Starting phenix.real_space_refine on Fri May 16 03:40:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpx_36489/05_2025/8jpx_36489.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpx_36489/05_2025/8jpx_36489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpx_36489/05_2025/8jpx_36489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpx_36489/05_2025/8jpx_36489.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpx_36489/05_2025/8jpx_36489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpx_36489/05_2025/8jpx_36489.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.116 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 78 5.49 5 Mg 6 5.21 5 S 38 5.16 5 C 9042 2.51 5 N 2386 2.21 5 O 2812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14362 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 6380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6380 Classifications: {'peptide': 770} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 740} Chain: "H" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 342 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 336 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 6380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6380 Classifications: {'peptide': 770} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 740} Chain: "G" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 342 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "T" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 336 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.64, per 1000 atoms: 0.60 Number of scatterers: 14362 At special positions: 0 Unit cell: (111.35, 106.25, 109.65, 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 38 16.00 P 78 15.00 Mg 6 11.99 O 2812 8.00 N 2386 7.00 C 9042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2956 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 18 sheets defined 36.2% alpha, 24.3% beta 28 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.524A pdb=" N ILE B 16 " --> pdb=" O ASN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.552A pdb=" N LEU B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 48 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.685A pdb=" N LYS B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 removed outlier: 3.629A pdb=" N LYS B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 206 through 222 removed outlier: 3.806A pdb=" N TYR B 221 " --> pdb=" O HIS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 236 removed outlier: 3.945A pdb=" N GLU B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.853A pdb=" N GLU B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.514A pdb=" N LEU B 347 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 393 through 411 removed outlier: 3.583A pdb=" N MET B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 421 removed outlier: 3.829A pdb=" N LEU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 467 Processing helix chain 'B' and resid 487 through 498 removed outlier: 3.718A pdb=" N LEU B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'B' and resid 523 through 538 Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.768A pdb=" N ASP B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 647 removed outlier: 3.523A pdb=" N LYS B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 645 " --> pdb=" O TYR B 641 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 647 " --> pdb=" O SER B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 removed outlier: 3.511A pdb=" N VAL B 717 " --> pdb=" O THR B 713 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 725 " --> pdb=" O PHE B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 753 removed outlier: 3.511A pdb=" N LYS B 746 " --> pdb=" O HIS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.619A pdb=" N GLY B 765 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.555A pdb=" N ILE A 16 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.538A pdb=" N LEU A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.682A pdb=" N LYS A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 removed outlier: 3.629A pdb=" N LYS A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 173 Processing helix chain 'A' and resid 206 through 222 removed outlier: 3.813A pdb=" N TYR A 221 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 removed outlier: 3.948A pdb=" N GLU A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.852A pdb=" N GLU A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.502A pdb=" N LEU A 347 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 393 through 411 removed outlier: 3.563A pdb=" N MET A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 421 removed outlier: 3.832A pdb=" N LEU A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 467 Processing helix chain 'A' and resid 487 through 498 removed outlier: 3.711A pdb=" N LEU A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 513 Processing helix chain 'A' and resid 523 through 538 Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.772A