk 64 optimal weight: 0.0370 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 85 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.116341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090875 restraints weight = 25861.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.092584 restraints weight = 20165.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.093365 restraints weight = 14755.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.093260 restraints weight = 14372.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.093413 restraints weight = 13150.050| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14173 Z= 0.097 Angle : 0.519 8.298 19317 Z= 0.260 Chirality : 0.040 0.131 2280 Planarity : 0.004 0.041 2451 Dihedral : 5.943 79.422 1974 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.29 % Allowed : 14.24 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.20), residues: 1792 helix: 1.04 (0.19), residues: 858 sheet: -1.02 (0.44), residues: 140 loop : -1.94 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 226 TYR 0.015 0.001 TYR A 698 PHE 0.012 0.001 PHE A 807 TRP 0.010 0.001 TRP A 54 HIS 0.008 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00213 (14173) covalent geometry : angle 0.51878 (19317) hydrogen bonds : bond 0.03326 ( 607) hydrogen bonds : angle 3.71149 ( 1776) ********************** 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 149 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.7843 (tmmt) cc_final: 0.7168 (ttpt) REVERT: A 381 ASP cc_start: 0.8009 (t70) cc_final: 0.7682 (t0) REVERT: A 840 MET cc_start: 0.7943 (tpp) cc_final: 0.7434 (mmt) REVERT: B 144 LYS cc_start: 0.8093 (tmmt) cc_final: 0.7375 (ttpt) REVERT: B 381 ASP cc_start: 0.7704 (t0) cc_final: 0.7492 (t0) REVERT: B 431 ARG cc_start: 0.8365 (ttp-110) cc_final: 0.8019 (ttm110) REVERT: B 840 MET cc_start: 0.7639 (mmt) cc_final: 0.7389 (mmt) outliers start: 19 outliers final: 19 residues processed: 145 average time/residue: 0.0941 time to fit residues: 20.6759 Evaluate side-chains 147 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 467 CYS 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 326 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 533 SER 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 29 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.114607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.089193 restraints weight = 25946.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.090220 restraints weight = 21288.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.091194 restraints weight = 17142.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.091351 restraints weight = 14030.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091499 restraints weight = 13141.812| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14173 Z= 0.125 Angle : 0.540 8.472 19317 Z= 0.272 Chirality : 0.041 0.131 2280 Planarity : 0.004 0.040 2451 Dihedral : 5.960 80.826 1974 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.42 % Allowed : 14.37 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.20), residues: 1792 helix: 1.01 (0.19), residues: 860 sheet: -1.02 (0.44), residues: 140 loop : -1.93 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 226 TYR 0.022 0.001 TYR A 698 PHE 0.011 0.001 PHE B 364 TRP 0.012 0.001 TRP A 54 HIS 0.008 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00300 (14173) covalent geometry : angle 0.53965 (19317) hydrogen bonds : bond 0.03752 ( 607) hydrogen bonds : angle 3.79824 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.40 seconds wall clock time: 29 minutes 5.86 seconds (1745.86 seconds total)