pdb=" N ASP A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 647 removed outlier: 3.524A pdb=" N LYS A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 645 " --> pdb=" O TYR A 641 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 725 removed outlier: 3.580A pdb=" N VAL A 717 " --> pdb=" O THR A 713 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 725 " --> pdb=" O PHE A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 removed outlier: 3.512A pdb=" N LYS A 746 " --> pdb=" O HIS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.702A pdb=" N GLY A 765 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.663A pdb=" N SER B 317 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLU B 320 " --> pdb=" O ASN B 672 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN B 672 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU B 696 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE B 656 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LYS B 698 " --> pdb=" O ASP B 654 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP B 654 " --> pdb=" O LYS B 698 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 553 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP B 628 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 559 " --> pdb=" O ASP B 628 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 570 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY B 591 " --> pdb=" O GLY B 570 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER B 572 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS B 589 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 574 " --> pdb=" O PRO B 587 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE B 576 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 585 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.663A pdb=" N SER B 317 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLU B 320 " --> pdb=" O ASN B 672 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN B 672 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 54 removed outlier: 6.387A pdb=" N ILE B 59 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE B 21 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU B 77 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 23 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA6, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 195 removed outlier: 4.851A pdb=" N LYS B 200 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 333 removed outlier: 3.747A pdb=" N VAL B 544 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 445 through 448 removed outlier: 3.500A pdb=" N GLU B 448 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY B 473 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLN B 503 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 475 " --> pdb=" O GLN B 503 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL B 505 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 477 " --> pdb=" O VAL B 505 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.664A pdb=" N SER A 317 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLU A 320 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN A 672 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU A 696 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE A 656 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS A 698 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP A 654 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 553 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 628 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 559 " --> pdb=" O ASP A 628 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 570 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY A 591 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER A 572 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LYS A 589 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 574 " --> pdb=" O PRO A 587 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE A 576 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 585 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.664A pdb=" N SER A 317 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLU A 320 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN A 672 " --> pdb=" O GLU A 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 9 through 11 Processing sheet with id=AB4, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.386A pdb=" N ILE A 59 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE A 21 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU A 77 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 23 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AB6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AB7, first strand: chain 'A' and resid 194 through 195 removed outlier: 4.865A pdb=" N LYS A 200 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 332 through 333 removed outlier: 3.724A pdb=" N VAL A 544 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.560A pdb=" N GLY A 473 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLN A 503 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA A 475 " --> pdb=" O GLN A 503 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL A 505 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 477 " --> pdb=" O VAL A 505 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3610 1.33 - 1.45: 2848 1.45 - 1.57: 8108 1.57 - 1.69: 152 1.69 - 1.81: 74 Bond restraints: 14792 Sorted by residual: bond pdb=" CB PRO B 185 " pdb=" CG PRO B 185 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.20e+00 bond pdb=" C LEU B 263 " pdb=" N LEU B 264 " ideal model delta sigma weight residual 1.328 1.305 0.023 1.67e-02 3.59e+03 1.83e+00 bond pdb=" CB ASP B 310 " pdb=" CG ASP B 310 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.22e+00 bond pdb=" O4' DG H 15 " pdb=" C1' DG H 15 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.01e-01 bond pdb=" C4' DG G 12 " pdb=" O4' DG G 12 " ideal model delta sigma weight residual 1.450 1.431 0.019 2.00e-02 2.50e+03 8.98e-01 ... (remaining 14787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 19930 2.04 - 4.08: 292 4.08 - 6.12: 23 6.12 - 8.16: 0 8.16 - 10.20: 1 Bond angle restraints: 20246 Sorted by residual: angle pdb=" N LEU A 158 " pdb=" CA LEU A 158 " pdb=" C LEU A 158 " ideal model delta sigma weight residual 114.62 109.88 4.74 1.14e+00 7.69e-01 1.73e+01 angle pdb=" N LEU B 158 " pdb=" CA LEU B 158 " pdb=" C LEU B 158 " ideal model delta sigma weight residual 114.62 109.94 4.68 1.14e+00 7.69e-01 1.69e+01 angle pdb=" CA LEU A 158 " pdb=" C LEU A 158 " pdb=" N VAL A 159 " ideal model delta sigma weight residual 119.71 116.28 3.43 1.17e+00 7.31e-01 8.62e+00 angle pdb=" CA LEU B 158 " pdb=" C LEU B 158 " pdb=" N VAL B 159 " ideal model delta sigma weight residual 119.71 116.35 3.36 1.17e+00 7.31e-01 8.27e+00 angle pdb=" C ASP B 577 " pdb=" N SER B 578 " pdb=" CA SER B 578 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 ... (remaining 20241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.45: 8043 31.45 - 62.90: 780 62.90 - 94.34: 43 94.34 - 125.79: 0 125.79 - 157.24: 4 Dihedral angle restraints: 8870 sinusoidal: 4294 harmonic: 4576 Sorted by residual: dihedral pdb=" C4' DT F 2 " pdb=" C3' DT F 2 " pdb=" O3' DT F 2 " pdb=" P DT F 3 " ideal model delta sinusoidal sigma weight residual 220.00 62.76 157.24 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DT E 2 " pdb=" C3' DT E 2 " pdb=" O3' DT E 2 " pdb=" P DT E 3 " ideal model delta sinusoidal sigma weight residual 220.00 76.92 143.08 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" CA ASP B 438 " pdb=" C ASP B 438 " pdb=" N PHE B 439 " pdb=" CA PHE B 439 " ideal model delta harmonic sigma weight residual -180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1468 0.034 - 0.067: 503 0.067 - 0.101: 153 0.101 - 0.134: 104 0.134 - 0.168: 6 Chirality restraints: 2234 Sorted by residual: chirality pdb=" CB ILE B 616 " pdb=" CA ILE B 616 " pdb=" CG1 ILE B 616 " pdb=" CG2 ILE B 616 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB ILE A 616 " pdb=" CA ILE A 616 " pdb=" CG1 ILE A 616 " pdb=" CG2 ILE A 616 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE B 694 " pdb=" N ILE B 694 " pdb=" C ILE B 694 " pdb=" CB ILE B 694 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2231 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 583 " 0.237 9.50e-02 1.11e+02 1.06e-01 7.02e+00 pdb=" NE ARG B 583 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 583 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 583 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 583 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 162 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO B 163 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 163 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 163 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 29 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO B 30 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.028 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 56 2.50 - 3.10: 9340 3.10 - 3.70: 20429 3.70 - 4.30: 31713 4.30 - 4.90: 53439 Nonbonded interactions: 114977 Sorted by model distance: nonbonded pdb=" OP1 DT U 10 " pdb="MG MG B 801 " model vdw 1.900 2.170 nonbonded pdb=" OP1 DT T 10 " pdb="MG MG A 801 " model vdw 1.900 2.170 nonbonded pdb=" OD2 ASP A 558 " pdb="MG MG A 801 " model vdw 1.900 2.170 nonbonded pdb=" OD2 ASP B 558 " pdb="MG MG B 801 " model vdw 1.903 2.170 nonbonded pdb=" ND1 HIS A 745 " pdb="MG MG A 801 " model vdw 2.008 2.250 ... (remaining 114972 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' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.920 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 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 : 0.003 0.074 14792 Z= 0.141 Angle : 0.562 10.203 20246 Z= 0.322 Chirality : 0.043 0.168 2234 Planarity : 0.005 0.106 2296 Dihedral : 21.049 157.240 5914 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.50 % Allowed : 34.07 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1536 helix: 0.50 (0.25), residues: 496 sheet: 1.00 (0.28), residues: 342 loop : -1.80 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.002 0.001 HIS B 144 PHE 0.032 0.001 PHE A 439 TYR 0.013 0.001 TYR A 212 ARG 0.007 0.000 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.15584 ( 575) hydrogen bonds : angle 5.68211 ( 1601) covalent geometry : bond 0.00316 (14792) covalent geometry : angle 0.56157 (20246) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 287 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7671 (tm-30) REVERT: B 443 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6326 (mt-10) REVERT: A 31 GLU cc_start: 0.7551 (tp30) cc_final: 0.7227 (tp30) REVERT: A 36 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7360 (mttm) REVERT: A 443 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6259 (mt-10) outliers start: 7 outliers final: 6 residues processed: 174 average time/residue: 1.5488 time to fit residues: 291.5285 Evaluate side-chains 166 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 596 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 143 optimal weight: 0.2980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097028 restraints weight = 19256.518| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.22 r_work: 0.2967 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14792 Z= 0.171 Angle : 0.561 8.850 20246 Z= 0.314 Chirality : 0.044 0.144 2234 Planarity : 0.005 0.054 2296 Dihedral : 18.267 169.274 2540 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.48 % Allowed : 34.77 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1536 helix: 0.74 (0.24), residues: 502 sheet: 0.79 (0.27), residues: 354 loop : -1.71 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 222 HIS 0.003 0.001 HIS B 144 PHE 0.031 0.001 PHE A 439 TYR 0.013 0.001 TYR A 743 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 575) hydrogen bonds : angle 4.42333 ( 1601) covalent geometry : bond 0.00400 (14792) covalent geometry : angle 0.56070 (20246) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 GLU cc_start: 0.8134 (tp30) cc_final: 0.7627 (tt0) REVERT: B 443 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6808 (mt-10) REVERT: B 592 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: B 611 PHE cc_start: 0.6165 (m-10) cc_final: 0.5643 (m-80) REVERT: B 635 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8722 (mt-10) REVERT: A 31 GLU cc_start: 0.8026 (tp30) cc_final: 0.7584 (tp30) REVERT: A 36 LYS cc_start: 0.7371 (ttmt) cc_final: 0.7016 (mttm) REVERT: A 150 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: A 443 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6786 (mm-30) REVERT: A 592 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: A 635 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8709 (mt-10) outliers start: 35 outliers final: 17 residues processed: 196 average time/residue: 1.4820 time to fit residues: 315.2195 Evaluate side-chains 181 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 709 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 111 optimal weight: 0.0570 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.098128 restraints weight = 19357.787| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.22 r_work: 0.2983 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14792 Z= 0.148 Angle : 0.539 7.930 20246 Z= 0.302 Chirality : 0.044 0.136 2234 Planarity : 0.004 0.055 2296 Dihedral : 17.976 157.175 2532 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer: Outliers : 3.40 % Allowed : 34.49 % Favored : 62.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1536 helix: 0.91 (0.24), residues: 500 sheet: 0.80 (0.27), residues: 354 loop : -1.67 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 222 HIS 0.002 0.001 HIS A 144 PHE 0.028 0.001 PHE A 439 TYR 0.011 0.001 TYR B 743 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 575) hydrogen bonds : angle 4.16609 ( 1601) covalent geometry : bond 0.00342 (14792) covalent geometry : angle 0.53890 (20246) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 287 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7830 (tm-30) REVERT: B 371 GLU cc_start: 0.8147 (tp30) cc_final: 0.7663 (tt0) REVERT: B 443 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6856 (mt-10) REVERT: B 611 PHE cc_start: 0.6214 (m-10) cc_final: 0.5887 (m-10) REVERT: B 635 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8742 (mt-10) REVERT: A 31 GLU cc_start: 0.8031 (tp30) cc_final: 0.7740 (tp30) REVERT: A 36 LYS cc_start: 0.7355 (ttmt) cc_final: 0.7009 (mttm) REVERT: A 287 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 443 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6791 (mm-30) REVERT: A 635 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8737 (mt-10) outliers start: 48 outliers final: 24 residues processed: 203 average time/residue: 1.4051 time to fit residues: 310.0475 Evaluate side-chains 186 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 576 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 78 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.098573 restraints weight = 19331.578| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.23 r_work: 0.2983 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14792 Z= 0.145 Angle : 0.535 7.392 20246 Z= 0.300 Chirality : 0.044 0.136 2234 Planarity : 0.004 0.055 2296 Dihedral : 17.978 156.493 2532 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.81 % Favored : 92.06 % Rotamer: Outliers : 3.47 % Allowed : 34.77 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.22), residues: 1536 helix: 0.96 (0.24), residues: 500 sheet: 0.81 (0.27), residues: 354 loop : -1.67 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 222 HIS 0.002 0.001 HIS B 144 PHE 0.028 0.001 PHE A 439 TYR 0.011 0.001 TYR B 212 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 575) hydrogen bonds : angle 4.06576 ( 1601) covalent geometry : bond 0.00334 (14792) covalent geometry : angle 0.53513 (20246) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8493 (tt) REVERT: B 287 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 371 GLU cc_start: 0.8144 (tp30) cc_final: 0.7662 (tt0) REVERT: B 443 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6918 (mt-10) REVERT: B 611 PHE cc_start: 0.6371 (m-10) cc_final: 0.6015 (m-10) REVERT: B 635 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8700 (mt-10) REVERT: A 31 GLU cc_start: 0.8107 (tp30) cc_final: 0.7856 (tp30) REVERT: A 36 LYS cc_start: 0.7307 (ttmt) cc_final: 0.6956 (mttm) REVERT: A 287 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 443 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6793 (mm-30) REVERT: A 622 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8536 (ttpt) REVERT: A 635 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8713 (mt-10) outliers start: 49 outliers final: 28 residues processed: 209 average time/residue: 1.4803 time to fit residues: 335.7745 Evaluate side-chains 191 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 39 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN A 346 GLN A 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.096210 restraints weight = 19562.328| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.23 r_work: 0.2944 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14792 Z= 0.198 Angle : 0.577 7.628 20246 Z= 0.322 Chirality : 0.045 0.142 2234 Planarity : 0.004 0.056 2296 Dihedral : 18.028 156.196 2530 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.68 % Favored : 92.19 % Rotamer: Outliers : 3.90 % Allowed : 34.99 % Favored : 61.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1536 helix: 1.05 (0.24), residues: 486 sheet: 0.86 (0.27), residues: 360 loop : -1.82 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 222 HIS 0.003 0.001 HIS B 742 PHE 0.030 0.002 PHE B 439 TYR 0.014 0.001 TYR B 743 ARG 0.007 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 575) hydrogen bonds : angle 4.16310 ( 1601) covalent geometry : bond 0.00469 (14792) covalent geometry : angle 0.57658 (20246) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8533 (tt) REVERT: B 371 GLU cc_start: 0.8101 (tp30) cc_final: 0.7603 (tt0) REVERT: B 440 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.6112 (tpt170) REVERT: B 443 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6911 (mt-10) REVERT: A 31 GLU cc_start: 0.8152 (tp30) cc_final: 0.7938 (tp30) REVERT: A 36 LYS cc_start: 0.7372 (ttmt) cc_final: 0.6931 (mttm) REVERT: A 443 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6841 (mt-10) REVERT: A 458 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: A 622 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8501 (ttpt) outliers start: 55 outliers final: 29 residues processed: 199 average time/residue: 1.4632 time to fit residues: 316.2097 Evaluate side-chains 190 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 76 optimal weight: 5.9990 chunk 88 optimal weight: 0.1980 chunk 133 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.098213 restraints weight = 19468.380| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.23 r_work: 0.2973 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14792 Z= 0.140 Angle : 0.540 7.003 20246 Z= 0.303 Chirality : 0.044 0.137 2234 Planarity : 0.004 0.053 2296 Dihedral : 17.984 156.770 2530 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.29 % Favored : 92.58 % Rotamer: Outliers : 3.61 % Allowed : 35.91 % Favored : 60.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1536 helix: 1.20 (0.24), residues: 484 sheet: 1.02 (0.28), residues: 336 loop : -1.78 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 222 HIS 0.002 0.001 HIS A 144 PHE 0.028 0.001 PHE A 439 TYR 0.011 0.001 TYR B 212 ARG 0.005 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 575) hydrogen bonds : angle 4.02454 ( 1601) covalent geometry : bond 0.00319 (14792) covalent geometry : angle 0.53967 (20246) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8514 (tt) REVERT: B 287 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 371 GLU cc_start: 0.8173 (tp30) cc_final: 0.7684 (tt0) REVERT: B 440 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.5880 (mmt-90) REVERT: B 443 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6910 (mt-10) REVERT: A 31 GLU cc_start: 0.8133 (tp30) cc_final: 0.7674 (tp30) REVERT: A 32 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8444 (mm-30) REVERT: A 36 LYS cc_start: 0.7368 (ttmt) cc_final: 0.6945 (mttm) REVERT: A 287 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 443 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6832 (mm-30) REVERT: A 458 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: A 622 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8367 (ttpt) outliers start: 51 outliers final: 32 residues processed: 206 average time/residue: 1.3875 time to fit residues: 311.0660 Evaluate side-chains 195 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 46 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095329 restraints weight = 19624.688| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.23 r_work: 0.2942 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14792 Z= 0.222 Angle : 0.595 7.526 20246 Z= 0.332 Chirality : 0.046 0.145 2234 Planarity : 0.004 0.054 2296 Dihedral : 18.090 156.092 2530 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.81 % Favored : 92.06 % Rotamer: Outliers : 3.97 % Allowed : 35.48 % Favored : 60.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1536 helix: 0.79 (0.24), residues: 502 sheet: 1.02 (0.28), residues: 350 loop : -1.83 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 222 HIS 0.003 0.001 HIS A 742 PHE 0.030 0.002 PHE B 439 TYR 0.017 0.001 TYR B 743 ARG 0.005 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 575) hydrogen bonds : angle 4.20533 ( 1601) covalent geometry : bond 0.00531 (14792) covalent geometry : angle 0.59497 (20246) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8577 (tt) REVERT: B 162 ASP cc_start: 0.7796 (t0) cc_final: 0.7517 (t0) REVERT: B 168 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8477 (mt-10) REVERT: B 371 GLU cc_start: 0.8102 (tp30) cc_final: 0.7618 (tt0) REVERT: B 440 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.6089 (tpt170) REVERT: B 443 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6908 (mt-10) REVERT: A 31 GLU cc_start: 0.8186 (tp30) cc_final: 0.7730 (tp30) REVERT: A 32 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 36 LYS cc_start: 0.7401 (ttmt) cc_final: 0.6966 (mttm) REVERT: A 443 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6859 (mt-10) REVERT: A 458 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8086 (mt-10) outliers start: 56 outliers final: 33 residues processed: 203 average time/residue: 1.4708 time to fit residues: 323.8681 Evaluate side-chains 192 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095767 restraints weight = 19561.042| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.23 r_work: 0.2951 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14792 Z= 0.196 Angle : 0.582 7.447 20246 Z= 0.325 Chirality : 0.045 0.167 2234 Planarity : 0.004 0.054 2296 Dihedral : 18.090 156.994 2530 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.94 % Favored : 91.93 % Rotamer: Outliers : 3.47 % Allowed : 35.69 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1536 helix: 0.81 (0.24), residues: 502 sheet: 1.14 (0.28), residues: 326 loop : -1.83 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 222 HIS 0.003 0.001 HIS A 742 PHE 0.029 0.002 PHE A 439 TYR 0.014 0.001 TYR A 743 ARG 0.005 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 575) hydrogen bonds : angle 4.14723 ( 1601) covalent geometry : bond 0.00466 (14792) covalent geometry : angle 0.58176 (20246) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8562 (tt) REVERT: B 162 ASP cc_start: 0.7804 (t0) cc_final: 0.7527 (t0) REVERT: B 371 GLU cc_start: 0.8105 (tp30) cc_final: 0.7624 (tt0) REVERT: B 440 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.6042 (tpt170) REVERT: B 443 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6921 (mt-10) REVERT: B 458 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: B 758 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7930 (tppp) REVERT: A 31 GLU cc_start: 0.8184 (tp30) cc_final: 0.7729 (tp30) REVERT: A 32 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8437 (mm-30) REVERT: A 36 LYS cc_start: 0.7399 (ttmt) cc_final: 0.6966 (mttm) REVERT: A 443 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6829 (mt-10) REVERT: A 458 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8108 (mt-10) outliers start: 49 outliers final: 35 residues processed: 190 average time/residue: 1.4453 time to fit residues: 298.1834 Evaluate side-chains 193 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 758 LYS Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 63 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.093392 restraints weight = 19537.045| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.23 r_work: 0.2931 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14792 Z= 0.249 Angle : 0.621 7.677 20246 Z= 0.345 Chirality : 0.047 0.149 2234 Planarity : 0.005 0.054 2296 Dihedral : 18.159 156.812 2530 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.68 % Favored : 92.19 % Rotamer: Outliers : 3.47 % Allowed : 35.62 % Favored : 60.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1536 helix: 0.67 (0.24), residues: 502 sheet: 0.96 (0.28), residues: 350 loop : -1.86 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 222 HIS 0.003 0.001 HIS B 742 PHE 0.031 0.002 PHE B 439 TYR 0.018 0.002 TYR B 743 ARG 0.005 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04806 ( 575) hydrogen bonds : angle 4.26379 ( 1601) covalent geometry : bond 0.00597 (14792) covalent geometry : angle 0.62101 (20246) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 GLU cc_start: 0.8074 (tp30) cc_final: 0.7767 (tp30) REVERT: B 66 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8602 (tt) REVERT: B 162 ASP cc_start: 0.7843 (t0) cc_final: 0.7559 (t0) REVERT: B 168 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8495 (mt-10) REVERT: B 371 GLU cc_start: 0.8102 (tp30) cc_final: 0.7616 (tt0) REVERT: B 440 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.6055 (tpt170) REVERT: B 758 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7988 (tppp) REVERT: A 31 GLU cc_start: 0.8201 (tp30) cc_final: 0.7755 (tp30) REVERT: A 32 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8430 (mm-30) REVERT: A 36 LYS cc_start: 0.7398 (ttmt) cc_final: 0.6972 (mttm) REVERT: A 443 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6894 (mt-10) REVERT: A 458 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: A 592 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: A 758 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7974 (tppp) outliers start: 49 outliers final: 36 residues processed: 194 average time/residue: 1.5735 time to fit residues: 334.5035 Evaluate side-chains 200 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 758 LYS Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 152 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN B 749 ASN A 499 ASN A 749 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.098010 restraints weight = 19389.516| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.23 r_work: 0.2987 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14792 Z= 0.140 Angle : 0.561 7.498 20246 Z= 0.317 Chirality : 0.044 0.145 2234 Planarity : 0.004 0.055 2296 Dihedral : 18.079 158.087 2530 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.36 % Favored : 92.51 % Rotamer: Outliers : 2.55 % Allowed : 36.69 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1536 helix: 0.75 (0.24), residues: 512 sheet: 0.93 (0.28), residues: 344 loop : -1.67 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 222 HIS 0.002 0.001 HIS A 144 PHE 0.028 0.001 PHE A 439 TYR 0.014 0.001 TYR A 212 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 575) hydrogen bonds : angle 4.00970 ( 1601) covalent geometry : bond 0.00317 (14792) covalent geometry : angle 0.56099 (20246) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLU cc_start: 0.8076 (tp30) cc_final: 0.7713 (tp30) REVERT: B 66 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8548 (tt) REVERT: B 371 GLU cc_start: 0.8173 (tp30) cc_final: 0.7681 (tt0) REVERT: B 440 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5960 (tpt170) REVERT: B 443 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6912 (mt-10) REVERT: A 31 GLU cc_start: 0.8171 (tp30) cc_final: 0.7714 (tp30) REVERT: A 32 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8407 (mm-30) REVERT: A 36 LYS cc_start: 0.7359 (ttmt) cc_final: 0.6926 (mttm) REVERT: A 443 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6836 (mt-10) REVERT: A 458 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8052 (mt-10) outliers start: 36 outliers final: 23 residues processed: 184 average time/residue: 1.5451 time to fit residues: 307.2941 Evaluate side-chains 180 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 139 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.092570 restraints weight = 19717.043| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.23 r_work: 0.2917 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 14792 Z= 0.300 Angle : 0.665 7.919 20246 Z= 0.368 Chirality : 0.049 0.153 2234 Planarity : 0.005 0.053 2296 Dihedral : 18.251 156.406 2530 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.88 % Favored : 91.99 % Rotamer: Outliers : 2.48 % Allowed : 36.97 % Favored : 60.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1536 helix: 0.54 (0.23), residues: 502 sheet: 1.02 (0.28), residues: 332 loop : -1.85 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 222 HIS 0.003 0.001 HIS B 742 PHE 0.035 0.002 PHE B 439 TYR 0.020 0.002 TYR B 743 ARG 0.005 0.001 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.05289 ( 575) hydrogen bonds : angle 4.35215 ( 1601) covalent geometry : bond 0.00725 (14792) covalent geometry : angle 0.66478 (20246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10087.97 seconds wall clock time: 174 minutes 11.67 seconds (10451.67 seconds total)